diff --git a/biblio/41388549.mdwn b/biblio/41388549.mdwn
new file mode 100644
index 00000000..594389a3
--- /dev/null
+++ b/biblio/41388549.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The repertoire of short tandem repeats across the tree of life."]]
+[[!tag repeats]]
+
+Chantzi N, Georgakopoulos-Soares I.
+
+The repertoire of short tandem repeats across the tree of life.
+
+Genome Biol. 2025 Dec 12;26(1):425. doi:10.1186/s13059-025-03893-z
+
+[[!pmid 41388549 desc="“The average STR density was 1.51 STR bp per kB” “_Plasmodium falciparum_ shows the highest STR genomic density (109 bp/kB)” “19,645 viruses and 5 bacteria lacked STRs altogether” “the bacterial kingdom Fusobacteriati is depleted of STRs” “for prokaryotic genomes, we notice that one bp repeat unit STRs are highly depleted. Notably, trinucleotide and hexanucleotide tandem repeats are also enriched in most prokaryotic phyla” “bacterial and archaeal genomes are, on average, not more repetitive than expected by chance in contrast to eukaryotic and viral genomes.”"]]

diff --git a/index.en.po b/index.en.po
index 99c35b76..1f68e443 100644
--- a/index.en.po
+++ b/index.en.po
@@ -2,7 +2,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2026-01-11 07:20+0000\n"
+"POT-Creation-Date: 2026-01-12 05:57+0000\n"
 "PO-Revision-Date: 2019-06-04 11:11+0900\n"
 "Last-Translator: Charles Plessy <>\n"
 "Language-Team: Hopla\n"
@@ -19,34 +19,16 @@ msgid "[[!meta stylesheet=\"accueil\" rel=\"stylesheet\" title=\"Page d'accueil\
 msgstr "[[!meta stylesheet=\"accueil\" rel=\"stylesheet\" title=\"Home page\"]]\n"
 
 #. type: Plain text
-msgid ""
-"Voici quelques [photos][] (Antarctique, Japon, montagne, divers, …) que j'ai "
-"numérisé.  Ma [[page japon|Japon]] (qui ne se remplit plus vraiment), avec "
-"la traduction du vocabulaire de certains manuels de japonais. Enfin, "
-"quelques nouvelles de moi avec le [[kanji du moment|Japon/kanji]], et des "
-"nouvelles de mes [[contributions|Debian/planète]] en tant que [développeur "
-"Debian][]."
-msgstr ""
-"Here are some [pictures][photos] (Antarctica, Japan, mountain, others, …) "
-"that I scanned.  My [[Japan page|Japon]] (rarely updated), with the "
-"translation of the vocabulary for some Japanese language textbooks.  Lastly, "
-"some personal news with the [[kanji of the day|Japon/kanji]], news of my "
-"[[contributions|Debian/planet]] as [Debian developer][développeur Debian]."
-
-#. type: Link reference
-#, no-wrap
-msgid "[photos]:\t\thttp://photo.charles.plessy.org/"
-msgstr ""
-
-#. type: Link reference
-#, fuzzy, no-wrap
-#| msgid "[photos]:\t\thttp://photo.charles.plessy.org/ [développeur Debian]:\thttp://qa.debian.org/developer.php?login=plessy"
-msgid "[développeur Debian]:\thttp://qa.debian.org/developer.php?login=plessy"
-msgstr ""
-"[photos]:\t\thttp://photo.charles.plessy.org/\n"
-"[développeur Debian]:\thttp://qa.debian.org/developer.php?login=plessy"
-
-#. type: Plain text
+#, fuzzy
+#| msgid ""
+#| "Je travaille à [OIST][] depuis août 2018, et j'y étudie la séquence des "
+#| "chromosomes d'un petit animal planctonique appellé _[Oikopleura dioica]"
+#| "[]_.  Auparavant, j'ai travaillé au [RIKEN][] pendant 14 ans, pour y "
+#| "développer des technologies pour mesurer l'activité des cellules en "
+#| "séquençant leurs ARN messagers.  Je publie mes [résultats en anglais][].  "
+#| "Avant de déménager au Japon, j'étudiais le [poisson-zèbre][zfin] à "
+#| "Illkirch.  J'ai encore quelques images de mes [poissons transgéniques]"
+#| "[gfp] sur ce site."
 msgid ""
 "Je travaille à [OIST][] depuis août 2018, et j'y étudie la séquence des "
 "chromosomes d'un petit animal planctonique appellé _[Oikopleura dioica][]_.  "
@@ -54,7 +36,8 @@ msgid ""
 "des technologies pour mesurer l'activité des cellules en séquençant leurs "
 "ARN messagers.  Je publie mes [résultats en anglais][].  Avant de déménager "
 "au Japon, j'étudiais le [poisson-zèbre][zfin] à Illkirch.  J'ai encore "
-"quelques images de mes [poissons transgéniques][gfp] sur ce site."
+"quelques images de mes [poissons transgéniques][gfp] sur ce site.  Plus de "
+"détails sur [[open-source-biologist]]."
 msgstr ""
 "I am working at [OIST] since August 2018, where I study the sequence of the "
 "chromosomes of a small planktonic animal called _[Oikopleura dioica][]_. "
@@ -95,14 +78,26 @@ msgid "[résultats en anglais]:   http://www.ncbi.nlm.nih.gov/pubmed?term=plessy
 msgstr ""
 
 #. type: Plain text
-#, no-wrap
+#, fuzzy, no-wrap
+#| msgid ""
+#| "Mes pages (plus ou moins à jour) dans des annuaires ou des réseaux :\n"
+#| "[viadeo][], [linkedin][], ou [copains d'avant][copainsdavant].  J'ai\n"
+#| "[[signé ici|réseauxsociaux.txt]] les URLs ci-dessus avec la [[!wikipediafr signature_numérique desc=\"clef électronique\"]] que j'utilise chez Debian. <form method=\"get\"\n"
+#| "action=\"http://pgp.cs.uu.nl/mk_path.cgi?\"\n"
+#| "id=\"clef\">Si vous avez aussi une clef pour signer des documents électroniques, vous\n"
+#| "pouvez vérifier si elle est connectée à <a\n"
+#| "href=\"https://sks-keyservers.net/pks/lookup?op=vindex&search=0xC5BD6C8F2295D502\"\n"
+#| "title=\"Ma clef GPG\">ma clef</a> en entrant son identifiant\n"
+#| "ici&nbsp;:&nbsp;<input name=\"FROM\" size=\"10\" type=\"text\"><input name=\"TO\"\n"
+#| "value=\"2295D502\" type=\"hidden\"><input name=\"PATHS\" value=\"Rechercher un chaîne\n"
+#| "de confiance.\" type=\"submit\"></form>\n"
 msgid ""
-"Mes pages (plus ou moins à jour) dans des annuaires ou des réseaux :\n"
-"[viadeo][], [linkedin][], ou [copains d'avant][copainsdavant].  J'ai\n"
-"[[signé ici|réseauxsociaux.txt]] les URLs ci-dessus avec la [[!wikipediafr signature_numérique desc=\"clef électronique\"]] que j'utilise chez Debian. <form method=\"get\"\n"
-"action=\"http://pgp.cs.uu.nl/mk_path.cgi?\"\n"
-"id=\"clef\">Si vous avez aussi une clef pour signer des documents électroniques, vous\n"
-"pouvez vérifier si elle est connectée à <a\n"
+"J'ai [[signé ici|réseauxsociaux.txt]] les URLs des réseaux sociaux où on peut\n"
+"me trouver, avec la [[!wikipediafr signature_numérique desc=\"clef\n"
+"électronique\"]] que j'utilise chez Debian. <form method=\"get\"\n"
+"action=\"http://pgp.cs.uu.nl/mk_path.cgi?\" id=\"clef\">Si vous avez aussi une clef\n"
+"pour signer des documents électroniques, vous pouvez vérifier si elle est\n"
+"connectée à <a\n"
 "href=\"https://sks-keyservers.net/pks/lookup?op=vindex&search=0xC5BD6C8F2295D502\"\n"
 "title=\"Ma clef GPG\">ma clef</a> en entrant son identifiant\n"
 "ici&nbsp;:&nbsp;<input name=\"FROM\" size=\"10\" type=\"text\"><input name=\"TO\"\n"
@@ -110,31 +105,33 @@ msgid ""
 "de confiance.\" type=\"submit\"></form>\n"
 msgstr "My (more or less up to date) pages in social networks: [viadeo][], [linkedin][], or [copains d'avant][].  I [[signed here|réseauxsociaux.txt]] these URLs with the [[!wikipedia Digital_signature desc=\"electronic key\"]] that I use at Debian.<form method=\"get\" action=\"http://pgp.cs.uu.nl/mk_path.cgi?\" id=\"clef\">If you have a key for signing electronic documents, you can check if it is connected to <a href=\"http://pgpkeys.mit.edu:11371/pks/lookup?op=vindex&search=0xC5BD6C8F2295D502\" title=\"Ma clef GPG\">my key</a> by entering its ID here:<input name=\"FROM\" size=\"10\" type=\"text\"><input name=\"TO\" value=\"2295D502\" type=\"hidden\"><input name=\"PATHS\" value=\"Search for a chain of trust.\" type=\"submit\"></form>\n"
 
-#. type: Link reference
-#, no-wrap
-msgid "[viadeo]:     http://www.viadeo.com/fr/profile/charles.plessy"
-msgstr ""
-
-#. type: Link reference
-#, no-wrap
-msgid "[linkedin]:   http://jp.linkedin.com/in/charlesplessy"
-msgstr ""
-
-#. type: Link reference
-#, no-wrap
-msgid "[annuaire]:   http://annuaire.sciencescope.org/"
-msgstr ""
-
-#. type: Link reference
-#, no-wrap
-msgid "[copainsdavant]:   http://copainsdavant.linternaute.com/membre/520697/7398950458/charles_plessy/"
-msgstr ""
-
 #. type: Plain text
 #, no-wrap
 msgid "<p class=\"thanks\">propulsé par <a href=\"http://ikiwiki.info/\">ikiwiki</a></p>\n"
 msgstr "<p class=\"thanks\">powered by <a href=\"http://ikiwiki.info/\">ikiwiki</a></p>\n"
 
+#~ msgid ""
+#~ "Voici quelques [photos][] (Antarctique, Japon, montagne, divers, …) que "
+#~ "j'ai numérisé.  Ma [[page japon|Japon]] (qui ne se remplit plus "
+#~ "vraiment), avec la traduction du vocabulaire de certains manuels de "
+#~ "japonais. Enfin, quelques nouvelles de moi avec le [[kanji du moment|"
+#~ "Japon/kanji]], et des nouvelles de mes [[contributions|Debian/planète]] "
+#~ "en tant que [développeur Debian][]."
+#~ msgstr ""
+#~ "Here are some [pictures][photos] (Antarctica, Japan, mountain, others, …) "
+#~ "that I scanned.  My [[Japan page|Japon]] (rarely updated), with the "
+#~ "translation of the vocabulary for some Japanese language textbooks.  "
+#~ "Lastly, some personal news with the [[kanji of the day|Japon/kanji]], "
+#~ "news of my [[contributions|Debian/planet]] as [Debian developer]"
+#~ "[développeur Debian]."
+
+#, fuzzy, no-wrap
+#~| msgid "[photos]:\t\thttp://photo.charles.plessy.org/ [développeur Debian]:\thttp://qa.debian.org/developer.php?login=plessy"
+#~ msgid "[développeur Debian]:\thttp://qa.debian.org/developer.php?login=plessy"
+#~ msgstr ""
+#~ "[photos]:\t\thttp://photo.charles.plessy.org/\n"
+#~ "[développeur Debian]:\thttp://qa.debian.org/developer.php?login=plessy"
+
 #, no-wrap
 #~ msgid ""
 #~ "[OIST]:   https://www.oist.jp/\n"

diff --git a/index.mdwn b/index.mdwn
index 1ec3a23d..491b0056 100644
--- a/index.mdwn
+++ b/index.mdwn
@@ -1,24 +1,14 @@
 [[!meta stylesheet="accueil" rel="stylesheet" title="Page d'accueil"]]
 
 
-Voici quelques [photos][] (Antarctique, Japon, montagne, divers, …) que j'ai
-numérisé.  Ma [[page japon|Japon]] (qui ne se remplit plus vraiment), avec la
-traduction du vocabulaire de certains manuels de japonais. Enfin, quelques
-nouvelles de moi avec le [[kanji du moment|Japon/kanji]], et des nouvelles de
-mes [[contributions|Debian/planète]] en tant que [développeur Debian][].
-
-
-[photos]:		http://photo.charles.plessy.org/
-[développeur Debian]:	http://qa.debian.org/developer.php?login=plessy
-
-
 Je travaille à [OIST][] depuis août 2018, et j'y étudie la séquence des
 chromosomes d'un petit animal planctonique appellé _[Oikopleura dioica][]_.
 Auparavant, j'ai travaillé au [RIKEN][] pendant 14 ans, pour y développer des
 technologies pour mesurer l'activité des cellules en séquençant leurs ARN
 messagers.  Je publie mes [résultats en anglais][].  Avant de déménager au
 Japon, j'étudiais le [poisson-zèbre][zfin] à Illkirch.  J'ai encore quelques
-images de mes [poissons transgéniques][gfp] sur ce site.
+images de mes [poissons transgéniques][gfp] sur ce site.  Plus de détails
+sur [[open-source-biologist]].
 
 
 [OIST]:   https://www.oist.jp/
@@ -29,12 +19,12 @@ images de mes [poissons transgéniques][gfp] sur ce site.
 [résultats en anglais]:   http://www.ncbi.nlm.nih.gov/pubmed?term=plessy%20c
 
 
-Mes pages (plus ou moins à jour) dans des annuaires ou des réseaux :
-[viadeo][], [linkedin][], ou [copains d'avant][copainsdavant].  J'ai
-[[signé ici|réseauxsociaux.txt]] les URLs ci-dessus avec la [[!wikipediafr signature_numérique desc="clef électronique"]] que j'utilise chez Debian. <form method="get"
-action="http://pgp.cs.uu.nl/mk_path.cgi?"
-id="clef">Si vous avez aussi une clef pour signer des documents électroniques, vous
-pouvez vérifier si elle est connectée à <a
+J'ai [[signé ici|réseauxsociaux.txt]] les URLs des réseaux sociaux où on peut
+me trouver, avec la [[!wikipediafr signature_numérique desc="clef
+électronique"]] que j'utilise chez Debian. <form method="get"
+action="http://pgp.cs.uu.nl/mk_path.cgi?" id="clef">Si vous avez aussi une clef
+pour signer des documents électroniques, vous pouvez vérifier si elle est
+connectée à <a
 href="https://sks-keyservers.net/pks/lookup?op=vindex&search=0xC5BD6C8F2295D502"
 title="Ma clef GPG">ma clef</a> en entrant son identifiant
 ici&nbsp;:&nbsp;<input name="FROM" size="10" type="text"><input name="TO"
@@ -42,12 +32,6 @@ value="2295D502" type="hidden"><input name="PATHS" value="Rechercher un chaîne
 de confiance." type="submit"></form>
 
 
-[viadeo]:     http://www.viadeo.com/fr/profile/charles.plessy
-[linkedin]:   http://jp.linkedin.com/in/charlesplessy
-[annuaire]:   http://annuaire.sciencescope.org/
-[copainsdavant]:   http://copainsdavant.linternaute.com/membre/520697/7398950458/charles_plessy/
-
-
 ---
 
 <p class="thanks">propulsé par <a href="http://ikiwiki.info/">ikiwiki</a></p>

diff --git a/.gitignore b/.gitignore
index b84c8066..7977173d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,2 +1,3 @@
 /.ikiwiki
 /recentchanges
+*.pot

diff --git a/Debian/debiâneries/bioperl-et-tests.en.po b/Debian/debiâneries/bioperl-et-tests.en.po
index b1c0184d..215fb4d2 100644
--- a/Debian/debiâneries/bioperl-et-tests.en.po
+++ b/Debian/debiâneries/bioperl-et-tests.en.po
@@ -56,7 +56,7 @@ msgstr ""
 "are disabled by default as the Internet is not available in our [build farm]"
 "(http://buildd.debian.org).  Nevertheless, they can be triggered through the "
 "environment variable [DEB_MAINTAINER_MODE](http://lists.debian.org/debian-"
-"perl/2009/09/msg00044.html) when building the package locally.\n"
+"perl/2009/09/msg00044.html) when building the package locally."
 
 #. type: Plain text
 msgid ""
@@ -76,7 +76,7 @@ msgstr ""
 "gmap-run.  In some cases, like EMBOSS, it is because a command has been "
 "renamed in Debian.  In other cases, in particular [[!debpkg wise desc=\"DBA "
 "et Genewise\"]], it is much more difficult to figure out on which side is "
-"the problem.\n"
+"the problem."
 
 #. type: Plain text
 #, no-wrap
@@ -111,7 +111,7 @@ msgstr ""
 "test it comprehensively.  In the example of bioperl-run, it makes it "
 "impossible to build on armel as long as t-coffee is broken there.  Second, "
 "this approach does not help the user to test similarly a program installed "
-"on his computer.\n"
+"on his computer."
 
 #. type: Plain text
 msgid ""
@@ -121,7 +121,7 @@ msgid ""
 msgstr ""
 "Maybe the [Debian Enhancement Proposal 8](http://dep.debian.net/deps/dep8/), "
 "to test binary packages with material provided by their source packages, "
-"will solve these two problems.\n"
+"will solve these two problems."
 
 #~| msgid ""
 #~| "Deuxièmement, cela ne fournit pas un moyen simple à l'utilisateur de "
diff --git a/Debian/debiâneries/bonjour.en.po b/Debian/debiâneries/bonjour.en.po
index 7938e67a..9c6b540b 100644
--- a/Debian/debiâneries/bonjour.en.po
+++ b/Debian/debiâneries/bonjour.en.po
@@ -2,7 +2,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2011-02-10 10:19+0900\n"
+"POT-Creation-Date: 2026-01-11 07:20+0000\n"
 "PO-Revision-Date: 2011-01-15 15:36+0900\n"
 "Last-Translator: Charles Plessy <https://launchpad.net/~plessy>\n"
 "Language-Team: Hopla\n"
@@ -49,20 +49,40 @@ msgstr ""
 "not much to translate anyway. Conversions will be via ikiwiki’s [po plugin] "
 "[]. This blog is hosted on [Branchable] []."
 
-#. type: Plain text
-msgid ""
-"[Planet Debian]: http://planet.debian.org/ [po4a]: http://po4a.alioth.debian."
-"org/ [Virtaal]: http://translate.sourceforge.net/wiki/virtaal/ [Poedit]: "
-"http://www.poedit.net/ [plugin po]: http://ikiwiki.info/plugins/po/ "
-"[ikiwiki]: http://ikiwiki.info/ [Branchable]: http://www.branchable.com/"
+#. type: Link reference
+#, no-wrap
+msgid "[Planet Debian]: http://planet.debian.org/"
+msgstr ""
+
+#. type: Link reference
+#, no-wrap
+msgid "[po4a]: http://po4a.alioth.debian.org/"
+msgstr ""
+
+#. type: Link reference
+#, no-wrap
+msgid "[Virtaal]: http://translate.sourceforge.net/wiki/virtaal/"
+msgstr ""
+
+#. type: Link reference
+#, no-wrap
+msgid "[Poedit]: http://www.poedit.net/"
+msgstr ""
+
+#. type: Link reference
+#, no-wrap
+msgid "[plugin po]: http://ikiwiki.info/plugins/po/"
+msgstr ""
+
+#. type: Link reference
+#, no-wrap
+msgid "[ikiwiki]: http://ikiwiki.info/"
+msgstr ""
+
+#. type: Link reference
+#, no-wrap
+msgid "[Branchable]: http://www.branchable.com/"
 msgstr ""
-"[Planète Debian]: http://planet-fr.debian.net/\n"
-"[po4a]: http://po4a.alioth.debian.org/\n"
-"[Virtaal]: http://translate.sourceforge.net/wiki/virtaal/\n"
-"[Poedit]: http://www.poedit.net/\n"
-"[po plugin]: http://ikiwiki.info/plugins/po/\n"
-"[ikiwiki]: http://ikiwiki.info/\n"
-"[Branchable]: http://www.branchable.com/\n"
 
 #. type: Plain text
 msgid ""
@@ -81,12 +101,31 @@ msgstr ""
 "the general public in the future. And given the stakes, I hope that some of "
 "them will be free and we'll manage to distribute them in Debian!"
 
-#. type: Plain text
-msgid ""
-"[bioinformatique]: http://qa.debian.org/developer.php?login=plessy [Debian "
-"Med]: http://www.debian.org/devel/debian-med/ [séquençage de l'ADN]: http://"
-"fr.wikipedia.org/wiki/S%C3%A9quenceur_d%27ADN#S.C3.A9quenceur_haut_d.C3.A9bit"
+#. type: Link reference
+#, no-wrap
+msgid "[bioinformatique]: http://qa.debian.org/developer.php?login=plessy"
 msgstr ""
-"[bioinformatics]: http://qa.debian.org/developer.php?login=plessy\n"
-"[Debian Med]: http://www.debian.org/devel/debian-med/\n"
-"[DNA sequencing]: http://en.wikipedia.org/wiki/Next-generation_sequencing\n"
+
+#. type: Link reference
+#, no-wrap
+msgid "[Debian Med]: http://www.debian.org/devel/debian-med/"
+msgstr ""
+
+#. type: Link reference
+#, fuzzy, no-wrap
+#| msgid "[bioinformatique]: http://qa.debian.org/developer.php?login=plessy [Debian Med]: http://www.debian.org/devel/debian-med/ [séquençage de l'ADN]: http://fr.wikipedia.org/wiki/S%C3%A9quenceur_d%27ADN#S.C3.A9quenceur_haut_d.C3.A9bit"
+msgid "[séquençage de l'ADN]: http://fr.wikipedia.org/wiki/S%C3%A9quenceur_d%27ADN#S.C3.A9quenceur_haut_d.C3.A9bit"
+msgstr "[bioinformatics]: http://qa.debian.org/developer.php?login=plessy[Debian Med]: http://www.debian.org/devel/debian-med/[DNA sequencing]: http://en.wikipedia.org/wiki/Next-generation_sequencing"
+
+#~ msgid ""
+#~ "[Planet Debian]: http://planet.debian.org/ [po4a]: http://"
+#~ "po4a.alioth.debian.org/ [Virtaal]: http://translate.sourceforge.net/wiki/"
+#~ "virtaal/ [Poedit]: http://www.poedit.net/ [plugin po]: http://"
+#~ "ikiwiki.info/plugins/po/ [ikiwiki]: http://ikiwiki.info/ [Branchable]: "
+#~ "http://www.branchable.com/"
+#~ msgstr ""
+#~ "[Planète Debian]: http://planet-fr.debian.net/[po4a]: http://"
+#~ "po4a.alioth.debian.org/[Virtaal]: http://translate.sourceforge.net/wiki/"
+#~ "virtaal/[Poedit]: http://www.poedit.net/[po plugin]: http://ikiwiki.info/"
+#~ "plugins/po/[ikiwiki]: http://ikiwiki.info/[Branchable]: http://"
+#~ "www.branchable.com/"
diff --git a/Debian/debiâneries/bts.en.po b/Debian/debiâneries/bts.en.po
index a64e2f0f..d9cb0332 100644
--- a/Debian/debiâneries/bts.en.po
+++ b/Debian/debiâneries/bts.en.po
@@ -6,14 +6,14 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2019-12-17 14:33+0000\n"
+"POT-Creation-Date: 2026-01-11 07:20+0000\n"
 "PO-Revision-Date: 2019-12-17 23:36+0900\n"
+"Last-Translator: Charles Plessy <toto@example.com>\n"
+"Language-Team: \n"
 "Language: en\n"
 "MIME-Version: 1.0\n"
 "Content-Type: text/plain; charset=UTF-8\n"
 "Content-Transfer-Encoding: 8bit\n"
-"Last-Translator: Charles Plessy <toto@example.com>\n"
-"Language-Team: \n"
 "X-Generator: Poedit 2.2.1\n"
 
 #. type: Plain text
diff --git a/Debian/debiâneries/cloud-init.en.po b/Debian/debiâneries/cloud-init.en.po
index 3e425fca..1c16d94b 100644
--- a/Debian/debiâneries/cloud-init.en.po
+++ b/Debian/debiâneries/cloud-init.en.po
@@ -7,7 +7,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: PACKAGE VERSION\n"
-"POT-Creation-Date: 2012-05-26 02:14+0000\n"
+"POT-Creation-Date: 2026-01-11 07:20+0000\n"
 "PO-Revision-Date: 2012-05-26 11:14+0900\n"
 "Last-Translator: Charles Plessy <>\n"
 "Language-Team: LANGUAGE <LL@li.org>\n"
@@ -53,7 +53,7 @@ msgstr ""
 "connect to it.  If the machine image is public and if the instance is open "
 "to the Internet, which is common when using commercial providers such as "
 "[Amazon][], an attacker could connect randomly to known IPs from the cloud, "
-"and eventually access to an instance before its owner.\n"
+"and eventually access to an instance before its owner."
 
 #. type: Plain text
 msgid ""
@@ -67,7 +67,7 @@ msgstr ""
 "at startup, called [instance metadata][métadonnées d'instance], which will "
 "be available to this instance only at a fixed HTTP URL.  If the owner "
 "provides a [public SSH key][clé publique SSH], this can be used to ensure "
-"that only the owner of the private key can connect.\n"
+"that only the owner of the private key can connect."
 
 #. type: Plain text
 #, no-wrap

(Diff truncated)

diff --git a/tags/repeats.mdwn b/tags/repeats.mdwn
new file mode 100644
index 00000000..4fe8b274
--- /dev/null
+++ b/tags/repeats.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged repeats"]]
+
+[[!inline pages="tagged(repeats)" actions="no" archive="yes"
+feedshow=10]]

diff --git a/tags/sequence_tag.mdwn b/tags/sequence_tag.mdwn
new file mode 100644
index 00000000..244d1cd6
--- /dev/null
+++ b/tags/sequence_tag.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged sequence tag"]]
+
+[[!inline pages="tagged(sequence_tag)" actions="no" archive="yes"
+feedshow=10]]

diff --git a/tags/cephalochordate.mdwn b/tags/cephalochordate.mdwn
new file mode 100644
index 00000000..2ef316f1
--- /dev/null
+++ b/tags/cephalochordate.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged cephalochordate"]]
+
+[[!inline pages="tagged(cephalochordate)" actions="no" archive="yes"
+feedshow=10]]

diff --git a/tags/tags.mdwn b/tags/tags.mdwn
new file mode 100644
index 00000000..1b8430b8
--- /dev/null
+++ b/tags/tags.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged tags"]]
+
+[[!inline pages="tagged(tags)" actions="no" archive="yes"
+feedshow=10]]

diff --git a/tags/reverse-transcription.mdwn b/tags/reverse-transcription.mdwn
new file mode 100644
index 00000000..a6d340df
--- /dev/null
+++ b/tags/reverse-transcription.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged reverse-transcription"]]
+
+[[!inline pages="tagged(reverse-transcription)" actions="no" archive="yes"
+feedshow=10]]

diff --git a/tags/cell_line.mdwn b/tags/cell_line.mdwn
new file mode 100644
index 00000000..6e03a931
--- /dev/null
+++ b/tags/cell_line.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged cell line"]]
+
+[[!inline pages="tagged(cell_line)" actions="no" archive="yes"
+feedshow=10]]

diff --git a/tags/sequence.mdwn b/tags/sequence.mdwn
new file mode 100644
index 00000000..6a90b3fd
--- /dev/null
+++ b/tags/sequence.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged sequence"]]
+
+[[!inline pages="tagged(sequence)" actions="no" archive="yes"
+feedshow=10]]

diff --git a/tags/operon.mdwn b/tags/operon.mdwn
new file mode 100644
index 00000000..cbea2bd3
--- /dev/null
+++ b/tags/operon.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged operon"]]
+
+[[!inline pages="tagged(operon)" actions="no" archive="yes"
+feedshow=10]]

diff --git a/tags/ANI.mdwn b/tags/ANI.mdwn
new file mode 100644
index 00000000..e06c8b9a
--- /dev/null
+++ b/tags/ANI.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged ANI"]]
+
+[[!inline pages="tagged(ANI)" actions="no" archive="yes"
+feedshow=10]]

diff --git a/tags/pangenome.mdwn b/tags/pangenome.mdwn
new file mode 100644
index 00000000..6f980f78
--- /dev/null
+++ b/tags/pangenome.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged pangenome"]]
+
+[[!inline pages="tagged(pangenome)" actions="no" archive="yes"
+feedshow=10]]

diff --git a/biblio/10.1007_s00343-025-503.mdwn b/biblio/10.1007_s00343-025-503.mdwn
new file mode 100644
index 00000000..07c8a51b
--- /dev/null
+++ b/biblio/10.1007_s00343-025-503.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Limited growth and recruitment of _Oikopleura dioica_ (Tunicata: Appendicularia) in the Jiaozhou Bay, China"]]
+[[!tag Oikopleura]]
+
+Shuai Li, Mengtan Liu, Aiyong Wan, Zhiqiang Xu, Shiwei Wang, Yi Liang, Zengxia Zhao & Guangtao Zhang
+
+Limited growth and recruitment of _Oikopleura dioica_ (Tunicata: Appendicularia) in the Jiaozhou Bay, China
+
+J. Ocean. Limnol. (2025). doi: 10.1007/s00343-025-503
+
+[[!doi 10.1007_s00343-025-503 desc="_O. dioica was mostly found from June to December 2011.  Salinity varied between ~31 and ~28, and temperature between ~25 and ~5.  Chlorophyl peaked in both winter and summer, but cyanobacteria only peaked in summer.  Wild animals never reached the size of lab animals during the whole year."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index c49fe7b5..10c24094 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -712,8 +712,7 @@ Ecology
  - A study near an eddy of the Kuroshio extension defined three communities, including
    one coastal characterised by high species diversity and the presence of _O. dioica_,
    one dominated by _O. longicauda_ and one with a higher contribution of _Fritillaria_
-    [[Sato, Kodama and Hidaka, 2024|biblio/10.1093_plankt_fbaf029]].
-
+   [[Sato, Kodama and Hidaka, 2024|biblio/10.1093_plankt_fbaf029]].
 
 ### Distribution near Taiwan and China
 
@@ -734,6 +733,10 @@ Ecology
    ([[Franco, Chen and Li, 2014|biblio/10.1007_s11802-014-2376-0]]).  Abundance peaked
    is spring, but the animals could also be found in winter when water temperature
    went below 10°C.
+ - _O. dioica_ was found mostly from June to December in Jiaozhou Bay,
+   especially when both chlorophyl and cyanobacteria peaked.  Nevertheless, the
+   size of wild catches was consistently smaller than lab animals
+   [[Li and coll., 2025|biblio/10.1007_s00343-025-503]].
 
 ### Elsewhere in the Pacific ocean
 

diff --git a/biblio/40773350.mdwn b/biblio/40773350.mdwn
new file mode 100644
index 00000000..b1ad7671
--- /dev/null
+++ b/biblio/40773350.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Protocol for the isolation, culture, and transfection of squid primary cells"]]
+[[!tag cell_culture]]
+
+Kim Y, Tanner HM, Rosenthal JJC, Brangwynne CP
+
+STAR Protoc. 2025 Sep 19;6(3):103994. doi:10.1016/j.xpro.2025.103994
+
+Protocol for the isolation, culture, and transfection of squid primary cells
+
+[[!pmid 40773350 desc="Fibroblast-like cells migrate out of optic lobe, eye or gill explants after trypsin digestion, and can be transfected, but no cell division was observed.  Insulin-transferrin-selenium (ITS-G), FGF and EGF are present in the cell culture medium."]]
diff --git a/tags/cell_culture.mdwn b/tags/cell_culture.mdwn
index 4383346d..7ee49049 100644
--- a/tags/cell_culture.mdwn
+++ b/tags/cell_culture.mdwn
@@ -10,5 +10,6 @@ A few notes that just scratch the surface of a vast field…
  - [[Kawamura and coll. (2021)|biblio/33899125]] reported the use of plasmin to establish coral cell lines.
  - Shark cells need high osmolarity and a supplement of 333 mM urea, 188 mM NaCl and 54 mM trimethylamine N-oxide ([[Uno and coll., 2020|biblio/33159152]]).
  - RasV12 could immortalise _Drosophila_ cells ([[Simcox and coll. 2008|biblio/18670627]]).  Such lines seem to preferentially originate from adult muscle precursor cells ([[Dequéant and coll., 2015|biblio/26438832]]).
+ - Primary squid cell culture from explants in ITS-G, FGF and EGF ([[Kai and coll., 2025|biblio/40773350]]).
 
 [[!inline pages="tagged(cell_culture)" limit=0]]

diff --git a/biblio/10.64898_2025.12.03.692109.mdwn b/biblio/10.64898_2025.12.03.692109.mdwn
new file mode 100644
index 00000000..09e3fbe4
--- /dev/null
+++ b/biblio/10.64898_2025.12.03.692109.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Behavioral ontogeny in a pelagic tunicate reveals the deep origins of chordate behavioral developmental plasticity"]]
+[[!tag bioRxiv Oikopleura]]
+
+Oleg Tolstenkov, Rodolfo da Silva Mazzarini Baldinotti, Sissel Norland, Anne Elin Aasjord, Daniel Chourrout, Marios Chatzigeorgiou
+
+bioRxiv 2025.12.03.692109; doi: 10.64898/2025.12.03.692109
+
+Behavioral ontogeny in a pelagic tunicate reveals the deep origins of chordate behavioral developmental plasticity
+
+[[!doi 10.64898/2025.12.03.692109 desc="“We built a behavioral atlas of the planktonic tunicate Oikopleura dioica across its life cyclefrom larval to adult stages using high-throughput tracking and unsupervised analysis.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index a9a445d1..c49fe7b5 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -538,8 +538,8 @@ Anatomy
  - The brain of _B. stygius_ contains a number of cells comparable to the one of
    _O. dioica_ ([[Zemann and coll., 2003|biblio/37313762]]).
 
-Physiology
-----------
+Physiology and behaviour
+------------------------
 
  - Searching for an immune system, [[Denoeud et al., 2010|biblio/21097902]] excluded
    LRR proteins, as none of the 74 models found had a transmembrane domain.
@@ -563,6 +563,7 @@ Physiology
  - In line with the absence of peroxisomes in _O. dioica_, no wax esters
    (storage lipids) were found in _O vanhoeffenni_, which is mostly containing
    phospholipids [[Deibel and coll.,1992|biblio/m088p297]].
+ - Quantitative study of _O. dioica_ behaviour: [[Tolstenkov and coll., 2025|biblio/10.64898_2025.12.03.692109]].
 
 House
 -----

diff --git a/biblio/10.64898_2025.12.09.693291.mdwn b/biblio/10.64898_2025.12.09.693291.mdwn
new file mode 100644
index 00000000..c197ba6b
--- /dev/null
+++ b/biblio/10.64898_2025.12.09.693291.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evolution of Tunicate lifestyles shaped by Myosin heavy chain gene duplications, losses, and the diversification of tail muscle cell identities in Oikopleura dioica"]]
+[[!tag biorXiv Oikopleura]]
+
+Marc Fabregà-Torrus, Alfonso Ferrández-Roldán, Gaspar Sánchez-Serna, Beatriz Iralde Cárdenas, Cristian Cañestro
+
+bioRxiv 2025.12.09.693291; doi: 10.64898/2025.12.09.693291
+
+Evolution of Tunicate lifestyles shaped by Myosin heavy chain gene duplications, losses, and the diversification of tail muscle cell identities in Oikopleura dioica
+
+[[!doi 10.64898/2025.12.09.693291 desc="_O. dioica_ lost the jaw/body wall myosin heavy chain and amplified the paraxial ones."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index e682b010..a9a445d1 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -286,9 +286,11 @@ Genes and pathways
  - There are two copies of Aurora, _OdAur1_ and _OdAur2_.  In meiosis, they
    localise to the centrosomes and the spindle respectively ([[Feng and
    Thompson, 2023|biblio/38130951]]).
+ - _O. doica_ amplified the paraxial myosin heavy chains ([[Marc Fabregà-Torrus and coll., 2025|biblio/10.64898_2025.12.09.693291]]).
 
 ### Lost
 
+ - _O. doica_ lost the jaw/body wall myosin heavy chain ([[Marc Fabregà-Torrus and coll., 2025|biblio/10.64898_2025.12.09.693291]]).
  - _O. dioica_ lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]],
    [[Albalat, Martí-Solans and Cañestro, 2012|biblio/22389042]]).
    It has Dnmt2, but this is a tRNA methyltransferase and it was later renamed Trdmt1 accordingly.

diff --git a/biblio/10.64898_2025.12.09.693154.mdwn b/biblio/10.64898_2025.12.09.693154.mdwn
new file mode 100644
index 00000000..9f5c7ca5
--- /dev/null
+++ b/biblio/10.64898_2025.12.09.693154.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Downstream effects of the “Less, but More” Fgf signaling in Oikopleura dioica: Fgf receptor expansion and RTK pathway simplification"]]
+[[!tag bioRxiv Oikopleura]]
+
+Gaspar Sánchez-Serna, Paula Bujosa, Alfonso Ferrández-Roldán, Marc Fabregá-Torrus, Ana Alonso-Bartolomé, Laura Reyner-Laplana, Nuria P. Torres-Águila, Cristian Cañestro
+
+bioRxiv 2025.12.09.693154; doi: 10.64898/2025.12.09.693154
+
+Downstream effects of the “Less, but More” Fgf signaling in Oikopleura dioica: Fgf receptor expansion and RTK pathway simplification
+
+[[!doi 10.64898/2025.12.09.693154 desc="Like in ascidians, the classical Ras protein is lost but was probably substituted by other related Ras proteins"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 21304551..e682b010 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -330,6 +330,8 @@ Genes and pathways
  - None of the genes encoding Bcl-2 proteins or their BH3-only ligands could be found
    in _O. dioica_ [[Suraweera and coll., 2022|biblio/35409052]].
  - Three caspases related to the CSP3/7 family were found by [[Weil and coll, 2005|biblio/15826240]].
+ - The classical Ras proteins were lost like in ascidians but their function was
+   probably taken over by other protein of the Ras-family [[Sánchez-Serna and coll. 2025|biblio/10.64898_2025.12.09.693154]].
 
 Epigenome
 ---------

diff --git a/biblio/30415838.mdwn b/biblio/30415838.mdwn
new file mode 100644
index 00000000..73e03cbb
--- /dev/null
+++ b/biblio/30415838.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum."]]
+[[!tag yeast]]
+
+Shen XX, Opulente DA, Kominek J, Zhou X, Steenwyk JL, Buh KV, Haase MAB, Wisecaver JH, Wang M, Doering DT, Boudouris JT, Schneider RM, Langdon QK, Ohkuma M, Endoh R, Takashima M, Manabe RI, Čadež N, Libkind D, Rosa CA, DeVirgilio J, Hulfachor AB, Groenewald M, Kurtzman CP, Hittinger CT, Rokas A.
+
+Cell. 2018 Nov 29;175(6):1533-1545.e20. doi:10.1016/j.cell.2018.10.023
+
+Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum.
+
+[[!pmid 30415838 desc="Survey of 45 metabolic traits over 400 million years of yeast evolutionary history suggests that lineages evolved by gene loss from a generalist ancestor.  “We estimate the origin of the subphylum between 317 and 523 (95% credibility interval; posterior mean date: 404) million years ago (mya); the origin of the CUG-Ser1 clade, which contains the major opportunistic pathogen C. albicans, between 178 and 248 (210) mya, the origin of the whole-genome duplication (WGD) clade between 82 and 105 (93) mya, and the divergence of S. cerevisiae and C. albicans from their sister species (Saccharomyces paradoxus and Candida dubliniensis) between 4.0 and 5.8 (4.9) mya and 5.0 and 14.0 (8.7) mya, respectively”"]]
diff --git a/tags/yeast.mdwn b/tags/yeast.mdwn
index 2e16ab37..5fc10487 100644
--- a/tags/yeast.mdwn
+++ b/tags/yeast.mdwn
@@ -2,5 +2,9 @@
 
 # Yeast and other unicellular fungi
 
+## Phylogeny
+
+ - [[Shen and coll., 2018|biblio/30415838]]: “We estimate the origin of the subphylum between 317 and 523 (95% credibility interval; posterior mean date: 404) million years ago (mya); the origin of the CUG-Ser1 clade, which contains the major opportunistic pathogen C. albicans, between 178 and 248 (210) mya, the origin of the whole-genome duplication (WGD) clade between 82 and 105 (93) mya, and the divergence of S. cerevisiae and C. albicans from their sister species (Saccharomyces paradoxus and Candida dubliniensis) between 4.0 and 5.8 (4.9) mya and 5.0 and 14.0 (8.7) mya, respectively”
+
 [[!inline pages="tagged(yeast)" actions="no" archive="yes"
 feedshow=10]]

diff --git a/biblio/41379974.mdwn b/biblio/41379974.mdwn
new file mode 100644
index 00000000..d14065da
--- /dev/null
+++ b/biblio/41379974.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Multispecies pangenomes reveal a pervasive influence of population size on structural variation."]]
+[[!tag repeat]
+
+Edwards SV, Fang B, Khost D, Kolyfetis GE, Cheek RG, DeRaad DA, Chen N, Fitzpatrick JW, McCormack JE, Funk WC, Ghalambor CK, Garrison E, Guarracino A, Li H, Sackton TB. 
+
+Science. 2025 Dec 11;390(6778):eadw1931. doi:10.1126/science.adw1931
+
+Multispecies pangenomes reveal a pervasive influence of population size on structural variation.
+
+[[!pmid 41379974 desc="“We find rapid evolution of genome architecture, including ~100-megabase decreases in genome size driven by shifts in complex satellite landscapes”"]]

diff --git a/biblio/40349337.mdwn b/biblio/40349337.mdwn
index 3e94ef4a..08ed26ba 100644
--- a/biblio/40349337.mdwn
+++ b/biblio/40349337.mdwn
@@ -7,4 +7,4 @@ Cell Rep. 2025 May 27;44(5):115697. doi:10.1016/j.celrep.2025.115697
 
 Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves.
 
-[[!pmid 40349337 desc=""]]
+[[!pmid 40349337 desc="“contiguous shell/core gene block[s …] consisted of singletons (80.4% in B. belcheri, 74.9% in B. floridae) or contained fewer than 5 genes (99.0% in B. belcheri, 99.1% in B. floridae).”  “in the B. belcheri reference genome [and] 20 of the analysed resequenced samples [we found] the integrated genome of a herpes-like virus spanning 149,856 bp in length. […] Overall, BelcheriHV-1 was 24 × less impacted by nucleotide variations than the B. belcheri genome, with an average of one SNP per 5,958 nt, vs one SNP per 174 nt, respectively.” “[the dispensable genes] found in hemizygosity in only one of the two parental genotypes […] were absent in 40% of the offspring (expected 50%) and those found in hemizygosity in both parental genomes […] were absent in 19% of the offspring (expected 25%).”"]]

diff --git a/biblio/34289044.mdwn b/biblio/34289044.mdwn
new file mode 100644
index 00000000..029c9244
--- /dev/null
+++ b/biblio/34289044.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Nonparametric Bootstrap Support"]]
+[[!tag ANI]]
+
+Gosselin S, Fullmer MS, Feng Y, Gogarten JP.
+
+Improving Phylogenies Based on Average Nucleotide Identity, Incorporating Saturation Correction and Nonparametric Bootstrap Support.
+
+Syst Biol. 2022 Feb 10;71(2):396-409. doi:10.1093/sysbio/syab060
+
+[[!pmid 34289044 desc="“The distance (abbreviated Total Average Nucleotide Identity, or tANI) was calculated by using the formula: tANI  -ln(AF*ANI). The natural log added to this calculation counteracts saturation for low AF*ANI values” Mostly tested on bacteria but also briefly on primates and yeasts"]]
diff --git a/biblio/40349337.mdwn b/biblio/40349337.mdwn
new file mode 100644
index 00000000..3e94ef4a
--- /dev/null
+++ b/biblio/40349337.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves."]]
+[[!tag cephalochordate pangenome]]
+
+Liu S, Shi C, Chen C, Tan Y, Tian Y, Macqueen DJ, Li Q.
+
+Cell Rep. 2025 May 27;44(5):115697. doi:10.1016/j.celrep.2025.115697
+
+Haplotype-resolved genomes provide insights into the origins and functional significance of genome diversity in bivalves.
+
+[[!pmid 40349337 desc=""]]

diff --git a/biblio/30504855.mdwn b/biblio/30504855.mdwn
index fc8aa412..78c3736b 100644
--- a/biblio/30504855.mdwn
+++ b/biblio/30504855.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries."]]
-[[!tag speciation]]
+[[!tag ANI speciation]]
 
 Nat Commun. 2018 Nov 30;9(1):5114. doi:10.1038/s41467-018-07641-9
 
diff --git a/biblio/39878503.mdwn b/biblio/39878503.mdwn
new file mode 100644
index 00000000..20d2c49c
--- /dev/null
+++ b/biblio/39878503.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism."]]
+[[!tag ANI speciation]]
+
+Ndovie W, Havránek J, Leconte J, Koszucki J, Chindelevitch L, Adriaenssens EM, Mostowy RJ.
+
+Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism.
+
+mSystems. 2025 Feb 18;10(2):e0166124. doi:10.1128/msystems.01661-24
+
+[[!pmid 39878503 desc="“revealed a multimodal ANI distribution, with a distinct gap around 80%, akin to the bacterial ANI gap (~90%)”  “accuracy and scalability compared to existing approaches, even to data sets of hundreds of thousands of viral genomes”"]]

diff --git a/biblio/10.1101_2025.09.17.676786v1.mdwn b/biblio/10.1101_2025.09.17.676786v1.mdwn
new file mode 100644
index 00000000..03e90c34
--- /dev/null
+++ b/biblio/10.1101_2025.09.17.676786v1.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The mutation landscape of Daphnia obtusa reveals evolutionary forces shaping genome stability"]]
+[[!tag mutation]]
+
+The mutation landscape of Daphnia obtusa reveals evolutionary forces shaping genome stability
+
+Ruyun Deng, Feng Guo, Wen Wei, Michael E. Pfrender, Jeff L. Dudycha, Michael Lynch, Zhiqiang Ye
+
+bioRxiv 2025.09.17.676786; doi:10.1101/2025.09.17.676786
+
+[[!doi 10.1101/2025.09.17.676786v1 desc="“For D. pulex, the estimated mutation rates range from 2.3 × 10⁻⁹ to 4.53 × 10⁻⁹ substitutions per site per generation […] the estimate for D. magna is somewhat higher, ~8.9 × 10⁻⁹ per site per generation.”  “Genetically, D. obtusa is moderately divergent from the D. pulex–D. pulicaria species complex, with a silent-sit divergence of ~0.12”  “The primary draft genome assembly presented here, FS6_V2, consists of 129.4 Mb of DNA sequences located on 12 chromosomes”  “over 20 years […],  142  eight lines survived for deep whole-genome sequencing, having been propagated asexually for an average of 482 generations”  “we restricted our analysis to genomic sites with read depths between 20 and 300, resulting in an average of 87 million callable sites per sample”  “Across the D. obtusa genome, 99.43% of sites were homozygous, with only 0.57% being heterozygous”  “we defined a de novo mutation as a site that was unique to a single MA line and represented a change from the ancestral homozygous state to a heterozygous state”  “The overall SNM rate is estimated to be 2.23 × 10−9 mutations per base per generation […] while the indel rate is 2.75 × 10−10”  “Among the base substitutions, the most frequent type is C:G > T:A, occurring at a frequency 5.6 × higher than the least common type, C:G > G:C. The transition-to-transversion (Ts/Tv) ratio is 1.31”  “To estimate the expected GC-content of the genome at mutation–equilibrium, we used the rate of G/C → A/T substitutions (v) and the rate of A/T → G/C substitutions (u). The equilibrium GC-content […] is calculated as u / (u + v) [and was] estimated to be 0.320, which is much lower than the observed GC content of 0.409.”  “ we observed a significant deficit of mutations at  nonsynonymous sites”. “While chromosomes 11 and 12 showed slightly elevated mutation rates, a Chi-square test indicated no significant deviation from a uniform distribution”. “Using a minor allele frequency (MAF) threshold of >0.02 to define the presence of  alternative alleles, we found that 210 (29%) and 248 (34%) of the SNMs from the MA lines were also present in the EBG and RAP populations”  “we identified a total of 48 LOH events, with the number of events per MA line ranging from 0 to 22”  “We estimated a genome-wide LOH rate of 2.93 × 10−5 per heterozygous site per generation.”  “Among the 48 identified LOH events, 8 were attributed to heterozygous deletions, while 40 were attributed to gene conversion. The average length of conversion tracts was 320 kb. The estimated genome-wide rate of conversion-induced LOH was 2.62 × 10−5 per heterozygous site per generation.”"]]
diff --git a/tags/mutation.mdwn b/tags/mutation.mdwn
index 32831029..95773955 100644
--- a/tags/mutation.mdwn
+++ b/tags/mutation.mdwn
@@ -1,5 +1,9 @@
 [[!meta title="pages tagged mutation"]]
 
-De novo mutation rate in _Branchiostoma floridae_ was estimated to 5.10 × 10-9 per base per generation by [[Xue and coll. (2025)|biblio/10.1101_2025.07.14.664012]]
+### De novo mutation rates
+
+_Branchiostoma floridae_ was estimated to 5.10 × 10-9 per base per generation by [[Xue and coll. (2025)|biblio/10.1101_2025.07.14.664012]]
+
+_Daphnia obtusa_: [[Deng and coll. (2025)|biblio/10.1101_2025.09.17.676786v1]] estimated a spontaneous single nucleotide mutation (SNM) rate of 2.23 × 10-9 and an indel mutation rate of 2.75 × 10-10 per site per generation“ using mutation accumulation lines.
 
 [[!inline pages="tagged(mutation)" actions="no" limit=0]]

diff --git a/biblio/18278033.mdwn b/biblio/18278033.mdwn
index 46cdfbd5..238e749a 100644
--- a/biblio/18278033.mdwn
+++ b/biblio/18278033.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Direct multiplexed measurement of gene expression with color-coded probe pairs."]]
-[[!tag in_situ imaging method]]
+[[!tag imaging method]]
 
 Geiss GK, Bumgarner RE, Birditt B, Dahl T, Dowidar N, Dunaway DL, Fell HP, Ferree S, George RD, Grogan T, James JJ, Maysuria M, Mitton JD, Oliveri P, Osborn JL, Peng T, Ratcliffe AL, Webster PJ, Davidson EH, Hood L, Dimitrov K.
 
diff --git a/tags/in_situ.mdwn b/tags/in_situ.mdwn
deleted file mode 100644
index f1b60a12..00000000
--- a/tags/in_situ.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged in situ"]]
-
-[[!inline pages="tagged(in_situ)" actions="no" archive="yes"
-feedshow=10]]

diff --git a/biblio/10.1101_2020.05.07.078311.mdwn b/biblio/10.1101_2020.05.07.078311.mdwn
deleted file mode 100644
index be6a0ea9..00000000
--- a/biblio/10.1101_2020.05.07.078311.mdwn
+++ /dev/null
@@ -1,10 +0,0 @@
-[[!meta title="Conservative route to genome compaction in a miniature annelid"]]
-[[!tag genome synteny]]
-
-José M. Martín-Durán, Bruno C. Vellutini, Ferdinand Marlétaz, Viviana Cetrangolo, Nevena Cvetesic, Daniel Thiel, Simon Henriet, Xavier Grau-Bové, Allan M. Carrillo-Baltodano, Wenjia Gu, Alexandra Kerbl, Yamile Marquez, Nicolas Bekkouche, Daniel Chourrout, Jose Luis Gómez-Skarmeta, Manuel Irimia, Boris Lenhard, Katrine Worsaae, Andreas Hejnol
-
-bioRxiv 2020.05.07.078311; doi:10.1101/2020.05.07.078311 
-
-Conservative route to genome compaction in a miniature annelid
-
-[[!doi 10.1101/2020.05.07.078311 desc="Genome assembly (PacBio, 73.8 Mb, 95.8% BUSCO genes, 2.24 Mb N50, 4.87% transposable elements, 14,203 protein-coding genes) for the annelid Dimorphilus gyrociliatus, a meiobenthic segmented worm.  Synteny with the scallop genome is visible.  The Hox cluster is present and lacks only one gene, post1.  However, in situ hybridisation suggests lack of temporal colinearity.  The Myc pathway  “lacks the regulators mad (in D. gyrociliatus) and mnt (in all Dinophilidae), a condition also shared with the appendicularian O. dioica”.  “Open chromatin regions [ATAC-seq peaks] are short and mostly found in promoters.”  “Promoters [CAGE] are narrow (<150 bp) and use pyrimidine-purine dinucleotides as preferred initiators.”"]]
diff --git a/biblio/33199869.mdwn b/biblio/33199869.mdwn
new file mode 100644
index 00000000..c15d5690
--- /dev/null
+++ b/biblio/33199869.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Conservative route to genome compaction in a miniature annelid"]]
+[[!tag genome synteny]]
+
+José M. Martín-Durán, Bruno C. Vellutini, Ferdinand Marlétaz, Viviana Cetrangolo, Nevena Cvetesic, Daniel Thiel, Simon Henriet, Xavier Grau-Bové, Allan M. Carrillo-Baltodano, Wenjia Gu, Alexandra Kerbl, Yamile Marquez, Nicolas Bekkouche, Daniel Chourrout, Jose Luis Gómez-Skarmeta, Manuel Irimia, Boris Lenhard, Katrine Worsaae, Andreas Hejnol
+
+Nat Ecol Evol. 2021 Feb;5(2):231-242. doi: 10.1038/s41559-020-01327-6
+
+Conservative route to genome compaction in a miniature annelid
+
+[[!pmid 33199869 10.1101/2020.05.07.078311 desc="Genome assembly (PacBio, 73.8 Mb, 95.8% BUSCO genes, 2.24 Mb N50, 4.87% transposable elements, 14,203 protein-coding genes) for the annelid Dimorphilus gyrociliatus, a meiobenthic segmented worm.  Synteny with the scallop genome is visible.  The Hox cluster is present and lacks only one gene, post1.  However, in situ hybridisation suggests lack of temporal colinearity.  The Myc pathway  “lacks the regulators mad (in D. gyrociliatus) and mnt (in all Dinophilidae), a condition also shared with the appendicularian O. dioica”.  “Open chromatin regions [ATAC-seq peaks] are short and mostly found in promoters.”  “Promoters [CAGE] are narrow (<150 bp) and use pyrimidine-purine dinucleotides as preferred initiators.”"]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index b0d18deb..c98378ba 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -84,7 +84,7 @@ Chiton species of very similar morphology can have different karyotypes
    chordate chromosomes.  _Drosophila_ has no synteny with scallop, but _C.
    elegans_ still has some [[Wang and coll., 2017|biblio/28812685]].  The annelid
    worm _Dimorphilus gyrociliatus_ also has
-   ([[Martín-Durán and coll., 2020|biblio/10.1101_2020.05.07.078311]]).
+   ([[Martín-Durán and coll., 2021|biblio/33199869]]).
 
  - The ancestral amniote has 49 chromosomes ([[Sacerdot and coll., 2018|biblio/30333059]]).
 

diff --git a/biblio/10.1101_2022.05.30.494079.mdwn b/biblio/10.1101_2022.05.30.494079.mdwn
deleted file mode 100644
index 85b47e27..00000000
--- a/biblio/10.1101_2022.05.30.494079.mdwn
+++ /dev/null
@@ -1,10 +0,0 @@
-[[!meta title="Finding rearrangements in nanopore DNA reads with last and dnarrange"]]
-[[!tag bioRxiv LAST]]
-
-Martin C. Frith, Satomi Mitsuhashi
-
-Posted August 15, 2022. doi:10.1101/2022.05.30.494079
-
-Finding rearrangements in nanopore DNA reads with last and dnarrange
-
-[[!doi 10.1101/2022.05.30.494079 desc="Tutorial on how to use `dnarrange`.  Examples of gene conversion, repeat insertion in the reference, pseudogene insertion in the query, etc."]]
diff --git a/biblio/36781728.mdwn b/biblio/36781728.mdwn
new file mode 100644
index 00000000..7f124f04
--- /dev/null
+++ b/biblio/36781728.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Finding Rearrangements in Nanopore DNA Reads with LAST and dnarrange"]]
+[[!tag LAST]]
+
+Martin C. Frith, Satomi Mitsuhashi
+
+Methods Mol Biol. 2023;2632:161-175. doi:10.1007/978-1-0716-2996-3_12
+
+Finding Rearrangements in Nanopore DNA Reads with LAST and dnarrange
+
+[[!pmid 36781728 desc="Tutorial on how to use `dnarrange`.  Examples of gene conversion, repeat insertion in the reference, pseudogene insertion in the query, etc."]]
diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn
index 5a360e45..0900b438 100644
--- a/tags/LAST.mdwn
+++ b/tags/LAST.mdwn
@@ -38,6 +38,6 @@ _bibliography in progress..._
  - JRA (Joint Read Alignment) uses LAST [[Shrestha and coll., 2018|biblio/29182778]].
 
  - A tutorial for the use of `dnarrange` is published in [[Frith and
-   Mitsuhashi, 2022|biblio/10.1101_2022.05.30.494079]].
+   Mitsuhashi, 2023|biblio/36781728]].
 
 [[!inline pages="tagged(LAST)" actions="no" limit=0]]

diff --git a/biblio/10.1101_2025.07.14.664012.mdwn b/biblio/10.1101_2025.07.14.664012.mdwn
new file mode 100644
index 00000000..f709a4d2
--- /dev/null
+++ b/biblio/10.1101_2025.07.14.664012.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Germline de novo mutation rate of the highly heterozygous amphioxus genome"]]
+[[!tag bioRxiv mutation]]
+
+Jing Xue, Lei Tao, Junwei Cao, Guang Li, Cai Li
+
+bioRxiv 2025.07.14.664012; doi:https://doi.org/10.1101/2025.07.14.664012
+
+Germline de novo mutation rate of the highly heterozygous amphioxus genome
+
+[[!doi 10.1101/2025.07.14.664012 desc="“genome assembly for each parent using the allele-aware assembler Platanus-allee”   “the mean genome-wide mutation rate was calculated to be 5.10×10-9.”  “The ligation product was amplified by PCR” "]]
diff --git a/tags/mutation.mdwn b/tags/mutation.mdwn
index 25c5397d..32831029 100644
--- a/tags/mutation.mdwn
+++ b/tags/mutation.mdwn
@@ -1,4 +1,5 @@
 [[!meta title="pages tagged mutation"]]
 
-[[!inline pages="tagged(mutation)" actions="no" archive="yes"
-feedshow=10]]
+De novo mutation rate in _Branchiostoma floridae_ was estimated to 5.10 × 10-9 per base per generation by [[Xue and coll. (2025)|biblio/10.1101_2025.07.14.664012]]
+
+[[!inline pages="tagged(mutation)" actions="no" limit=0]]

diff --git a/biblio/10.1093_plankt_fbaf029.mdwn b/biblio/10.1093_plankt_fbaf029.mdwn
new file mode 100644
index 00000000..cf8ffc49
--- /dev/null
+++ b/biblio/10.1093_plankt_fbaf029.mdwn
@@ -0,0 +1,10 @@
+[[!meta title=" Community structure and distribution pattern of appendicularians in the Kuroshio–Oyashio transitional zone during summer"]]
+[[!tag Oikopleura]]
+
+Riki Sato, Taketoshi Kodama, Kiyotaka Hidaka
+
+Journal of Plankton Research, Volume 46, Issue 2, March/April 2024, Pages 141–157, doi:10.1093/plankt/fbad056
+
+Community structure and distribution pattern of appendicularians in the Kuroshio–Oyashio transitional zone during summer
+
+[[!doi 10.1093/plankt/fbaf029 desc="“Our cluster analysis separated appendicularian communities into three groups, corresponding to distinct hydrological regions namely the anticyclonic eddy, the edge and inner area of the Kuroshio Extension and nearshore area and the area between the eddy and the Kuroshio Extension. The first group, characterized by a low abundance and diversity, was regarded to comprise surviving or deteriorating communities after isolation from the ambient communities. [In this group, more than 97.7% of the total abundance was composed of only _O. longicauda_ and _O. fusiformis_.] The second group may comprise heterogeneous communities of various origins from several different water systems due to the higher numerical contribution of coastal species, _O. dioica_, and high species diversity. The third group displaced a higher numerical contribution of _F. formica digitata_ or _F. haplostoma_ and appeared to be related to the advection of offshore waters, which may be optimal for these fritillarid forms. Among these groups, only temperature and salinity in the surface layer and CI were significantly different.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index ee1ae587..21304551 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -704,6 +704,11 @@ Ecology
    more abundant in slope waters, compared with Kuroshio and subtropical
    waters, on the Pacific side of the Japan coast ([[Hidaka,
    2008|biblio/10.3800_pbr.3.152]]).
+ - A study near an eddy of the Kuroshio extension defined three communities, including
+   one coastal characterised by high species diversity and the presence of _O. dioica_,
+   one dominated by _O. longicauda_ and one with a higher contribution of _Fritillaria_
+    [[Sato, Kodama and Hidaka, 2024|biblio/10.1093_plankt_fbaf029]].
+
 
 ### Distribution near Taiwan and China
 

diff --git a/biblio/40327505.mdwn b/biblio/40327505.mdwn
new file mode 100644
index 00000000..3c6efd1a
--- /dev/null
+++ b/biblio/40327505.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="How repeats rearrange chromosomes: The molecular basis of chromosomal inversions in deer mice."]]
+[[!tag mouse variants]]
+
+Gozashti L, Harringmeyer OS, Hoekstra HE.
+
+Cell Rep. 2025 May 27;44(5):115644. doi:10.1016/j.celrep.2025.115644
+
+How repeats rearrange chromosomes: The molecular basis of chromosomal inversions in deer mice.
+
+[[!pmid 40327505 desc="Centromeres based on repeat analysis and methylation calls of PacBio HiFi data.  “at least 14 [inversions] are likely pericentric [...] based on our predicted centromere locations”  “[we] found examples of independently derived inversions sharing the same breakpoint (within 10 kb)”. “We found no evidence for the overrepresentation of LINE or SINE retrotransposons at the breakpoints of megabase-scale inversions [... where we observed ...] a 4-fold increase in SD occupancy with respect to random expectations.”  “We also observed a strong enrichment of PMSat at the breakpoints of large inversions”. “the inversion breakpoints often coincide with contig boundaries from the initial hifi-asm contig-level assemblies”. “highly similar LINE copies [occupy] >1% of the deer mouse genome”.  “9 [large] inversions had PMSat arrays at both breakpoints in at least one of the ancestral or derived haplotypes”"]]
diff --git a/tags/variants.mdwn b/tags/variants.mdwn
index c280fbe4..4b204848 100644
--- a/tags/variants.mdwn
+++ b/tags/variants.mdwn
@@ -91,6 +91,10 @@ on sister chromatids in G2 phase.
 recombination between X and Y chromosomes was low despite the absence of
 large-scale inversions.
 
+In deer mice, [[Gozashti, Harringmeyer and Hoekstra, 2025|biblio/40327505]]
+propose that megabase-scale inversions are caused by structural duplications,
+some of which being centromere-like repeats (possible ancient centromeres).
+
 ## Indels
 
 Indel-seq ([[Min and coll., 2023|biblio/37402370]]) shows insertions at

diff --git a/biblio/18670627.mdwn b/biblio/18670627.mdwn
new file mode 100644
index 00000000..8c0d38c0
--- /dev/null
+++ b/biblio/18670627.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Efficient genetic method for establishing Drosophila cell lines unlocks the potential to create lines of specific genotypes."]]
+[[!tag Drosophila cell_culture]]
+
+Efficient genetic method for establishing Drosophila cell lines unlocks the potential to create lines of specific genotypes.
+
+PLoS Genet. 2008 Aug 1;4(8):e1000142. doi:10.1371/journal.pgen.1000142.
+
+Simcox A, Mitra S, Truesdell S, Paul L, Chen T, Butchar JP, Justiniano S.
+
+[[!pmid 18670627 desc=""]]
diff --git a/biblio/26438832.mdwn b/biblio/26438832.mdwn
new file mode 100644
index 00000000..5e294fb5
--- /dev/null
+++ b/biblio/26438832.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization."]]
+[[!tag Drosophila cell_line]]
+
+Dequéant ML, Fagegaltier D, Hu Y, Spirohn K, Simcox A, Hannon GJ, Perrimon N.
+
+Discovery of progenitor cell signatures by time-series synexpression analysis during Drosophila embryonic cell immortalization.
+
+Proc Natl Acad Sci U S A. 2015 Oct 20;112(42):12974-9. doi:10.1073/pnas.1517729112
+
+[[!pmid 26438832 desc="“Common immortalized cells are related to adult muscle precursors (AMPs)”"]]
diff --git a/tags/cell_culture.mdwn b/tags/cell_culture.mdwn
index f4a0970c..4383346d 100644
--- a/tags/cell_culture.mdwn
+++ b/tags/cell_culture.mdwn
@@ -9,5 +9,6 @@ A few notes that just scratch the surface of a vast field…
    has been used at least once in invertebrates ([[Munroe and coll. (2019)|biblio/30747414]]).
  - [[Kawamura and coll. (2021)|biblio/33899125]] reported the use of plasmin to establish coral cell lines.
  - Shark cells need high osmolarity and a supplement of 333 mM urea, 188 mM NaCl and 54 mM trimethylamine N-oxide ([[Uno and coll., 2020|biblio/33159152]]).
+ - RasV12 could immortalise _Drosophila_ cells ([[Simcox and coll. 2008|biblio/18670627]]).  Such lines seem to preferentially originate from adult muscle precursor cells ([[Dequéant and coll., 2015|biblio/26438832]]).
 
 [[!inline pages="tagged(cell_culture)" limit=0]]

diff --git a/biblio/40274362.mdwn b/biblio/40274362.mdwn
new file mode 100644
index 00000000..78b1d2cd
--- /dev/null
+++ b/biblio/40274362.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad."]]
+[[!tag frog sex variants]]
+
+Xie S, Li J, Chen W, Fong LJM, Huang C, Feng Y, Ai Q, Zhao M, Mank JE, Wu H.
+
+Genome Res. 2025 Jun 2;35(6):1325-1336. doi:10.1101/gr.280161.124
+
+Extreme heterochiasmy and high rates of sex-reversed recombination result in large yet homomorphic sex chromosomes in the Emei moustache toad.
+
+[[!pmid 40274362 desc="	“Population genetic data showed high rates of sex-reversed XY-type females, and recombination between the X and Y Chromosomes in these individuals helps maintain the integrity of sequence and gene expression on the Y Chromosome.”  “Despite this large size and the assumption that inversions catalyze recombination suppression between the X and Y Chromosomes, we found little evidence of XY structural variation.”  “High collinearity and similarity between X and Y haplotypes implicate a pre-existing pattern of low recombination itself, likely predating the origin of Chr 1 as the sex chromosomes, rather than structural variation, in sex chromosome formation.” "]]
diff --git a/tags/variants.mdwn b/tags/variants.mdwn
index 001511c6..c280fbe4 100644
--- a/tags/variants.mdwn
+++ b/tags/variants.mdwn
@@ -87,6 +87,10 @@ the same transposon participate in an aberrant transposition event to a new
 site”.  They give an example where the two transposons are identical copies
 on sister chromatids in G2 phase.
 
+[[Xie and coll., 2025|biblio/40274362]] showed that in Emei moustache toad,
+recombination between X and Y chromosomes was low despite the absence of
+large-scale inversions.
+
 ## Indels
 
 Indel-seq ([[Min and coll., 2023|biblio/37402370]]) shows insertions at

diff --git a/biblio/20823260.mdwn b/biblio/20823260.mdwn
index b467b90f..b04a455a 100644
--- a/biblio/20823260.mdwn
+++ b/biblio/20823260.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="Selective cell death mediated by small conditional RNAs."]]
-[[!tag small_RNA PKR patent]]
+[[!tag small_RNA patent]]
 [[!pmid 20823260 desc="Conditional activation of the PKR pathway by exogenous small RNAs kills cell expressing marker sequence."]]
diff --git a/tags/PKR.mdwn b/tags/PKR.mdwn
deleted file mode 100644
index 3505e541..00000000
--- a/tags/PKR.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged PKR"]]
-
-[[!inline pages="tagged(PKR)" actions="no" archive="yes"
-feedshow=10]]

diff --git a/biblio/26571212.mdwn b/biblio/26571212.mdwn
index d6dc77c0..f6391732 100644
--- a/biblio/26571212.mdwn
+++ b/biblio/26571212.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition."]]
-[[!tag ES metabolome]]
+[[!tag ES]]
 
 Sperber H, Mathieu J, Wang Y, Ferreccio A, Hesson J, Xu Z, Fischer KA, Devi A,
 Detraux D, Gu H, Battle SL, Showalter M, Valensisi C, Bielas JH, Ericson NG,
diff --git a/tags/metabolome.mdwn b/tags/metabolome.mdwn
deleted file mode 100644
index 605e4c15..00000000
--- a/tags/metabolome.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged metabolome"]]
-
-[[!inline pages="tagged(metabolome)" actions="no" archive="yes"
-feedshow=10]]

diff --git a/biblio/24609268.mdwn b/biblio/24609268.mdwn
index 854533b5..1d2559cc 100644
--- a/biblio/24609268.mdwn
+++ b/biblio/24609268.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Isolated nuclei adapt to force and reveal a mechanotransduction pathway in the nucleus."]]
-[[!tag nucleus phosphorylation]]
+[[!tag nucleus]]
 
 Guilluy C, Osborne LD, Van Landeghem L, Sharek L, Superfine R, Garcia-Mata R, Burridge K
 
diff --git a/tags/phosphorylation.mdwn b/tags/phosphorylation.mdwn
deleted file mode 100644
index 60afd3c0..00000000
--- a/tags/phosphorylation.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged phosphorylation"]]
-
-[[!inline pages="tagged(phosphorylation)" actions="no" archive="yes"
-feedshow=10]]

diff --git a/biblio/40425826.mdwn b/biblio/40425826.mdwn
new file mode 100644
index 00000000..c6eb00e0
--- /dev/null
+++ b/biblio/40425826.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Conservation of regulatory elements with highly diverged sequences across large evolutionary distances."]]
+[[!tag synteny]]
+
+Nat Genet. 2025 Jun;57(6):1524-1534. doi: 10.1038/s41588-025-02202-5
+
+Phan MHQ, Zehnder T, Puntieri F, Magg A, Majchrzycka B, Antonović M, Wieler H, Lo BW, Baranasic D, Lenhard B, Müller F, Vingron M, Ibrahim DM.
+
+Conservation of regulatory elements with highly diverged sequences across large evolutionary distances.
+
+[[!pmid 40425826 desc="“Interspecies point projection (IPP) [is] a synteny-based algorithm designed to map corresponding genomic locations in highly diverged genomes”. “We term [...] sequence-diverged orthologs ‘indirectly conserved’ (IC)”"]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index ff936b28..b0d18deb 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -127,4 +127,8 @@ Chiton species of very similar morphology can have different karyotypes
  - “Chains” and “nets” of pairwise alignements between two genomes are described
    in [[Kent and coll, 2003|biblio/14500911]].
 
+ - [[Phan and coll., 2025|biblio/40425826]] use syntenic bridge alignments to
+   associate unalignable pairs of sequences in pairs of evolutionary distant
+   species, using an approach they call interspecies point projection (IPP).
+
 [[!inline pages="tagged(synteny)" limit=0]]

diff --git a/biblio/40244654.mdwn b/biblio/40244654.mdwn
new file mode 100644
index 00000000..c614ab0c
--- /dev/null
+++ b/biblio/40244654.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Still waters run deep in large-scale genome rearrangements of morphologically conservative Polyplacophora"]]
+[[!tag synteny]]
+
+Julia D Sigwart, Yunlong Li, Zeyuan Chen, Katarzyna Vončina, Jin Sun
+
+Elife 2025 Apr 17:13:RP102542. doi:10.7554/eLife.102542
+
+Still waters run deep in large-scale genome rearrangements of morphologically conservative Polyplacophora
+
+[[!pmid 40244654 desc="“Heterozygocity ranging from almost 1% in Deshayesiella to 4.12% in Callochiton” “There are major changes [of karyotype] between congeners in different ocean basins (the Pacific A. rubrolineata) but also between two species in the NE Atlantic (A. discrepans and A. crinita) that are morphologically and ecologically almost indistinguishable.” “Living species of Lepidopleurida retain more plesiomorphic morphology and this clade has a deep fossil record extending to the lower Carboniferous; yet the exemplar of this order shows the most deviations from the reconstructed ancestral karyotype.”"]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 1613dd3c..ff936b28 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -66,6 +66,9 @@ but higher than in plants ([[Li and coll., 2022|biblio/36334587]]).
 Kobayashi and coll ([[2023|biblio/37821828]]) showed that large structural variations
 can be observed in fungi even when ITS sequences are 100% identical.
 
+Chiton species of very similar morphology can have different karyotypes
+([[Sigwart and coll., 2025|biblio/40244654]]).
+
 ### Ancestral karyotpyes
 
  - The ancestral mammalian genome has 30 chromosomes ([[Zhou and coll.,

diff --git a/biblio/40164502.mdwn b/biblio/40164502.mdwn
new file mode 100644
index 00000000..21800733
--- /dev/null
+++ b/biblio/40164502.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes."]]
+[[!tag mitochondrion]]
+
+Chen YC, Vendrami DLJ, Huber ML, Handel LEY, Cooney CR, Hoffman JI, Gossmann TI.
+
+Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes.
+
+Genome Res. 2025 Jun 2;35(6):1313-1324. doi:10.1101/gr.279428.124
+
+[[!pmid 40164502 desc="“we demonstrate that many mitochondrial-coding NUMTs exhibit signs of long-term selection”"]]
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index a87a21ed..5b9ca29b 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -107,4 +107,6 @@ The presence of mtDNA concatemers in nuclear genomes was postulated by [[Balciun
 
 The Vertebrate Genome Project has a tool to remove NUMTs ([[Rhie and coll., 2021|biblio/30402909]]).
 
+[Chen and coll, 2025|biblio/40164502] found that the coding sequence of some NUMTs is under selection.
+
 [[!inline pages="tagged(mitochondrion)" limit=0]]

diff --git a/biblio/40347137.mdwn b/biblio/40347137.mdwn
new file mode 100644
index 00000000..53f42962
--- /dev/null
+++ b/biblio/40347137.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Laboratory evolution of the bacterial genome structure through insertion sequence activation."]]
+[[!tag variants]]
+
+Kanai Y, Shibai A, Yokoi N, Tsuru S, Furusawa C.
+
+Nucleic Acids Res. 2025 May 10;53(9):gkaf331. doi:10.1093/nar/gkaf331
+
+Laboratory evolution of the bacterial genome structure through insertion sequence activation.
+
+[[!pmid 40347137 desc="“we developed an E. coli strain with high IS activity and demonstrated rapid IS-mediated genome evolution under relaxed selection in the laboratory, simulating the natural evolution of symbionts and pathogens. In just ten weeks, we observed numerous IS insertions, IS-mediated duplications, and deletions, contributing to at most −4.4% to 9.2% genome size changes (Fig. 4).” “We detected a total of 457 large-scale rearrangements, including 54 inversions, 363 deletions, and 40 duplications. [...] The median size of inversions was 84 kbp (range: 2.2 kbp–1.7 Mbp). All three inversions exceeding 1 Mbp were nearly symmetric to the ori-ter axis, consistent with observations of large inversions in nature. [...] Deletions ranged from 102 bp to 163 kbp (Fig. 3C), with the largest deletion being a deletion of a duplicated region. [...] Duplications had a median size of 40 kbp (range: 4830 bp–372 kbp). Surprisingly, the majority of the duplications resulted from transpositions of composite transposons with a copy of IS at each end (25/40), rather than tandem duplications. [...] The rearrangements led to genome size changes ranging from 174 kbp reduction to 369 kbp increase or −4.4% to 9.2%. However, overall, deletions were offset by the genome size increase from duplications and IS insertions, resulting in negligible changes in the median genome sizes”"]]
diff --git a/tags/variants.mdwn b/tags/variants.mdwn
index db4d006f..001511c6 100644
--- a/tags/variants.mdwn
+++ b/tags/variants.mdwn
@@ -23,6 +23,10 @@ vicinity.  [[Donelly and coll., 2010|biblio/20116045]] gave a radically lower
 time estimate of 13,600 to 108,400 years, but an ancient origin was again
 supported by [[Steinberg and coll in 2012|biblio/22751100]].
 
+[[Kanai and coll., 2025|biblio/40347137]] engeneered _E. coli_ strains for high
+transposon activity accumulated hundreds of rearrangements in 10 weeks,
+including 54 inversions (range: 2.2 kbp–1.7 Mbp).
+
 ### Between-species
 
 ~1100 small-scale inversions are estimated to have happened between _S.

diff --git a/biblio/10.30550_j.azl_1974.mdwn b/biblio/10.30550_j.azl_1974.mdwn
new file mode 100644
index 00000000..e3231694
--- /dev/null
+++ b/biblio/10.30550_j.azl_1974.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="Nuevos registros de Appendicularia (Urochordata) y otras especies de zooplancton en el Pacífico tropical mexicano"]]
+[[!tag Oikopleura]]
+
+Sandoval-Navarrete, C. A., Hernández-Márquez, S., Zamudio-Resendiz, M. E. ., Núñez-Resendiz, M. L. ., Márquez-Valdelamar, L. M. ., & Sentíes, A
+
+Acta Zoológica Lilloana, 68(2), 309–341. doi:10.30550/j.azl/1974
+
+Nuevos registros de Appendicularia (Urochordata) y otras especies de zooplancton en el Pacífico tropical mexicano
+
+[[!doi 10.30550/j.azl/1974 desc="“the first molecular confirmation of
+Oikopleuradioicain Mexico stands out, revealing high genetic similarity with
+populations in Japan, highlighting the shared distribution between the
+northeastern and northwestern parts of the Pacific Ocean.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 81e065b9..ee1ae587 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -739,6 +739,8 @@ Ecology
  - Northern Chile: [[Aravena and Palma, 2002|biblio/10.4067_S0716-078X2002000200005]].
  - Might have been observed by Huxley ([[1851|biblio/108414]]) in New Guinea and the
    South Pacific.
+ - Mexico: [[Sandoval-Navarrete and coll., 2024|biblio/10.30550_j.azl_1974]] noted
+   the sequence similarity between _O. dioica_ of the American and Asian coasts.
 
 ### Elsewhere in the World
 

diff --git a/biblio/38278805.mdwn b/biblio/38278805.mdwn
new file mode 100644
index 00000000..3ce6a14e
--- /dev/null
+++ b/biblio/38278805.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae."]]
+[[!tag yeast synthetic]]
+
+Cheng L, Zhao S, Li T, Hou S, Luo Z, Xu J, Yu W, Jiang S, Monti M, Schindler D, Zhang W, Hou C, Ma Y, Cai Y, Boeke JD, Dai J.
+
+Nat Commun. 2024 Jan 26;15(1):770. doi:10.1038/s41467-023-44511-5
+
+Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae.
+
+[[!pmid 38278805 desc="“SparLox83R, a yeast strain containing 83 loxPsym sites distributed across all 16 chromosomes”  “LOH and aneuploidy are frequently detected in SCRaMbLEd heterozygous diploids”  “the proportion of rearrangement events was 10-fold higher in haploid than in diploid cells.”"]]
diff --git a/tags/synthetic.mdwn b/tags/synthetic.mdwn
index 07a6d002..47755312 100644
--- a/tags/synthetic.mdwn
+++ b/tags/synthetic.mdwn
@@ -14,6 +14,8 @@ Artificial genome scrambling in yeast 2.0 with loxPsym sites: [[Brooks and coll,
 
 Artificial 18 kbp random chromosome in yeast: [[Gvozdenov, Barcutean and Struhl, 2023|biblio/37137302]].
 
+SparLox83R contains 83 loxPsym sites distributed across all 16 chromosomes ([[Cheng and coll., 2024|biblio/38278805]]).
+
 ## Pathway
 
 Increasing the copy number of the endogenous aldehyde dehydrogenase Hfd1

diff --git a/biblio/38085182.mdwn b/biblio/38085182.mdwn
new file mode 100644
index 00000000..4dc56638
--- /dev/null
+++ b/biblio/38085182.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="DNA Conserved in Diverse Animals Since the Precambrian Controls Genes for Embryonic Development"]]
+[[!tag promoter enhancer evolution]]
+
+Frith MC, Ni S.
+
+Mol Biol Evol. 2023 Dec 1;40(12):msad275. doi: 10.1093/molbev/msad275
+
+DNA Conserved in Diverse Animals Since the Precambrian Controls Genes for Embryonic Development.
+
+[[!pmid 38085182 desc="“Here, we report 25 regulatory DNA segments conserved across bilaterian animals, of which 7 are also conserved in cnidaria (coral and sea anemone).” “On the other hand, no conserved segments were found in fly (Drosophila melanogaster), roundworm (Caenorhabditis elegans), or leech (Helobdella robusta).”"]]

diff --git a/biblio/39139705.mdwn b/biblio/39139705.mdwn
new file mode 100644
index 00000000..2e75b89f
--- /dev/null
+++ b/biblio/39139705.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evolution and subfamilies of HERVL human endogenous retrovirus"]]
+[[!tag repeat annotation]]
+
+Zhang H, Frith MC.
+
+Bioinform Adv. 2024 Jul 30;4(1):vbae110. doi:10.1093/bioadv/vbae110
+
+Evolution and subfamilies of HERVL human endogenous retrovirus
+
+[[!pmid 39139705 desc="Used last-split to discover a new subfamily of MLT2 that appears like a hybrid of MLT2A2 and MLT2B3."]]

diff --git a/biblio/39168123.mdwn b/biblio/39168123.mdwn
new file mode 100644
index 00000000..b334b6d1
--- /dev/null
+++ b/biblio/39168123.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Trehalose mediates salinity-stress tolerance in natural populations of a freshwater crustacean."]]
+[[!tag trehalose]]
+
+Santos JL, Nick F, Adhitama N, Fields PD, Stillman JH, Kato Y, Watanabe H, Ebert D.
+
+Curr Biol. 2024 Sep 23;34(18):4160-4169.e7. doi:10.1016/j.cub.2024.07.082
+
+Trehalose mediates salinity-stress tolerance in natural populations of a freshwater crustacean.
+
+[[!pmid 39168123 desc="The _Alpha,alpha-trehalose-phosphate synthase_ (_TPS_) gene was the only hit of a GWAS."]]

diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 79e407a3..81e065b9 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -171,7 +171,7 @@ Mitogenome
    mitochondrial sequences can be translated with the ascidian genetic code, and
    suggests that _O. lon_, _B. sty_ and perhaps _M. ery_ (all in the _Coecaria_ genus)
    use different code(s).
- - [[Albaina, Garić and Yebra, 2024|10.1093_plankt_fbae057]] report poly-T
+ - [[Albaina, Garić and Yebra, 2024|biblio/10.1093_plankt_fbae057]] report poly-T
    insertions in _O. dioica_, _O. albicans_, _Stegosoma magna_, _Appendicularia
    sicula_, _Fritillaria borealis saragossi_, _Fritillaria pellucida_, and
    _Fritillaria formica tuberculata_, but not in _O. longicauda_ and other members
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index e75b100f..a87a21ed 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -89,7 +89,7 @@ Echinoderms           S     S     I     N     W
  - [[Diercksens and coll., 2024|biblio/39162185]] and [[Klirs and coll.,
    2024|biblio/39162337]] found that occasional presences of Cs in the poly-T
    regions does not block editing.
- - [[Albaina, Garić and Yebra, 2024|10.1093_plankt_fbae057]] report poly-T
+ - [[Albaina, Garić and Yebra, 2024|biblio/10.1093_plankt_fbae057]] report poly-T
    insertions in _O. dioica_, _O. albicans_, _Stegosoma magna_, _Appendicularia
    sicula_, _Fritillaria borealis saragossi_, _Fritillaria pellucida_, and
    _Fritillaria formica tuberculata_.

diff --git a/biblio/10.1093_plankt_fbae057.mdwn b/biblio/10.1093_plankt_fbae057.mdwn
new file mode 100644
index 00000000..93907a3a
--- /dev/null
+++ b/biblio/10.1093_plankt_fbae057.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Know your limits; miniCOI metabarcoding fails with key marine zooplankton taxa"]]
+[[!tag Oikopleura mitochondrion]]
+
+Aitor Albaina, Rade Garić, Lidia Yebra
+
+Journal of Plankton Research, 2024;, fbae057 doi: 10.1093/plankt/fbae057
+
+Know your limits; miniCOI metabarcoding fails with key marine zooplankton taxa
+
+[[!doi 10.1093/plankt/fbae057 desc="Reports poly-T insertions in _O. dioica_, _O. albicans_, _Stegosoma magna_, _Appendicularia sicula_, _Fritillaria borealis saragossi_, _Fritillaria pellucida_, and _Fritillaria formica tuberculata_."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7fd5a6e2..79e407a3 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -171,6 +171,11 @@ Mitogenome
    mitochondrial sequences can be translated with the ascidian genetic code, and
    suggests that _O. lon_, _B. sty_ and perhaps _M. ery_ (all in the _Coecaria_ genus)
    use different code(s).
+ - [[Albaina, Garić and Yebra, 2024|10.1093_plankt_fbae057]] report poly-T
+   insertions in _O. dioica_, _O. albicans_, _Stegosoma magna_, _Appendicularia
+   sicula_, _Fritillaria borealis saragossi_, _Fritillaria pellucida_, and
+   _Fritillaria formica tuberculata_, but not in _O. longicauda_ and other members
+   of the _Coecaria_ group.
 
 Repeat elements
 ---------------
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index 9686a5ba..e75b100f 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -89,6 +89,10 @@ Echinoderms           S     S     I     N     W
  - [[Diercksens and coll., 2024|biblio/39162185]] and [[Klirs and coll.,
    2024|biblio/39162337]] found that occasional presences of Cs in the poly-T
    regions does not block editing.
+ - [[Albaina, Garić and Yebra, 2024|10.1093_plankt_fbae057]] report poly-T
+   insertions in _O. dioica_, _O. albicans_, _Stegosoma magna_, _Appendicularia
+   sicula_, _Fritillaria borealis saragossi_, _Fritillaria pellucida_, and
+   _Fritillaria formica tuberculata_.
 
 ## Other
 

diff --git a/biblio/10.1017_S0025315423000541.mdwn b/biblio/10.1017_S0025315423000541.mdwn
new file mode 100644
index 00000000..18894465
--- /dev/null
+++ b/biblio/10.1017_S0025315423000541.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="An improved cultivation device for appendicularians with notes on the biology of Fritillaria sp. collected in Sagami Bay, Japan."]]
+[[!tag Oikopleura]]
+
+An improved cultivation device for appendicularians with notes on the biology of _Fritillaria sp._ collected in Sagami Bay, Japan.
+
+Sato Riki
+
+Journal of the Marine Biological Association of the United Kingdom. 2023;103:e68. doi:10.1017/S0025315423000541
+
+[[!doi 10.1017/S0025315423000541 desc="Uses rotating cylinders to circulate water in buckets.  The cultivated _Fritillaria sp._ do not survive the use of rotating paddles.  Its house covered the body entirely."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 37c97843..7fd5a6e2 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -790,7 +790,8 @@ Culture protocols (incomplete list):
  - Thompson lab protocol: [[Bouquet and coll., 2009|biblio/19461862]].
  - Cañestro lab protocol: [[Martí-Solans and coll., 2015|biblio/25044679]].
  - OIST's culture protocol: [[Masunaga and coll., 2020|biblio/32628172]].
- - Report of _Fritilaria_ being cultured: [[Henriet, Aasjord and Chourrout, 2022|biblio/36307829]].
+ - _Fritilaria_ culture: [[Henriet, Aasjord and Chourrout, 2022|biblio/36307829]], [[Sato, 2023|biblio/10.1017_S0025315423000541]].
+ - Rotating cylinders instead of paddles: [[Sato, 2023|biblio/10.1017_S0025315423000541]].
 
 Food tested in laboratory (totally incomplete list):
 

diff --git a/biblio/39208629.mdwn b/biblio/39208629.mdwn
new file mode 100644
index 00000000..b10faf4f
--- /dev/null
+++ b/biblio/39208629.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Growth and reproductive toxicity of bisphenol A in Oikopleura dioica at environmentally relevant concentrations."]]
+[[!tag Oikopleura]]
+
+Li S, Liang Y, Zhang G.
+
+J Hazard Mater. 2024 Aug 16;479:135552. doi:10.1016/j.jhazmat.2024.135552.
+
+Growth and reproductive toxicity of bisphenol A in Oikopleura dioica at environmentally relevant concentrations.
+
+[[!pmid 39208629 desc="“Evaluation of the toxicity of environmentally relevant levels of BPA [(bisphenol a)] (2.5–150 μg/L) on the appendicularian _Oikopleura dioica_”  LC50 of 142 μg/L.  “125 μg/L BPA significantly inhibited the somatic growth, gonadal development and reproduction”  ”exposure to an environmentally safe concentration (2.5 μg/L) affected female fecundity and fitness”  “BPA exposure […] led to abnormal secretion of digestive enzymes and phospholipase A2”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 1456fbcc..37c97843 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -493,6 +493,8 @@ Development
  - Adult notochord cells proliferate ([[Søviknes and Glover, 2008|biblio/18258772]]).
  - Expression of development genes is retarded by polyunsaturated aldehydes produced
    by diatoms ([[Torres-Águila and coll., 2018|biblio/30272001]]).
+ - Bisphenol A (BPA) reduces fitness at concentration that are defined as
+   ”environmentally safe” by the European Union ([[Li, Liang and Zhang, 2024|biblio/39208629]]).
  - Epithelial cells divide by mitosis during embryogenesis.  Once the final number
    of cells is produce, they grow by endomitosis, with final ploidy ranging between
    ~30 to ~1300 C. Cells with higher ploidy have shorter gap phases.  Endomitoses
@@ -654,7 +656,7 @@ Ecology
    database of DNA barcodes.
  - Carbon output of _O. dioica_ is either their house or fecal pellets, the
    ratio of which may depend on food concentration ([[Acuña and
-   Kiefer, 2000|biblio/10.4319_lo.2000.45.3.0608.mdwn]]).
+   Kiefer, 2000|biblio/10.4319_lo.2000.45.3.0608]]).
  - Gravid _B mcnutti_ individuals are found at down to 800 m, but spawning is supposed to
    happen closer to the surface ([[Sherlock and coll., 2017|biblio/28042175]]).
  - Oikopleuridae have been reported to be able to ingest microplastics.
@@ -703,7 +705,7 @@ Ecology
  - In Taiwan, _O. dioica_ was reported in north east costal waters in summar
    2005 by [[Hsiao and coll.|biblio/10.1007/s10750-011-0628-1]] and in 2009
    (plus near the Kueishan island) by [[Kâ and Hwang,
-   2011|biblio/zoolstud_50.2_155.mdwn]].  In a coastal sampling sites visited in
+   2011|biblio/zoolstud_50.2_155]].  In a coastal sampling sites visited in
    2014, 2015, and 2017, it was almost always the most abundant appendicularian.
    It was most abundant in summer ([[Franco and coll,.
    2016|biblio/10.6620_ZS.2016.55-28]], [[Franco and coll.,

diff --git a/biblio/10.1101_2023.07.18.549157v1.mdwn b/biblio/39181419.mdwn
similarity index 58%
rename from biblio/10.1101_2023.07.18.549157v1.mdwn
rename to biblio/39181419.mdwn
index d46ce5e8..20e6ec79 100644
--- a/biblio/10.1101_2023.07.18.549157v1.mdwn
+++ b/biblio/39181419.mdwn
@@ -1,15 +1,15 @@
 [[!meta title="Pax37 gene function in Oikopleura dioica supports a neuroepithelial-like origin for its house-making Fol territory"]]
-[[!tag Oikopleura bioRxiv]]
+[[!tag Oikopleura]]
 
 David Lagman, Anthony Leon, Nadia Cieminska, Wei Deng, Marios Chatzigeorgiou, Simon Henriet, Daniel Chourrout
 
-bioRxiv 2023.07.18.549157; doi:10.1101/2023.07.18.549157
+Dev Biol. 2024 Aug 22:S0012-1606(24)00217-3. doi:10.1016/j.ydbio.2024.08.012.
 
 Pax37 gene function in Oikopleura dioica supports a neuroepithelial-like origin for its house-making Fol territory
 
-[[!doi 2023.07.18.549157v1 desc="Knock-out of Pax37B and Pax37A using
+[[!pmid 39181419 desc="Knock-out of Pax37B and Pax37A using
 CRISPR-Cas9.  Pax37B is essential to the proper patterning of the oikoblastic
 epithelium but not Pax37A.  Based on the analysis of single-cell and
-transcriptomic data in Oikopleura and Ciona, the authors propose a parallel
-between oikoblastic cells in Oikopleura and the neuroepithelial cells that
-produce gluing collocytes in Ciona."]]
+transcriptomic data in _Oikopleura_ and _Ciona_, the authors propose a parallel
+between oikoblastic cells in _Oikopleura_ and the neuroepithelial cells that
+produce gluing collocytes in _Ciona_."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index c09c7449..1456fbcc 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -501,7 +501,7 @@ Development
    of the nuclear envelopper are shown by simultaneous staining of DNA, RNA and membranes
    ([[Spada and coll., 2007|biblio/17288541]]).
  - Knock-out of _Pax37B_ shows it is essential to the proper patterning of the oikoblastic
-   epithelium ([[Langma an coll., 2023|biblio/10.1101_2023.07.18.549157v1]]). 
+   epithelium ([[Lagman an coll., 2024|biblio/39181419]]). 
 
 Anatomy
 -------

diff --git a/biblio/10.1101_2023.10.30.564762.mdwn b/biblio/10.1101_2023.10.30.564762.mdwn
deleted file mode 100644
index 8146af0f..00000000
--- a/biblio/10.1101_2023.10.30.564762.mdwn
+++ /dev/null
@@ -1,10 +0,0 @@
-[[!meta title="The brittle star genome illuminates the genetic basis of animal appendage regeneration"]]
-[[!tag synteny]]
-
-bioRxiv 2023.10.30.564762; doi:10.1101/2023.10.30.564762
-
-Elise Parey, Olga Ortega-Martinez, Jérôme Delroisse, Laura Piovani, Anna Czarkwiani, David Dylus, Srishti Arya, Samuel Dupont, Michael Thorndyke, Tomas Larsson, Kerstin Johannesson, Katherine M. Buckley, Pedro Martinez, Paola Oliveri, Ferdinand Marlétaz
-
-The brittle star genome illuminates the genetic basis of animal appendage regeneration
-
-[[!doi 10.1101/2023.10.30.564762 desc="“We showed that the ‘Eleutherozoa Linkage Groups’ descend from a single fusion of ancestral bilaterian linkages (B2+C2).”  “Interestingly, sea cucumbers have the lowest rate of inter-chromosomal rearrangements, yet the most derived echinoderm body plan (Rahman et al. 2019), which highlights the uncoupling of global genomic rearrangements from morphological evolution.”  “In contrast with its sea star sister-group, the A. filiformis genome is highly rearranged: our analyses identified 26 inter-chromosomal rearrangements since the Eleutherozoa ancestor.”"]]
diff --git a/biblio/39030276.mdwn b/biblio/39030276.mdwn
new file mode 100644
index 00000000..1e9abffd
--- /dev/null
+++ b/biblio/39030276.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The brittle star genome illuminates the genetic basis of animal appendage regeneration"]]
+[[!tag synteny]]
+
+Nat Ecol Evol. 2024 Aug;8(8):1505-1521. doi:10.1038/s41559-024-02456-y
+
+Elise Parey, Olga Ortega-Martinez, Jérôme Delroisse, Laura Piovani, Anna Czarkwiani, David Dylus, Srishti Arya, Samuel Dupont, Michael Thorndyke, Tomas Larsson, Kerstin Johannesson, Katherine M. Buckley, Pedro Martinez, Paola Oliveri, Ferdinand Marlétaz
+
+The brittle star genome illuminates the genetic basis of animal appendage regeneration
+
+[[!pmid 39030276 desc="“We showed that the ‘Eleutherozoa Linkage Groups’ descend from a single fusion of ancestral bilaterian linkages (B2+C2).”  “Interestingly, sea cucumbers have the lowest rate of inter-chromosomal rearrangements, yet the most derived echinoderm body plan (Rahman et al. 2019), which highlights the uncoupling of global genomic rearrangements from morphological evolution.”  “In contrast with its sea star sister-group, the A. filiformis genome is highly rearranged: our analyses identified 26 inter-chromosomal rearrangements since the Eleutherozoa ancestor.”"]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index ae81b65c..1613dd3c 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -96,7 +96,7 @@ can be observed in fungi even when ITS sequences are 100% identical.
    that this happened by chromoanagenesis.
 
  - The Eleutherozoa Linkage Groups descend from a single fusion of ancestral
-   bilaterian linkages B2 and C2 ([[Parey and coll., 2023|biblio/10.1101_2023.10.30.564762]]).
+   bilaterian linkages B2 and C2 ([[Parey and coll., 2023|biblio/39030276]]).
    Some clades there scrambled a lot, and some not (sea cucumbers).
 
  - [[Wright and coll., 2024|biblio/38383850]] found 32 ALGs in lepidopteran,

diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index 9b376047..9686a5ba 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -86,7 +86,7 @@ Echinoderms           S     S     I     N     W
  - Poly-T regions in _O. dioica_'s mitogenome were found by [[Denoeud and
    coll., 2010|biblio/21097902]] to be reduced to T hexamers in the
    transcriptome.
- - [[Diercksens and coll., 2024|39162185]] and [[Klirs and coll.,
+ - [[Diercksens and coll., 2024|biblio/39162185]] and [[Klirs and coll.,
    2024|biblio/39162337]] found that occasional presences of Cs in the poly-T
    regions does not block editing.
 

diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index 4844f53e..9b376047 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -81,6 +81,15 @@ Echinoderms           S     S     I     N     W
    ([[Gissi & Pessole, 2003|biblio/12915488]]).
 
 
+## Homopolymers in appendicularians
+
+ - Poly-T regions in _O. dioica_'s mitogenome were found by [[Denoeud and
+   coll., 2010|biblio/21097902]] to be reduced to T hexamers in the
+   transcriptome.
+ - [[Diercksens and coll., 2024|39162185]] and [[Klirs and coll.,
+   2024|biblio/39162337]] found that occasional presences of Cs in the poly-T
+   regions does not block editing.
+
 ## Other
 
 Mitochondria can be lost in eukaryotes, be them monocellular ([[Karnkowska and

diff --git a/biblio/39162185.mdwn b/biblio/39162185.mdwn
new file mode 100644
index 00000000..b185d547
--- /dev/null
+++ b/biblio/39162185.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Tracing Homopolymers in Oikopleura dioica's mitogenome."]]
+[[!tag Oikopleura mitochondrion OIST]]
+
+Tracing Homopolymers in Oikopleura dioica's mitogenome.
+
+Dierckxsens N, Watanabe K, Tan Y, Masunaga A, Mansfield MJ, Miao J, Luscombe NM, Plessy C.
+
+Genome Biol Evol. 2024 Aug 20:evae182. doi: 10.1093/gbe/evae182
+
+[[!pmid 39162185 desc="Our PacBio I25 assembly"]]
diff --git a/biblio/39162337.mdwn b/biblio/39162337.mdwn
new file mode 100644
index 00000000..3af777bd
--- /dev/null
+++ b/biblio/39162337.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss"]]
+[[!tag Oikopleura mitochondrion]]
+
+Klirs Y, Novosolov M, Gissi C, Garic R, Pupko T, Stach T, Huchon D.
+
+Genome Biol Evol. 2024 Aug 20:evae181. doi:10.1093/gbe/evae181
+
+Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss.
+
+[[!pmid 39162337 desc="“the nad3 gene has been transferred to the nucleus and acquired a mitochondria-targeting signal“ Cs are occasionally found in edited poly-T regions."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 2722d14c..c09c7449 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -121,19 +121,6 @@ Genome
    [[Schulmeister, Schmid and Thompson, 2007|biblio/17333540]].
  - Genome compaction in _Oikopleura_ and _Ciona_ have been reviewed in parallel
    by [[Berná and Alvarez-Valin (2014)|biblio/25008364]].
- - Only a partial mitochondrial genome was reconstituted in [[Denoeud et al.,
-   2010|biblio/21097902]], due to cloning and sequencing difficulties that may
-   have been caused by oligo-dT stretches.  A/T-rich codons are more frequent than
-   in human.  In other tunicates, all mitochondrial genes are on the same DNA strand
-   and 24 tRNAs are present, instead of 22 in other chordates (reviewed by [[Gissi and coll.,
-   2008|biblio/18612321]]).
- - The mitochondrial COI sequence AY116609 and the 18S rRNA sequence AB013014
-   in Genbank are probably a contamination and a misidentification, respectively
-   ([[Sakaguchi and coll., 2017|biblio/10.1007_s12562-017-1106-0]]).
- - [[Pichon, Luscombe and Plessy, 2019|biblio/32148763]] confirms that _O. dioica_'s
-   mitochondrial sequences can be translated with the ascidian genetic code, and
-   suggests that _O. lon_, _B. sty_ and perhaps _M. ery_ (all in the _Coecaria_ genus)
-   use different code(s).
  - Analysis of sex-linked markers supports genetic sex determination with male heterogamety –
    that is: X chromosomes for females and Y for males.  ([[Denoeud et al., 2010|biblio/21097902]])
  - The major spliceosome is hypothethised to have evolved
@@ -163,6 +150,28 @@ Genome
    pairwise non-coding conservation that “may have utility in the analysis of”
    conserved non-coding elements in _Oikopleura_.
 
+Mitogenome
+----------
+
+ - A partial mitochondrial genome was reconstituted in [[Denoeud et al.,
+   2010|biblio/21097902]], where edited oligo-dT stretches were discovered.
+   A/T-rich codons are more frequent than in human.
+ - Long-read mitochondrial assemblies confirmed the gene content (atp6, cob,
+   cox1, cox2, cox3, nad1, nad4, nad5 and a putative nad2 ORF), and showed
+   that the poly-T regions could contain Cs that do not interrupt editing
+   ([[Dierckxsens and coll, 2024|biblio/39162185]], [[Klirs et and coll., 2024|biblio/39162337]]).
+ - The _nad3_ gene was transferred to the nuclear genome ([[Klirs et and coll., 2024|biblio/39162337]]).
+ - In other tunicates, all mitochondrial genes are on the same DNA strand and 24
+   tRNAs are present, instead of 22 in other chordates (reviewed by [[Gissi and
+   coll., 2008|biblio/18612321]]).
+ - The mitochondrial COI sequence AY116609 and the 18S rRNA sequence AB013014
+   in Genbank are probably a contamination and a misidentification, respectively
+   ([[Sakaguchi and coll., 2017|biblio/10.1007_s12562-017-1106-0]]).
+ - [[Pichon, Luscombe and Plessy, 2019|biblio/32148763]] confirms that _O. dioica_'s
+   mitochondrial sequences can be translated with the ascidian genetic code, and
+   suggests that _O. lon_, _B. sty_ and perhaps _M. ery_ (all in the _Coecaria_ genus)
+   use different code(s).
+
 Repeat elements
 ---------------
 

diff --git a/biblio/10.3354_meps294201.mdwn b/biblio/10.3354_meps294201.mdwn
new file mode 100644
index 00000000..5b7f6122
--- /dev/null
+++ b/biblio/10.3354_meps294201.mdwn
@@ -0,0 +1,15 @@
+[[!meta title="Grazing of two common appendicularians on the natural prey assemblage of a tropical coastal ecosystem"]]
+[[!tag Oikopleura]]
+
+R. D. Scheinberg, M. R. Landry, A. Calbet
+
+MEPS 294:201-212 (2005) doi:10.3354/meps294201 
+
+Grazing of two common appendicularians on the natural prey assemblage of a tropical coastal ecosystem
+
+[[!doi 10.3354/meps294201 desc="Trunk length 0.7 ± 0.2 for _O. longicauda_ and
+0.8 ± 0.2 for O. fusiformis.  House length 3.9 ± 0.5 mm vs 7.0 ± 1.3,
+respectively.  Clearance rate 35 and 39 ml/ind/h respectively.  “The mean
+clearance rates of these 2 species on total sub-micron cells in Kaneohe Bay
+were not significantly different; however, O. fusiformis cleared Hbact at a
+marginally higher rate”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index f4f6e67d..2722d14c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -565,6 +565,11 @@ House
    that 35 ml of water were filtered per hour.  In comparison, the giant
    species _Bathochordaeus mcnutti_ was reported to filter as much as 76 L/h
    ([[Katija and coll., 2018|biblio/28508058]]).
+ - The clearance rate of _O. longicauda_ and _O. fusiformis_ are similar
+   (36 and 39 ml/h respectively).  _O. lon._ has a lower rate on bacteria, but as
+   their biomass is less than the one of eukaryotes, this does not result in a
+   significant difference in terms of carbon updake ([[Scheinberg, Landry and Calbet,
+   2005|biblio/10.3354_meps294201]]).
  - The inner house of _Bathochordaeus_ has been modeled in 3D by
    [[Katija and coll., 2020|biblio/32494011]].
  - Filter-feeding in marine animals has been reviewed by [[Conley, Lombard and

diff --git a/biblio/10.1017_S0025315400059038.mdwn b/biblio/10.1017_S0025315400059038.mdwn
new file mode 100644
index 00000000..87a3cb26
--- /dev/null
+++ b/biblio/10.1017_S0025315400059038.mdwn
@@ -0,0 +1,14 @@
+[[!meta title="A new mesopelagic appendicularian, Mesochordaeus bahamasi gen. nov., sp. nov."]]
+[[!tag Oikopleura]]
+
+Fenaux R, Youngbluth MJ.
+
+Journal of the Marine Biological Association of the United Kingdom. 1990;70(4):755-760. doi:10.1017/S0025315400059038
+
+A new mesopelagic appendicularian, _Mesochordaeus bahamasi_ gen. nov., sp. nov.
+
+[[!doi 10.1017/S0025315400059038desc="Primary publication for the
+_Mesochordaeus_ genus.  “collected […] on 5 October 1981, off the Bahamas (Dive
+no. 634, 25°58-2'N, 77°25-6'W) at a depth of 595 m”  “In dorsal view, the trunk
+is oval, 3360 µm long and 1800 µm wide. Maximum height (in pharyngeal region)
+is 1400 µM”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 0d94afdb..f4f6e67d 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -73,6 +73,8 @@ Phylogeny
  - There are two subgenus of _Oikopleura_: _Vexillaria_ and _Coecaria_.  _Vexillaria_,
    to which _dioica_ and _rufescens_ belong, have oral glands and bioluminescence
    ([[Galt, Grober and Sykes, 1985|biblio/10.2307_1541178]]).
+ - Other appendicularians: _Mesochordaeus_ ([[Fenaux and Youngbluth,
+   1990|biblio/10.1017_S0025315400059038]]), etc.
 
 
 Karyotype

diff --git a/biblio/33752599.mdwn b/biblio/33752599.mdwn
index 88029aa7..ae7a3862 100644
--- a/biblio/33752599.mdwn
+++ b/biblio/33752599.mdwn
@@ -3,8 +3,8 @@
 
 Marius Wenzel, Berndt Mueller, Jonathan Pettitt
 
-bioRxiv 2020.12.23.423594; doi:10.1101/2020.12.23.423594
+BMC Bioinformatics. 2021 Mar 22;22(1):140. doi:10.1186/s12859-021-04009-7
 
 SLIDR and SLOPPR: Flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data
 
-[[!doi 10.1101/2020.12.23.423594 desc="Median intercistronic distance of 33 nt in Oikopleura. Calculated as the the distance between two “gene” annotations."]]
+[[!pmid 33752599 desc="Median intercistronic distance of 33 nt in Oikopleura. Calculated as the the distance between two “gene” annotations."]]

diff --git a/biblio/38807159.mdwn b/biblio/38807159.mdwn
new file mode 100644
index 00000000..304ad4ca
--- /dev/null
+++ b/biblio/38807159.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Reproductive isolation arises during laboratory adaptation to a novel hot environment."]]
+[[!tag Drosophila temperature evolution]]
+
+Hsu SK, Lai WY, Novak J, Lehner F, Jakšić AM, Versace E, Schlötterer C.
+
+Genome Biol. 2024 May 28;25(1):141. doi:10.1186/s13059-024-03285-9
+
+Reproductive isolation arises during laboratory adaptation to a novel hot environment.
+
+[[!pmid 38807159 desc="“After more than 100 generations of adaptation to a novel high temperature regime, we [...] observed significant mate discrimination between ancestral and hot-evolved populations but not for replicate populations evolved independently to the same selection regime.”  “We detected 18 major CHC [(cuticular hydrocarbons)] compounds across both sexes, which differ in length of carbon chain or numbers of double bonds”  “similar modifications in CHC compositions have been documented for multiple Drosophila species in latitudinal clines, implying that the same causal link with temperature adaptation is also present in natural populations.”  “Crosses between replicates of the evolved populations produced on average 8.3% fewer viable offspring than crosses within the same replicates of the evolved populations”"]]

diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index a2d355c6..ae81b65c 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -91,7 +91,9 @@ can be observed in fungi even when ITS sequences are 100% identical.
  - The ancestral annelid had 20 chromosomes, syntenic to the ancestral
    bilaterian linkage groups, but the genome of leeches and earthworms was
    extensively reshuffled ([[Lewin, Liao and Luo,
-   2024|biblio/10.1101_2024.05.15.594353]]).
+   2024|biblio/10.1101_2024.05.15.594353]], [[Vargas-Chávez and coll.,
+   2024|biblio/10.1101_2024.05.16.594344]]).   Vargas-Chávez and coll. proposed
+   that this happened by chromoanagenesis.
 
  - The Eleutherozoa Linkage Groups descend from a single fusion of ancestral
    bilaterian linkages B2 and C2 ([[Parey and coll., 2023|biblio/10.1101_2023.10.30.564762]]).

diff --git a/biblio/10.1016_j.pocean.2022.102822.mdwn b/biblio/10.1016_j.pocean.2022.102822.mdwn
new file mode 100644
index 00000000..47df60f2
--- /dev/null
+++ b/biblio/10.1016_j.pocean.2022.102822.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Global ecological and biogeochemical impacts of pelagic tunicates"]]
+[[!tag Oikopleura]]
+
+Jessica Y Luo, Charles A. Stock, Natasha Henschke, John P. Dunne and Todd D. O'Brien
+
+Progress in Oceanography Volume 205, July 2022, 102822
+
+Global ecological and biogeochemical impacts of pelagic tunicates
+
+[[!doi 10.1016_j.pocean.2022.102822 desc="“Our results suggest that pelagic tunicates play important trophic roles in both directly competing with microzooplankton and indirectly shunting carbon export away from the microbial loop.”"]]
diff --git a/biblio/10.1101_2022.03.01.482560.mdwn b/biblio/10.1101_2022.03.01.482560.mdwn
deleted file mode 100644
index 52525776..00000000
--- a/biblio/10.1101_2022.03.01.482560.mdwn
+++ /dev/null
@@ -1,10 +0,0 @@
-[[!meta title="Global ecological and biogeochemical impacts of pelagic tunicates"]]
-[[!tag bioRxiv]]
-
-Jessica Y Luo, Charles A. Stock, Natasha Henschke, John P. Dunne and Todd D. O'Brien
-
-Posted March 04, 2022.
-
-Global ecological and biogeochemical impacts of pelagic tunicates
-
-[[!doi 10.1101/2022.03.01.482560 desc="“Our results suggest that pelagic tunicates play important trophic roles in both directly competing with microzooplankton and indirectly shunting carbon export away from the microbial loop.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index bac98b52..0d94afdb 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -615,6 +615,8 @@ Ecology
 
  - The ecological role of appendicularians was reviewed by [[Jaspers and coll,
    2023|biblio/37277269]].
+ - Luo and coll. [[(2022)|biblio/10.1016_j.pocean.2022.102822]] reported that
+   pelagic tunicates indirectly shunt the microbial loop.
  - _O. dioica_ grazes on bacterioplankton, which can be a significant share
    of its own diet, but the grazing has only “minimal influence on the
    population dynamics of the free-living bacteria” ([[King, Hollibaugh and

diff --git a/biblio/10.1101_2024.05.15.594353.mdwn b/biblio/10.1101_2024.05.15.594353.mdwn
new file mode 100644
index 00000000..9315c8b2
--- /dev/null
+++ b/biblio/10.1101_2024.05.15.594353.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Annelid comparative genomics and the evolution of massive lineage-specific genome rearrangement in bilaterians"]]
+[[!tag bioRxiv synteny]]
+
+Thomas D. Lewin, Isabel Jiah-Yih Liao, Yi-Jyun Luo
+
+bioRxiv 2024.05.15.594353 doi:10.1101/2024.05.15.594353
+
+Annelid comparative genomics and the evolution of massive lineage-specific genome rearrangement in bilaterians
+
+[[!doi 10.1101/2024.05.15.594353 desc="“the last annelid common ancestor retained the ancestral lophotrochozoan karyotype with 20 chromosomes“  “The genomes of all sampled species have at least three ALG fusions compared to the ancestral annelid genome.”  “almost all the chromosome fusion events in annelids can be categorized as fusion-with-mixing”  “we found no correlation between the ALG fusion rate and the length of chromosomes”  “In contrast to fusions, the splitting of ALGs is relatively rare, with only three cases in this dataset of 16 annelid species.”  “in both leeches and earthworms, there is complete shuffling of the ancient bilaterian genome [...] there has also been massive genome shuffling between these two groups.“  “within the Clitellata, M. vulgaris has a lineage-specific tetraploidization that is not shared by other earthworms or leeches”  “we developed a macrosynteny rearrangement index [...] to quantify both ALG fusion and fission into a single value between 0 (no rearrangement) and 1 (maximum rearrangement).”  “dramatic genome rearrangement in clitellates correlates with the evolution of a new ecological niche, alongside divergent genomic location and altered expression of key developmental genes”"]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 70cb6be3..a2d355c6 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -88,6 +88,11 @@ can be observed in fungi even when ITS sequences are 100% identical.
  - The ancestral bilaterian had 24 linkage groups according to [[Simakov and
    coll., 2022|biblio/35108053]].
 
+ - The ancestral annelid had 20 chromosomes, syntenic to the ancestral
+   bilaterian linkage groups, but the genome of leeches and earthworms was
+   extensively reshuffled ([[Lewin, Liao and Luo,
+   2024|biblio/10.1101_2024.05.15.594353]]).
+
  - The Eleutherozoa Linkage Groups descend from a single fusion of ancestral
    bilaterian linkages B2 and C2 ([[Parey and coll., 2023|biblio/10.1101_2023.10.30.564762]]).
    Some clades there scrambled a lot, and some not (sea cucumbers).

diff --git a/biblio/10.1007_s00227-022-04145-5.mdwn b/biblio/10.1007_s00227-022-04145-5.mdwn
new file mode 100644
index 00000000..1458c722
--- /dev/null
+++ b/biblio/10.1007_s00227-022-04145-5.mdwn
@@ -0,0 +1,8 @@
+[[!meta title="The cosmopolitan appendicularian Oikopleura dioica reveals hidden genetic diversity around the globe."]]
+[[!tag Oikopleura OIST]]
+
+Aki Masunaga, Michael J. Mansfield, Yongkai Tan, Andrew W. Liu, Aleksandra Bliznina, Paolo Barzaghi, Tamara L. Hodgetts, Alfonso Ferrández-Roldán, Cristian Cañestro, Takeshi A. Onuma, Charles Plessy & Nicholas M. Luscombe.
+
+The cosmopolitan appendicularian Oikopleura dioica reveals hidden genetic diversity around the globe.
+
+[[!doi 10.1007/s00227-022-04145-5 desc="Three (cryptic) _O. dioica_ species.  The only robust morphological change found was egg diameter."]]
diff --git a/biblio/38621828.mdwn b/biblio/38621828.mdwn
new file mode 100644
index 00000000..9d037455
--- /dev/null
+++ b/biblio/38621828.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species."]]
+[[!tag Oikopleura OIST]]
+
+Plessy C, Mansfield MJ, Bliznina A, Masunaga A, West C, Tan Y, Liu AW, Grašič J, Del Río Pisula MS, Sánchez-Serna G, Fabrega-Torrus M, Ferrández-Roldán A, Roncalli V, Navratilova P, Thompson EM, Onuma T, Nishida H, Cañestro C, Luscombe NM.
+
+Genome Res. 2024 Apr 25;34(3):426-440. doi:10.1101/gr.278295.123
+
+Extreme genome scrambling in marine planktonic Oikopleura dioica cryptic species. 
+
+[[!pmid 38621828 desc="Gene order is scrambled between _O. dioica_ species.  Molecular clock analysis of 177 single-copy orthologs places appendicularian sister to all tunicates."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 5d18ecf7..bac98b52 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -57,10 +57,16 @@ Phylogeny
    sister to all other tunicates.
  - Study of 117 phenotypic characters in 49 tunicate species also support basal
    position of appendicularians ([[Braun, Leubner and Stach, 2019|biblio/10.1111_cla.12405]].
- - “The difference between coding sequences was considerably higher in
-   comparisons between strains of different oceans than within the Bergen gene
-   pool.  We ignore whether and how Oikopleura dioica is subdivided into multiple
-   species” ([[Denoeud et al., 2010|biblio/21097902]]).
+ - Molecular clock analysis of 177 single-copy orthologs also places appendicularians
+   sister to all tunicates ([[Plessy, Mansfield and coll., 2024|biblio/38621828]]).
+ - _O. dioica_ is actually mutliple species.  “The difference between coding
+   sequences was considerably higher in comparisons between strains of
+   different oceans than within the Bergen gene pool.  We ignore whether and how
+   Oikopleura dioica is subdivided into multiple species” ([[Denoeud et al.,
+   2010|biblio/21097902]]).  Masunaga and coll. ([[2022|biblio/10.1007_s00227-022-04145-5]])
+   demonstrated the existence of at least 3 species using molecular markers, and
+   found that egg diameter distinguishes the “okinawan” one from the others.
+   Gene order is scrambled between the 3 species ([[Plessy, Mansfield and coll., 2024|biblio/38621828]]).
  - Giant Oikopleurid species, such as  exist in deeper waters. _Bathochordaeus charon_'s 18S
    RNA is 97% identical to the one of _O. dioica_ ([[Sherlock and coll, 2016|biblio/10.1186_s41200-016-0075-9]]).
  - CO1 DNA of _B. mcnutti_ and _B. strygius_ are ~12% different ([[Sherlock and coll., 2017|biblio/28042175]]).

diff --git a/biblio/38493164.mdwn b/biblio/38493164.mdwn
new file mode 100644
index 00000000..44b9704b
--- /dev/null
+++ b/biblio/38493164.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Temporospatial hierarchy and allele-specific expression of zygotic genome activation revealed by distant interspecific urochordate hybrids."]]
+[[!tag Ciona]]
+
+Wei J, Zhang W, Jiang A, Peng H, Zhang Q, Li Y, Bi J, Wang L, Liu P, Wang J, Ge Y, Zhang L, Yu H, Li L, Wang S, Leng L, Chen K, Dong B.
+
+Nat Commun. 2024 Mar 16;15(1):2395. doi:10.1038/s41467-024-46780-0
+
+Temporospatial hierarchy and allele-specific expression of zygotic genome activation revealed by distant interspecific urochordate hybrids
+
+[[!pmid 38493164 desc="_robusta_ / _savignyi_ reciprocal crosses after dechorionation.  “Gene expression and regulatory profiles revealed that the initiation of ZGA in Ciona began at the 8-cell stage, with the minor wave mainly occurring from the 16- to 32-cell stage and the major wave from the 64- to 112-cell stage during ascidian embryogenesis”"]]
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index 09e91b65..3e82c17f 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -28,6 +28,8 @@ different computations presented in that work.
 
 _C. intestinalis_ and _C. savignyi_ can cross-fertilise after removal of the
 vitelline enveloppe ([[Byrd and Lambert, 2000|biblio/10602281]]).
+Allele-specific expression in these crosses was studied by [[Wei and coll.,
+2024|biblio/38493164]].
 
 _Ciona robusta_'s sperm can efficiently fertilise _C. intestinalis_ eggs, but
 the fertilisation rates are much lower in the reciprocal crosses ([[Suzuki,

diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index 1b06c15b..09e91b65 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -37,8 +37,8 @@ Hybrids were infertile and a _C. rob_ - _C. int_ cross from two sympatric
 strains from Plymouth did not develop beyond cleavage ([[Caputi and coll.,
 2007|biblio/17517633]]).  In line with this, the only hybdids found by the SNP
 analysis of wild animals of ([[Bouchemousse and coll., 2016|biblio/27662427]])
-were F1 and of _C. int_ maternal origin.  [[Ohta and coll, 2020|bilbio/32518083]]
-reported fertile hybrids between _C. rob_ from San Diego
+were F1 and of _C. int_ maternal origin.  [[Ohta and coll,
+2020|biblio/32518083]] reported fertile hybrids between _C. rob_ from San Diego
 (CA) and _C. int_ from Woods Hole (MA), but viability was reduced, especially
 when maternal or grand-maternal origin was _C. int_.
 

diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index 6fa03c8e..1b06c15b 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -37,8 +37,8 @@ Hybrids were infertile and a _C. rob_ - _C. int_ cross from two sympatric
 strains from Plymouth did not develop beyond cleavage ([[Caputi and coll.,
 2007|biblio/17517633]]).  In line with this, the only hybdids found by the SNP
 analysis of wild animals of ([[Bouchemousse and coll., 2016|biblio/27662427]])
-were F1 and of _C. int_ maternal origin.  [[Ohta and coll,
-2020|bilbio/32518083]] reported fertile hybrids between _C. rob_ from San Diego
+were F1 and of _C. int_ maternal origin.  [[Ohta and coll, 2020|bilbio/32518083]]
+reported fertile hybrids between _C. rob_ from San Diego
 (CA) and _C. int_ from Woods Hole (MA), but viability was reduced, especially
 when maternal or grand-maternal origin was _C. int_.
 

diff --git a/biblio/38383850.mdwn b/biblio/38383850.mdwn
new file mode 100644
index 00000000..7887a912
--- /dev/null
+++ b/biblio/38383850.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera."]]
+[[!tag synteny]]
+
+Wright CJ, Stevens L, Mackintosh A, Lawniczak M, Blaxter M.
+
+Comparative genomics reveals the dynamics of chromosome evolution in Lepidoptera.
+
+Nat Ecol Evol. 2024 Feb 21. doi:10.1038/s41559-024-02329-4
+
+[[!pmid  38383850 desc="“We assigned 4,112 orthologues (78%) to 32 ALGs: 31 autosomes and Z, the sex chromosome. Hereafter, we refer to these ALGs as Merian elements, named after the seventeenth-century lepidopterist and botanical artist, Maria Sibylla Merian”  ”Merian elements have remained intact in most species”  “Lepidopteran chromosomes arising from fusions retain syntenic domains that reflect the original elements. Remarkably, this includes the M17 + M20 fusion, which occurred ~200 million years ago”"]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 6672f561..70cb6be3 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -92,6 +92,10 @@ can be observed in fungi even when ITS sequences are 100% identical.
    bilaterian linkages B2 and C2 ([[Parey and coll., 2023|biblio/10.1101_2023.10.30.564762]]).
    Some clades there scrambled a lot, and some not (sea cucumbers).
 
+ - [[Wright and coll., 2024|biblio/38383850]] found 32 ALGs in lepidopteran,
+   which they termed Merian elements.  There is a case where scrambling has
+   not erased traces of a fusion that occured 200 million years ago.
+
 ### Computational aspects
 
  - [[Rocha (2003)|biblio/14585609]] defines a Gene Order Conservation (GOC)

diff --git a/biblio/10.1101_2024.02.15.580425.mdwn b/biblio/10.1101_2024.02.15.580425.mdwn
new file mode 100644
index 00000000..3df64157
--- /dev/null
+++ b/biblio/10.1101_2024.02.15.580425.mdwn
@@ -0,0 +1,12 @@
+[[!meta title=" Fusion, fission, and scrambling of the bilaterian genome in Bryozoa"]]
+[[!tag bioRxiv synteny]]
+
+Thomas D. Lewin, Isabel Jiah-Yih Liao, Mu-En Chen, John D. D. Bishop, Peter W. H. Holland, Yi-Jyun Luo
+
+bioRxiv 2024.02.15.580425; doi:10.1101/2024.02.15.580425
+
+Fusion, fission, and scrambling of the bilaterian genome in Bryozoa.
+
+[[!doi 10.1101/2024.02.15.580425 desc="Defines a “microsynteny mixing score” as
+1 minus the absolute value of the spearman correlation coefficient of the
+ranked positions of orthologous genes on orthologous chromosome pairs."]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 98f5d95b..6672f561 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -105,6 +105,11 @@ can be observed in fungi even when ITS sequences are 100% identical.
    that a given gene has its orthologue in a homologous chromosome of a related
    species.
 
+ - [[Lewin and coll., 2024|biblio/10.1101_2024.02.15.580425]] defined a
+   “microsynteny mixing score” as 1 minus the Spearman correlation coefficient
+   of the ranked positional indices of orthologous genes on orthologous
+   chromosomes.
+
  - “Chains” and “nets” of pairwise alignements between two genomes are described
    in [[Kent and coll, 2003|biblio/14500911]].
 

diff --git a/biblio/30504855.mdwn b/biblio/30504855.mdwn
new file mode 100644
index 00000000..fc8aa412
--- /dev/null
+++ b/biblio/30504855.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries."]]
+[[!tag speciation]]
+
+Nat Commun. 2018 Nov 30;9(1):5114. doi:10.1038/s41467-018-07641-9
+
+Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S.
+
+High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. 
+
+[[!pmid 30504855 desc="Less than 0.2% of the genome pairs had an average nucleotide identity between 83% and 95%."]]

diff --git a/tags/subgenome.mdwn b/tags/subgenome.mdwn
new file mode 100644
index 00000000..2d8d901a
--- /dev/null
+++ b/tags/subgenome.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged subgenome"]]
+
+[[!inline pages="tagged(subgenome)" actions="no" archive="yes"
+feedshow=10]]

diff --git a/biblio/37335429.mdwn b/biblio/37335429.mdwn
new file mode 100644
index 00000000..29e0693e
--- /dev/null
+++ b/biblio/37335429.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Novel chromosomes and genomes provide new insights into evolution and adaptation of the whole genome duplicated yeast-like fungus TN3-1 isolated from natural honey."]]
+[[!tag yeast synteny subgenome]]
+
+Jia SL, Zhang M, Liu GL, Chi ZM, Chi Z.
+
+Funct Integr Genomics. 2023 Jun 19;23(3):206. doi:10.1007/s10142-023-01127-8
+
+Novel chromosomes and genomes provide new insights into evolution and adaptation of the whole genome duplicated yeast-like fungus TN3-1 isolated from natural honey.
+
+[[!pmid 37335429 desc="A new _Aureobasidium melanogenum_ strain that has two subgenomes that diverged ~10 million years ago."]]

diff --git a/biblio/10.1101_2020.11.25.392936.mdwn b/biblio/35762203.mdwn
similarity index 65%
rename from biblio/10.1101_2020.11.25.392936.mdwn
rename to biblio/35762203.mdwn
index 5d33692b..52de2f6c 100644
--- a/biblio/10.1101_2020.11.25.392936.mdwn
+++ b/biblio/35762203.mdwn
@@ -1,10 +1,10 @@
 [[!meta title="Robotic Search for Optimal Cell Culture in Regenerative Medicine"]]
-[[!tag bioRxiv automation]]
+[[!tag automation]]
 
 Genki N. Kanda, Taku Tsuzuki, Motoki Terada, Noriko Sakai, Naohiro Motozawa, Tomohiro Masuda, Mitsuhiro Nishida, Chihaya T. Watanabe, Tatsuki Higashi, Shuhei A. Horiguchi, Taku Kudo, Motohisa Kamei, Genshiro A. Sunagawa, Kenji Matsukuma, Takeshi Sakurada, Yosuke Ozawa, Masayo Takahashi, Koichi Takahashi, Tohru Natsume
 
-bioRxiv 2020.11.25.392936; doi: https://doi.org/10.1101/2020.11.25.392936
+Elife. 2022 Jun 28;11:e77007. doi:10.7554/eLife.77007
 
 Robotic Search for Optimal Cell Culture in Regenerative Medicine
 
-[[!doi 10.1101/2020.11.25.392936  desc="Uses the Maholo LabDroid and Batch Bayesian optimization (BBO) to screen a 7-dimensions parameter space."]]
+[[!pmid 35762203 desc="Uses the Maholo LabDroid and Batch Bayesian optimization (BBO) to screen a 7-dimensions parameter space."]]

diff --git a/biblio/10.1111_j.1558-5646.1958.tb02962.x.mdwn b/biblio/10.1111_j.1558-5646.1958.tb02962.x.mdwn
new file mode 100644
index 00000000..75ab5c62
--- /dev/null
+++ b/biblio/10.1111_j.1558-5646.1958.tb02962.x.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Rapid evolution in Clarkia"]]
+[[!tag ]]
+
+Harlan Lewis and Peter H. Raven
+
+Evolution, Volume 12, Issue 3, 1 September 1958, Pages 319–336 doi:10.1111/j.1558-5646.1958.tb02962.x
+
+Rapid evolution in Clarkia
+
+[[!doi 10.1111/j.1558-5646.1958.tb02962.x desc="Frequent translocations cause bridges and circles in meiosis of hybrids."]]
diff --git a/biblio/10100754.mdwn b/biblio/10100754.mdwn
index d7d8d55d..40491a3c 100644
--- a/biblio/10100754.mdwn
+++ b/biblio/10100754.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="Comparison of T-cell receptor Jβ gene usage in spleen cells of different mouse strains."]]
-[[!tag J_segment TCR mouse β_chain]]
-[[!pmid 10100754 desc="“As a possible factor responsible for this skewed TCR Jβ gene usage, rearrangement itself may be crucial”."]]
+[[!tag TCR mouse β_chain]]
+[[!pmid 10100754 desc="“As a possible factor responsible for this skewed TCR J segment Jβ gene usage, rearrangement itself may be crucial”."]]
diff --git a/biblio/22579286.mdwn b/biblio/22579286.mdwn
index 17f97448..7d25e98d 100644
--- a/biblio/22579286.mdwn
+++ b/biblio/22579286.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Nuclear Envelope Budding Enables Large Ribonucleoprotein Particle Export during Synaptic Wnt Signaling."]]
-[[!tag RNA_granule]]
+[[!tag RNP_granules]]
 
 Cell. 2012 May 11;149(4):832-46.
 
diff --git a/tags/J_segment.mdwn b/tags/J_segment.mdwn
deleted file mode 100644
index 9899bfce..00000000
--- a/tags/J_segment.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged J segment"]]
-
-[[!inline pages="tagged(J_segment)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/RNA_granule.mdwn b/tags/RNA_granule.mdwn
deleted file mode 100644
index eefe9b02..00000000
--- a/tags/RNA_granule.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged RNA granule"]]
-
-[[!inline pages="tagged(RNA_granule)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/variants.mdwn b/tags/variants.mdwn
index d23fcca7..db4d006f 100644
--- a/tags/variants.mdwn
+++ b/tags/variants.mdwn
@@ -89,6 +89,11 @@ Indel-seq ([[Min and coll., 2023|biblio/37402370]]) shows insertions at
 double-strand breaks originating from donor regions possibly single-stranded by
 transcription (R-loops) or repair.  Proximity and contact appear to be important.
 
+## Translocations
+
+Translocations are frequent in _Clarkia_ ([[Lewis and Raven,
+1958|biblio/10.1111_j.1558-5646.1958.tb02962.x]]).
+
 ## Software
 
  - _NanoSV_ ([[Cretu Stancu and coll., 2017|biblio/29109544]]) uses nanopore long

diff --git a/biblio/10.1101_2024.01.10.574808.mdwn b/biblio/10.1101_2024.01.10.574808.mdwn
new file mode 100644
index 00000000..5baf93d3
--- /dev/null
+++ b/biblio/10.1101_2024.01.10.574808.mdwn
@@ -0,0 +1,8 @@
+[[!meta title=" Developmental toxicity of pre-production plastic pellets affects a large swathe of invertebrate taxa"]]
+[[!tag Oikopleura microplastic]]
+
+Eva Jimenez Guri, Periklis Paganos, Claudia La Vecchia, Giovanni Annona, Filomena Caccavale, M Dolores Molina, Alfonso Ferrandez-Roldan, Rory Daniel Donnellan, Federica Salatiello, Adam N Johnstone, Maria Concetta Eliso, Antonietta Spagnuolo, Cristian Canestro, Ricard Albalat, Jose M Martin-Duran, Elisabeth A Williams, Enrico D'Aniello, Maria Ina Arnone.
+
+bioRxiv 2024.01.10.574808; doi: https://doi.org/10.1101/2024.01.10.574808 
+
+[[!doi 10.1101/2024.01.10.574808 doi desc="_O. dioica's development_ less affected by leachates than other tested animals."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 3c2a35be..5d18ecf7 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -637,6 +637,8 @@ Ecology
    Example(s): _B. stygius_ ([[Katija and coll., 2017b|biblio/28835922]]).  3
    to 17 microplastic particles were found in sinking houses in the Monterey Bay
    [[Choy and coll., 2019|biblio/31171833]].
+ - The development of _O. dioica_ is comparatively less affected by microplastic leachates
+   than some other invertebrates ([[Guri and coll., 2024|10.1101_2024.01.10.574808]]).
  - _O. dioica_ can filter, ingest and defecate the _Emiliania huxleyi_ virus
    ([[Lawrence and coll., 2018|biblio/10.1002_lno.10734]]).  This study does not assess
    whether the viruses are digested.

diff --git a/biblio/18615017.mdwn b/biblio/18615017.mdwn
index 03256b31..dc995b64 100644
--- a/biblio/18615017.mdwn
+++ b/biblio/18615017.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="High-resolution mapping of meiotic crossovers and non-crossovers in yeast."]]
-[[!tag Yeast chromosome microarray genetics]]
+[[!tag yeast chromosome microarray genetics]]
 
 Mancera E, Bourgon R, Brozzi A, Huber W, Steinmetz LM.
 
diff --git a/biblio/20937878.mdwn b/biblio/20937878.mdwn
index c66e29a9..7e6cf7d3 100644
--- a/biblio/20937878.mdwn
+++ b/biblio/20937878.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="Cell-permeable Foxp3 protein alleviates autoimmune disease associated with inflammatory bowel disease and allergic airway inflammation."]]
-[[!tag lymphocyte FoxP3 Treg therapy]]
+[[!tag lymphocyte FoxP3 therapy]]
 [[!pmid 20937878 desc=""]]
diff --git a/biblio/22761473.mdwn b/biblio/22761473.mdwn
index 316bb186..72cc0c21 100644
--- a/biblio/22761473.mdwn
+++ b/biblio/22761473.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="A New Approach to Simultaneously Quantify Both TCR α- and β-Chain Diversity after Adoptive Immunotherapy."]]
-[[!tag TCR clonotype]]
+[[!tag TCR repertoire]]
 
 Zhang M, Maiti S, Bernatchez C, Huls H, Rabinovich B, Champlin RE, Vence LM, Hwu P, Radvanyi L, Cooper LJ.
 
@@ -7,4 +7,4 @@ Clin Cancer Res. 2012 Sep 1;18(17):4733-42.
 
 A New Approach to Simultaneously Quantify Both TCR α- and β-Chain Diversity after Adoptive Immunotherapy.
 
-[[!pmid 22761473 desc="Using “NanoStrings” to count α and β segments."]]
+[[!pmid 22761473 desc="Using “NanoStrings” to count α and β segments.  Clonotypes"]]
diff --git a/biblio/22933635.mdwn b/biblio/22933635.mdwn
index 1e1e7216..2cd52b7e 100644
--- a/biblio/22933635.mdwn
+++ b/biblio/22933635.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="The TCR repertoires of regulatory and conventional T cells specific for the same foreign antigen are distinct."]]
-[[!tag mouse Treg TCR α_chain repertoire]]
+[[!tag mouse lymphocyte TCR α_chain repertoire]]
 
 Relland LM, Williams JB, Relland GN, Haribhai D, Ziegelbauer J, Yassai M, Gorski J, Williams CB.
 
diff --git a/biblio/23290140.mdwn b/biblio/23290140.mdwn
index 63804636..ea7d2d1f 100644
--- a/biblio/23290140.mdwn
+++ b/biblio/23290140.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Generation of rejuvenated antigen-specific T cells by reprogramming to pluripotency and redifferentiation."]]
-[[!tag iPS T_cell reprogramming]]
+[[!tag iPS lymphocyte reprogramming]]
 
 Nishimura T, Kaneko S, Kawana-Tachikawa A, Tajima Y, Goto H, Zhu D, Nakayama-Hosoya K, Iriguchi S, Uemura Y, Shimizu T, Takayama N, Yamada D, Nishimura K, Ohtaka M, Watanabe N, Takahashi S, Iwamoto A, Koseki H, Nakanishi M, Eto K, Nakauchi H.
 
diff --git a/biblio/24156252.mdwn b/biblio/24156252.mdwn
index aa7583ed..4ee8ad75 100644
--- a/biblio/24156252.mdwn
+++ b/biblio/24156252.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Temporal dynamics and transcriptional control using single-cell gene expression analysis."]]
-[[!tag single_cell OSC CLST]]
+[[!tag single_cell OSC]]
 
 Kouno T, de Hoon M, Mar JC, Tomaru Y, Kawano M, Carninci P, Suzuki H, Hayashizaki Y, Shin JW.
 
diff --git a/biblio/27071608.mdwn b/biblio/27071608.mdwn
index f3103177..69fcb3b8 100644
--- a/biblio/27071608.mdwn
+++ b/biblio/27071608.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Bioanalyzer chips can be used interchangeably for many analyses of DNA or RNA."]]
-[[!tag Bioanalyzer method]]
+[[!tag size method]]
 
 Davies J, Denyer T, Hadfield J
 
diff --git a/biblio/28623350.mdwn b/biblio/28623350.mdwn
index 49d9f8db..c696260a 100644
--- a/biblio/28623350.mdwn
+++ b/biblio/28623350.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Multiplexed Spliced-Leader Sequencing: A high-throughput, selective method for RNA-seq in Trypanosomatids."]]
-[[!tag trans-splicing method random priming.]]
+[[!tag trans-splicing method random_priming]]
 
 Cuypers B, Domagalska MA, Meysman P, Muylder G, Vanaerschot M, Imamura H, Dumetz F, Verdonckt TW, Myler PJ, Ramasamy G, Laukens K, Dujardin JC.
 
diff --git a/biblio/33093512.mdwn b/biblio/33093512.mdwn
index 9e32a576..ab2bc187 100644
--- a/biblio/33093512.mdwn
+++ b/biblio/33093512.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Use of Cap Analysis Gene Expression to detect human papillomavirus promoter activity patterns at different disease stages."]]
-[[!tag RIKEN OIST nanoCAGE HPV]]
+[[!tag OIST nanoCAGE HPV]]
 
 Taguchi A, Nagasaka K, Plessy C, Nakamura H, Kawata Y, Kato S, Hashimoto K, Nagamatsu T, Oda K, Kukimoto I, Kawana K, Carninci P, Osuga Y, Fujii T.
 
diff --git a/biblio/8894123.mdwn b/biblio/8894123.mdwn
index 10498a0f..116cd5f8 100644
--- a/biblio/8894123.mdwn
+++ b/biblio/8894123.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Zipf-scaling behavior in the immune system."]]
-[[!tag T_cell repertoire scale-free]]
+[[!tag lymphocyte repertoire scale-free]]
 
 Burgos JD, Moreno-Tovar P.
 
diff --git a/tags/Bioanalyzer.mdwn b/tags/Bioanalyzer.mdwn
deleted file mode 100644
index 05e91ae0..00000000
--- a/tags/Bioanalyzer.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged Bioanalyzer"]]
-
-[[!inline pages="tagged(Bioanalyzer)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/CLST.mdwn b/tags/CLST.mdwn
deleted file mode 100644
index 4af404bc..00000000
--- a/tags/CLST.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged CLST"]]
-
-[[!inline pages="tagged(CLST)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/RIKEN.mdwn b/tags/RIKEN.mdwn
deleted file mode 100644
index b77112a6..00000000
--- a/tags/RIKEN.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged RIKEN"]]
-
-[[!inline pages="tagged(RIKEN)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/T_cell.mdwn b/tags/T_cell.mdwn
deleted file mode 100644
index 1244a948..00000000
--- a/tags/T_cell.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged T cell"]]
-
-[[!inline pages="tagged(T_cell)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/Treg.mdwn b/tags/Treg.mdwn
deleted file mode 100644
index 744bf6a9..00000000
--- a/tags/Treg.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged Treg"]]
-
-[[!inline pages="tagged(Treg)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/clonotype.mdwn b/tags/clonotype.mdwn
deleted file mode 100644
index 25e95135..00000000
--- a/tags/clonotype.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged clonotype"]]
-
-[[!inline pages="tagged(clonotype)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/priming..mdwn b/tags/priming..mdwn
deleted file mode 100644
index bee9db76..00000000
--- a/tags/priming..mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged priming."]]
-
-[[!inline pages="tagged(priming.)" actions="no" archive="yes"
-feedshow=10]]
diff --git a/tags/random.mdwn b/tags/random.mdwn
deleted file mode 100644
index ee7ac848..00000000
--- a/tags/random.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged random"]]
-
-[[!inline pages="tagged(random)" actions="no" archive="yes"
-feedshow=10]]

diff --git a/biblio/37821828.mdwn b/biblio/37821828.mdwn
index 4d4c07a6..731154f7 100644
--- a/biblio/37821828.mdwn
+++ b/biblio/37821828.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny."]]
-[[!tag ]]
+[[!tag yeast synteny]]
 
 Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny.
 
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 74ea072d..98f5d95b 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -63,6 +63,9 @@ branched at the base of the animal tree.
 At equal evolutionary distance, yeast microsynteny is lower than in animals,
 but higher than in plants ([[Li and coll., 2022|biblio/36334587]]).
 
+Kobayashi and coll ([[2023|biblio/37821828]]) showed that large structural variations
+can be observed in fungi even when ITS sequences are 100% identical.
+
 ### Ancestral karyotpyes
 
  - The ancestral mammalian genome has 30 chromosomes ([[Zhou and coll.,

diff --git a/biblio/38130951.mdwn b/biblio/38130951.mdwn
new file mode 100644
index 00000000..aa2e426b
--- /dev/null
+++ b/biblio/38130951.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Functional specialization of Aurora kinase homologs during oogenic meiosis in the tunicate Oikopleura dioica."]]
+[[!tag Oikopleura H3S28p H3S10p]]
+
+Feng H, Thompson EM.
+
+Front Cell Dev Biol. 2023 Dec 7;11:1323378. doi:10.3389/fcell.2023.1323378
+
+Functional specialization of Aurora kinase homologs during oogenic meiosis in the tunicate Oikopleura dioica.
+
+[[!pmid 38130951 desc="“a C-terminal GFP fusion [of OdAur1] was localized on centrosomes throughout mitosis”  “a commercial phospho-Aurora antibody that can recognize the phosphorylated forms of both Aurora1 and Aurora2 in O. dioica [localised] on centrosomes and chromosomes in prophase and metaphase, and on centrosomes and the central spindle in anaphase”  “This suggests that Aurora1 and Aurora2 in O. dioica represent the polar and equatorial forms of Aurora kinases”. “[Knockdown] suggests that Aurora1 is involved in promoting the progression of prometaphase I. In all the Aur2 KD oocytes, both H3-pS10 and H3-pS28 were absent, and chromosomes were decondensed, reminiscent of INCENPa knockdown phenotypes”"]]
diff --git a/tags/H3S28p.mdwn b/tags/H3S28p.mdwn
index 1963c8f2..c1ef8182 100644
--- a/tags/H3S28p.mdwn
+++ b/tags/H3S28p.mdwn
@@ -47,4 +47,8 @@ The rat monoclonal antibody (Abcam ab10543) stains the centromere-attracting
 body in _O. dioica_, Osaka lab. strain. ([[Nishida and coll.,
 2021|biblio/34755656]]), probably by cross-reactivity.
 
+In [[Feng and Thompson, 2023|biblio/38130951], the Abcam ab10543 antibody “was
+either spread along entire chromosomes in 38% of oocytes or enriched on
+centromeres in 62% of oocytes”.
+
 [[!inline pages="tagged(H3S28p)" limit=0]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index d95bb1a3..3c2a35be 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -261,6 +261,9 @@ Genes and pathways
  - 6 FGF genes were detected by Oulion, Bertrand and Escriva ([[2012|biblio/22919541]]).
  - _Eya_, _Pitx_, _Six1/2_, _Six3/6a_ and _Six3/6b_, with expression patterns supporting
    homology of larvacean and vertebrate placodes ([[Bassham and Postlethwait, 2005|biblio/16120641]]).
+ - There are two copies of Aurora, _OdAur1_ and _OdAur2_.  In meiosis, they
+   localise to the centrosomes and the spindle respectively ([[Feng and
+   Thompson, 2023|biblio/38130951]]).
 
 ### Lost
 

diff --git a/tags/calcium.mdwn b/tags/calcium.mdwn
new file mode 100644
index 00000000..b21e1368
--- /dev/null
+++ b/tags/calcium.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged calcium"]]
+
+[[!inline pages="tagged(calcium)" actions="no" archive="yes"
+feedshow=10]]

diff --git a/biblio/37821828.mdwn b/biblio/37821828.mdwn
new file mode 100644
index 00000000..4d4c07a6
--- /dev/null
+++ b/biblio/37821828.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny."]]
+[[!tag ]]
+
+Chromosome-level genome assemblies of Cutaneotrichosporon spp. (Trichosporonales, Basidiomycota) reveal imbalanced evolution between nucleotide sequences and chromosome synteny.
+
+BMC Genomics. 2023 Oct 11;24(1):609. doi:10.1186/s12864-023-09718-2.
+
+Kobayashi Y, Kayamori A, Aoki K, Shiwa Y, Matsutani M, Fujita N, Sugita T, Iwasaki W, Tanaka N, Takashima M.
+
+[[!pmid 37821828 desc="_Cutaneotrichosporon cavernicola_ sister species with same karyotype, ITS sequence similarity above the usual threshold for species boundaries, but scrambling of large-width regions.  “If [mating infertility caused by genome rearrangement] is universal, chromosome synteny should be considered the determinant of biological species”"]]

diff --git a/biblio/15786810.mdwn b/biblio/15786810.mdwn
index 15b4888e..610f21c9 100644
--- a/biblio/15786810.mdwn
+++ b/biblio/15786810.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="cDNA library construction from a small amount of RNA: adaptor-ligation approach for two-round cRNA amplification using T7 and SP6 RNA polymerases."]]
-[[!tag ]]
+[[!tag library amplification]]
 
 Biotechniques. 2005 Mar;38(3):451-8.
 
diff --git a/biblio/26001965.mdwn b/biblio/26001965.mdwn
index dc319085..e73f2eac 100644
--- a/biblio/26001965.mdwn
+++ b/biblio/26001965.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Global analysis of RNA cleavage by 5′-hydroxyl RNA sequencing."]]
-[[!tag ]]
+[[!tag mRNA]]
 
 Peach SE, York K, Hesselberth JR.
 
diff --git a/biblio/31857067.mdwn b/biblio/31857067.mdwn
index 19b1826a..0d4aac24 100644
--- a/biblio/31857067.mdwn
+++ b/biblio/31857067.mdwn
@@ -1,10 +1,10 @@
 [[!meta title="Protein phosphatase 2A is essential to maintain meiotic arrest, and to prevent Ca2+ burst at spawning and eventual parthenogenesis in the larvacean Oikopleura dioica."]]
-[[!tag ]]
+[[!tag Oikopleura calcium]]
+
+Matsuo M, Onuma TA, Omotezako T, Nishida H.
 
 Protein phosphatase 2A is essential to maintain meiotic arrest, and to prevent Ca2+ burst at spawning and eventual parthenogenesis in the larvacean Oikopleura dioica.
 
 Dev Biol. 2020 Apr 15;460(2):155-163. doi:10.1016/j.ydbio.2019.12.005
 
-Matsuo M, Onuma TA, Omotezako T, Nishida H.
-
 [[!pmid 31857067 desc="“PP2A is essential for the maintenance of meiotic arrest and prevention of parthenogenesis at spawning event in O. dioica. When PP2Ac is lost, the pH rise at spawning brings about an aberrant Ca burst by still unknown molecular mechanisms, and it activates eggs via CaMK II, reinitiates meiosis, and eventually results in improper initiation of embryogenesis.” Okadaic acid also induced parthenogenesis.  Termination of parthenogenetic migth be explain by failure to complete the cleavages because of the absence of the centrosome that should have been brought by the sperm."]]
diff --git a/biblio/m088p297.mdwn b/biblio/m088p297.mdwn
index 859a8104..a12defd4 100644
--- a/biblio/m088p297.mdwn
+++ b/biblio/m088p297.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Lipid and lipid class content of the pelagic tunicate Oikopleura vanhoeffeni"]]
-[[!tag ]]
+[[!tag Oikopleura ]]
 
 Deibel, D., Cavaletto, J. F., Riehl, M., Gardner, W. S.
 

diff --git a/biblio/37945377.mdwn b/biblio/37945377.mdwn
new file mode 100644
index 00000000..32645c12
--- /dev/null
+++ b/biblio/37945377.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The human genome contains over a million autonomous exons."]]
+[[!tag splicing]]
+
+Stepankiw N, Yang AWH, Hughes TR.
+
+Genome Res. 2023 Nov 9. doi:10.1101/gr.277792.123
+
+The human genome contains over a million autonomous exons.
+
+[[!pmid 37945377 desc="“∼4.2 billion paired end reads [...] mapped to ∼6 million clusters [which] encompassed ∼9% of the genome.”  “Internal exons from protein-coding genes [...] had an average of 10,636 reads, [...] encompassing 32% of all reads.”  “exon clusters with at least 100 reads [captured] 1,245,947 exons in total, encompassing 3.2% of the stranded genome (i.e., 6.2 Gb)“. “5.3% of all intergenic region bases [...] are part of a trapped exon [424,632], corresponding to an exon every 3311 bases on average”. “52% of GENCODE lncRNA internal exons were trapped with at least 100 reads, a figure comparable to that of mRNA internal exons (61%).”  “Known alternative cassette exons displayed, on average, 2.5-fold lower inclusion rates when compared to all internal mRNA exons.”  “the trapped exons are very significantly depleted from introns, but not the mRNA antisense strand, and trapped exons that are detected in introns tend to have low read counts”"]]

diff --git a/biblio/10.1101_2023.10.30.564762.mdwn b/biblio/10.1101_2023.10.30.564762.mdwn
new file mode 100644
index 00000000..8146af0f
--- /dev/null
+++ b/biblio/10.1101_2023.10.30.564762.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The brittle star genome illuminates the genetic basis of animal appendage regeneration"]]
+[[!tag synteny]]
+
+bioRxiv 2023.10.30.564762; doi:10.1101/2023.10.30.564762
+
+Elise Parey, Olga Ortega-Martinez, Jérôme Delroisse, Laura Piovani, Anna Czarkwiani, David Dylus, Srishti Arya, Samuel Dupont, Michael Thorndyke, Tomas Larsson, Kerstin Johannesson, Katherine M. Buckley, Pedro Martinez, Paola Oliveri, Ferdinand Marlétaz
+
+The brittle star genome illuminates the genetic basis of animal appendage regeneration
+
+[[!doi 10.1101/2023.10.30.564762 desc="“We showed that the ‘Eleutherozoa Linkage Groups’ descend from a single fusion of ancestral bilaterian linkages (B2+C2).”  “Interestingly, sea cucumbers have the lowest rate of inter-chromosomal rearrangements, yet the most derived echinoderm body plan (Rahman et al. 2019), which highlights the uncoupling of global genomic rearrangements from morphological evolution.”  “In contrast with its sea star sister-group, the A. filiformis genome is highly rearranged: our analyses identified 26 inter-chromosomal rearrangements since the Eleutherozoa ancestor.”"]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index f1b16968..74ea072d 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -85,6 +85,10 @@ but higher than in plants ([[Li and coll., 2022|biblio/36334587]]).
  - The ancestral bilaterian had 24 linkage groups according to [[Simakov and
    coll., 2022|biblio/35108053]].
 
+ - The Eleutherozoa Linkage Groups descend from a single fusion of ancestral
+   bilaterian linkages B2 and C2 ([[Parey and coll., 2023|biblio/10.1101_2023.10.30.564762]]).
+   Some clades there scrambled a lot, and some not (sea cucumbers).
+
 ### Computational aspects
 
  - [[Rocha (2003)|biblio/14585609]] defines a Gene Order Conservation (GOC)

diff --git a/biblio/37947122.mdwn b/biblio/37947122.mdwn
new file mode 100644
index 00000000..7fafe168
--- /dev/null
+++ b/biblio/37947122.mdwn
@@ -0,0 +1,25 @@
+[[!meta title="The appendicularian Oikopleura dioica can enhance carbon export in a high CO2 ocean."]]
+[[!tag Oikopleura]]
+
+Taucher J, Lechtenbörger AK, Bouquet JM, Spisla C, Boxhammer T, Minutolo F, Bach LT, Lohbeck KT, Sswat M, Dörner I, Ismar-Rebitz SMH, Thompson EM, Riebesell U.
+
+The appendicularian _Oikopleura dioica_ can enhance carbon export in a high CO2 ocean.
+
+Glob Chang Biol. 2023 Nov 10:e17020. doi: 10.1111/gcb.17020.
+
+[[!pmid 37947122 desc=" “pelagic mesocosms [...], each extending to a depth of
+21 m (19 m cylindrical bag and 2 m full size/diameter conical sediment trap
+attached to the bottom of the bag) and enclosing about 60 m3 of the natural
+water column.”  “Average pCO2 during the experiment ranged between ~320
+(“ambient”) and 1700 μatm (“high CO2,” corresponding to a drop in pH by
+0.57 units compared to ambient conditions).”  “a custom-built net (50 μm mesh
+size; 20 cm in diameter) with a modified, non-filtering cod end (3.8 L clear
+polycarbonate beaker) and reduced towing speeds (0.15 m s−1) was applied in
+order to collect alive and undamaged O. dioica specimen.”  “The peak biomass of
+O. dioica was approximately twice as high in the high CO2 mesocosms (2.5 vs.
+1.3 μgC L−1) and occurred earlier (days 13–17) than under ambient conditions
+(day 21)”. “female O. dioica were cultured in mesocosm water (pre-filtered
+through a 50-μm mesh) of the respective CO2 conditions until they achieved
+maturity and produced eggs.”   “The fecundity of O. dioica was significantly
+elevated under lower pH, with females producing 278 (±107) eggs under ambient
+and 334 (±14) eggs in the OA treatment“"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index ea44efba..d95bb1a3 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -390,9 +390,11 @@ Development
    2014|biblio/24695788]]).
  - Meiosis is resumed by change of extracellular pH when the oocytes are released
    in seawater.  Partenogenesis starts if PP2A is inhibited by DNAi or with
-   okadaic acid ([[Matsuo and coll., 2020|biblio/31857067]).
+   okadaic acid ([[Matsuo and coll., 2020|biblio/31857067]]).
  - Colchicine treatment induced early differenciation of the oocytes
    ([[Ganot, Kallesøe, Thompson (2007)|biblio/17123503]]).
+ - In mesocosms under high-CO2 (low-pH) conditions, femals produce more eggs
+   (278 ±11 vs 334 ±14), Taucher and coll. ([[2023|biblio/37947122]]).
 
 ### Fertilization and early stages
 

diff --git a/biblio/37989229.mdwn b/biblio/37989229.mdwn
new file mode 100644
index 00000000..e41c4776
--- /dev/null
+++ b/biblio/37989229.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The hydrodynamics and kinematics of the appendicularian tail underpin peristaltic pumping."]]
+[[!tag Oikopleura]]
+
+Hiebert TC, Gemmell BJ, von Dassow G, Conley KR, Sutherland KR.
+
+J R Soc Interface. 2023 Nov;20(208):20230404. doi:10.1098/rsif.2023.0404
+
+The hydrodynamics and kinematics of the appendicularian tail underpin peristaltic pumping.
+
+[[!pmid 37989229 desc="“Flow tracers consisted of live, unicellular microalgae. Rhinomonas reticulata was used for observations at low magnifications (4×) and Isochrysis galbana was used for observations at high magnifications (40×).”  “Our micro-videography confirms that the beating tail in O. dioica acts as a positive displacement peristaltic pump when filtering”   “Temperature had a significant effect on tail beat frequency, which increased by 366% from 5 to 25°C.”  “Likewise, inlet particle speeds increased with increasing temperature”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 6c4d1336..ea44efba 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -581,6 +581,9 @@ House
  - Temperature and food availability increase house production from ~0.2 /h to ~0.4 / h
    ([[Fenaux 1985|biblio/WOSA1985AYN8600012]], of from ~0.4 /h to ~0.8 / h
    [[Sato, Tanaka and Ishimaru, 2001|biblio/10.1093_plankt_23.4.415]].
+ - The tail acts as a peristaltic pump to generate the flow in the house.  Tail
+   beat and particule speed increased with temperature (5, 15 and 25 ºC)
+   ([[Hiebert and coll., 2023|biblio/37989229]]).
 
 Phenotypes
 ----------

diff --git a/biblio/1571417125678584576.mdwn b/biblio/1571417125678584576.mdwn
new file mode 100644
index 00000000..5c630a82
--- /dev/null
+++ b/biblio/1571417125678584576.mdwn
@@ -0,0 +1,14 @@
+[[!meta title="Cycle vital d'un Appendiculaire Oikopleura dioica Fol, 1872 : description et chronologie"]]
+[[!tag Oikopleura]]
+
+Robert Fenaux
+
+Cycle vital d'un Appendiculaire _Oikopleura dioica_ Fol, 1872 : description et chronologie
+
+Ann. Inst. Oceanogr. Paris (1976) 52, 89-101 https://cir.nii.ac.jp/crid/1571417125678584576
+
+[[!url https://cir.nii.ac.jp/crid/1571417125678584576 desc="High sperm
+concentration leads to polyspermia, aborted cell divisions, and early
+developmental arrest.  Egg diameter between 97 and 107 µm.  The trunk / tail
+length ratio varies with age and can be matched with a Bertalanffy model.  Fed
+with _Nannochloris occulata_."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index eea3da10..6c4d1336 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -367,6 +367,8 @@ Tools
 Development
 -----------
 
+### Gametes
+
  - The oocytes originate from a specialised syncitium, the coenocyst, in which
    nurse cells and oocytes are connected by cytoplasmic bridges, the ring channels
    ([[Ganot and coll., 2007|biblio/17126826]]).
@@ -378,18 +380,34 @@ Development
  - Inhibition of the MAPK pathway cause some nurse cell nuclei to enter the
    oocyte through the ring channels ([[Ganot, Moosmann-Schulmeister and Thompson,
    2008|biblio/18845138]]).
+ - Egg diameter in females from (probably) Villefranche-sur-mer: 97 to 107 µm
+   ([[Fenaux, 1976|biblio/1571417125678584576]]). 
+ - Increased food abundance increases egg number but does not change diameter nor
+   generation time ([[Troedsson and coll., 2002|biblio/10.3354_meps243083]]).
+   Food reduction before day 4 causes growth arrest (GA), in which all cell cycles
+   eventually pause.  Animals in GA can survive ~18 days at 15°C.  GA can also be
+   induced by inhibiting the TOR pathway ([[Subramaniam, Campsteijn and Thompson,
+   2014|biblio/24695788]]).
+ - Meiosis is resumed by change of extracellular pH when the oocytes are released
+   in seawater.  Partenogenesis starts if PP2A is inhibited by DNAi or with
+   okadaic acid ([[Matsuo and coll., 2020|biblio/31857067]).
+ - Colchicine treatment induced early differenciation of the oocytes
+   ([[Ganot, Kallesøe, Thompson (2007)|biblio/17123503]]).
+
+### Fertilization and early stages
+
  - The sperm's mitochondrion enters the oocyte together with the nucleus
    ([[Holland, Gorsky and Fenaux, 1988|biblio/10.1007_BF00312223]]).
  - The first and second polar bodies are visible 5 and 15 min after fertilisation,
    respectively ([[Nishino and Morisawa, 1998|biblio/10.2108_zsj.15.723]]).
- - Meiosis is resumed by change of extracellular pH when the oocytes are released
-   in seawater.  Partenogenesis starts if PP2A is inhibited by DNAi or with
-   okadaic acid ([[Matsuo and coll., 2020|biblio/31857067]).
  - First embryonic cleavages are deterministic and “Clonal organization of the
    tissues is essentially invariant among individuals” ([[Stach and coll.,
    2008|biblio/18490654]]).
- - Colchicine treatment induced early differenciation of the oocytes
-   ([[Ganot, Kallesøe, Thompson (2007)|biblio/17123503]]).
+ - Fertilization in high sperm concentration leads to polyspermia
+   ([[Fenaux, 1976|biblio/1571417125678584576]]).
+
+### Other
+
  - Generation times shortens when temperature rises.  First spawnings are seen
    on day 6 at 14.2 °C, and on day 8 at 17.2 °C ([[Bouquet and coll.,
    2018|biblio/29298334]]).  Reported generation times in the litterature: 149 ± 2
@@ -402,12 +420,6 @@ Development
    1995|biblio/10.1016_0022-0981_95_00004-B]]).  Tôkyô bay _O. dioica_ under
    laboratory condiditons:  6 days at 15°C, 4 days at 20°C and 3 days at 25°C
    ([[Sato, Tanaka and Ishimaru, 2001|biblio/10.1093_plankt_23.4.415]]).
- - Increased food abundance increases egg number but does not change diameter nor
-   generation time ([[Troedsson and coll., 2002|biblio/10.3354_meps243083]]).
-   Food reduction before day 4 causes growth arrest (GA), in which all cell cycles
-   eventually pause.  Animals in GA can survive ~18 days at 15°C.  GA can also be
-   induced by inhibiting the TOR pathway ([[Subramaniam, Campsteijn and Thompson,
-   2014|biblio/24695788]]).
  - Large animals (~5 mm body length) could be cultivated when provided with large
    amounts of food ([[Li and Zhang, 2021|biblio/10.1007_s00343-020-0071-0]]).
  - Telomeres are localised at the nuclear envelope and do not overlap with nuclear
@@ -746,6 +758,9 @@ Culture protocols (incomplete list):
 
 Food tested in laboratory (totally incomplete list):
 
+ - [[Fenaux 1976|biblio/1571417125678584576]] reported the use of [_Nanochloropsis oceanica_][]
+   (under the name _Nanochloris occulata_) (2 to 3 µm according to Wikipedia).
+
  - Flagellates [_Isochrysis galbana_][] (4 µm width) and _Monochrysis lutheri_ (4 µm
    width), and the diatom _Cyclotella nana_ (Thalassiosira pseudonana) which had
    a width of 5 µm ([[G.-A. Paffenhöfer, 1973|biblio/10.1007_BF00391782]]).
@@ -776,5 +791,6 @@ Food tested in laboratory (totally incomplete list):
 [_Rhinomonas reticulata_]:  https://en.wikipedia.org/wiki/Rhinomonas
 [_Synechococcus sp._]:      https://en.wikipedia.org/wiki/Synechococcus
 [_Tetraselmis suecica_]:    https://en.wikipedia.org/wiki/Tetraselmis_suecica
+[_Nanochloropsis oceanica_]: https://en.wikipedia.org/wiki/Nannochloropsis
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

diff --git a/biblio/37819006.mdwn b/biblio/37819006.mdwn
new file mode 100644
index 00000000..c08cbcd2
--- /dev/null
+++ b/biblio/37819006.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="Where the minor things are: a pan-eukaryotic survey suggests neutral processes may explain much of minor intron evolution."]]
+[[!tag splicing]]
+
+Larue GE, Roy SW.
+
+Where the minor things are: a pan-eukaryotic survey suggests neutral processes may explain much of minor intron evolution.
+
+Nucleic Acids Res. 2023 Nov 10;51(20):10884-10908. doi: 10.1093/nar/gkad797
+
+[[!pmid 37819006 desc="Reports possible loss of the minor spliceosome in the
+Dipteran clade Chironomidae (_Clunio marinus_, _Polypedilum vanderplanki_ and
+_Belgica antarctica_) and in the copepod crustaceans _Tigriopus californicus_
+and _Eurytemora affinis_."]]

diff --git a/biblio/10.1016_j.slast.2023.10.004.mdwn b/biblio/10.1016_j.slast.2023.10.004.mdwn
new file mode 100644
index 00000000..c13fde4d
--- /dev/null
+++ b/biblio/10.1016_j.slast.2023.10.004.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Robotic cell processing facility for clinical research of retinal cell therapy"]]
+[[!tag robot]]
+
+Motoki Terada, Yu Kogawa, Yumiko Shibata, Michinori Kitagawa, Shinya Kato, Tomomitsu Iida, Tsuyoshi Yorimitsu, Akari Kato, Kenji Matsukuma, Tadao Maeda, Masayo Takahashi, Genki N. Kanda,
+
+SLAS Technology, 2023, ISSN 2472-6303, doi.org:10.1016/j.slast.2023.10.004
+
+Robotic cell processing facility for clinical research of retinal cell therapy
+
+[[!doi 10.1016/j.slast.2023.10.004 desc="10-day culture of iPS cells to be implanted in patients."]]

diff --git a/biblio/10.1007_BF00312223.mdwn b/biblio/10.1007_BF00312223.mdwn
new file mode 100644
index 00000000..821fd471
--- /dev/null
+++ b/biblio/10.1007_BF00312223.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Fertilization in Oikopleura dioica (Tunicata, Appendicularia): Acrosome reaction, cortical reaction and sperm-egg fusion."]]
+[[!tag Oikopleura]]
+
+Holland, L.Z., Gorsky, G. & Fenaux, R.
+
+Zoomorphology 108, 229–243 (1988). doi:10.1007/BF00312223
+
+Fertilization in Oikopleura dioica (Tunicata, Appendicularia): Acrosome reaction, cortical reaction and sperm-egg fusion.
+
+[[!doi 10.1007/BF00312223 desc="“Males [...] were placed in cold (4° C) seawater to induce testicular rupture.”  “Each egg is about 80-100 µm in diameter and is surrounded by a thin vitelline layer 80-100 nm thick [...] There is an asymmetrical perivitelline space ranging from 2 to 7 µm in width”. “The maximal diameter of the chromosomes in our section is about 150 nm”. “By 60 s after insemination, when the egg is regaining its spherical shape, the sperm nucleus, centriole, axoneme and mitochondrion have moved into the egg cortex”. “Fertilization [...] occurs almost simultaneously throughout an egg population after the addition of sperm”. “The central cytoplasm of the unfertilized appendicularian egg contains a preponderance of multivesicular bodies and the periphery has alternating areas rich in mitochondria and rich in endoplasmic reticulum”. “the anterior portion of the nuclear envelope evaginates together with the acrosomal membrane and may help to stiffen the resulting acrosomal tubule. The lumen of the tubule, which is consequently lined by the nuclear envelope, contains some fine fibrils that extend back into the nucleus.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index fa7ea4e7..eea3da10 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -378,6 +378,8 @@ Development
  - Inhibition of the MAPK pathway cause some nurse cell nuclei to enter the
    oocyte through the ring channels ([[Ganot, Moosmann-Schulmeister and Thompson,
    2008|biblio/18845138]]).
+ - The sperm's mitochondrion enters the oocyte together with the nucleus
+   ([[Holland, Gorsky and Fenaux, 1988|biblio/10.1007_BF00312223]]).
  - The first and second polar bodies are visible 5 and 15 min after fertilisation,
    respectively ([[Nishino and Morisawa, 1998|biblio/10.2108_zsj.15.723]]).
  - Meiosis is resumed by change of extracellular pH when the oocytes are released

diff --git a/biblio/34824214.mdwn b/biblio/34824214.mdwn
index 4725c16d..fcc4b8b7 100644
--- a/biblio/34824214.mdwn
+++ b/biblio/34824214.mdwn
@@ -1,4 +1,4 @@
-[[!meta title="Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer"]
+[[!meta title="Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer"]]
 [[!tag genome synteny chromosome epigenetic evolution]]
 
 Yin Y, Fan H, Zhou B, Hu Y, Fan G, Wang J, Zhou F, Nie W, Zhang C, Liu L, Zhong Z, Zhu W, Liu G, Lin Z, Liu C, Zhou J, Huang G, Li Z, Yu J, Zhang Y, Yang Y, Zhuo B, Zhang B, Chang J, Qian H, Peng Y, Chen X, Chen L, Li Z, Zhou Q, Wang W, Wei F.

diff --git a/biblio/29506021.mdwn b/biblio/29506021.mdwn
index e3cb72ad..b527789a 100644
--- a/biblio/29506021.mdwn
+++ b/biblio/29506021.mdwn
@@ -7,4 +7,8 @@ Bioinformatics. 2018 Jul 15;34(14):2371-2375. doi:10.1093/bioinformatics/bty113
 
 Updating the 97% identity threshold for 16S ribosomal RNA OTUs.
 
-[[!pmid 29506021 desc="Following a benchmark on V4 regions of the 16S rRNA, proposes to raise the threshold to 99% or to just use sequence variants (also called ZOTUS, Zero-radius OTUs."]]
+[[!pmid 29506021 desc="Following a benchmark on V4 regions of the 16S rRNA,
+proposes to raise the threshold to 99% or to just use sequence variants (also
+called ZOTUS, Zero-radius OTUs.  Identity computed as the number of columns
+containing identical letters divided by the number of columns containing at
+least one letter."]]

diff --git a/biblio/34824214.mdwn b/biblio/34824214.mdwn
new file mode 100644
index 00000000..4725c16d
--- /dev/null
+++ b/biblio/34824214.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer"]
+[[!tag genome synteny chromosome epigenetic evolution]]
+
+Yin Y, Fan H, Zhou B, Hu Y, Fan G, Wang J, Zhou F, Nie W, Zhang C, Liu L, Zhong Z, Zhu W, Liu G, Lin Z, Liu C, Zhou J, Huang G, Li Z, Yu J, Zhang Y, Yang Y, Zhuo B, Zhang B, Chang J, Qian H, Peng Y, Chen X, Chen L, Li Z, Zhou Q, Wang W, Wei F.
+
+Nat Commun. 2021 Nov 25;12(1):6858. doi:10.1038/s41467-021-27091-0
+
+Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer
+
+[[!pmid 34824214 desc="“we identified the rapidly evolving genes (REGs) and positively selected genes (PSGs) in the _M. crinifrons_, _M. gongshanensis_, and _M. muntjak vaginalis_ with large fused chromosomes, as well in their common ancestor node. The results showed that the PSGs and REGs in these lineages are enriched in GOs and pathways related to the maintenance of genomic stability.”  “the occurrence/frequency of genomic rearrangements (>10 kb) of _M. crinifrons_ and _M. gongshanensis_ (3.06~3.89 events/Mb) are not significantly higher than those in _M. reevesi_, _E. davidianus_, and _C. albirostris_ (3.11~4.56 events/Mb)”"]]

diff --git a/tags/publishing.mdwn b/tags/publishing.mdwn
new file mode 100644
index 00000000..3f7655ae
--- /dev/null
+++ b/tags/publishing.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged publishing"]]
+
+[[!inline pages="tagged(publishing)" actions="no" archive="yes"
+feedshow=10]]

diff --git a/biblio/29145518.mdwn b/biblio/29145518.mdwn
index 38ea5c74..9166c13c 100644
--- a/biblio/29145518.mdwn
+++ b/biblio/29145518.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="The prehistory of biology preprints: A forgotten experiment from the 1960s."]]
-[[!tag bioRxiv]]
+[[!tag publishing]]
 
 Cobb M.
 
diff --git a/biblio/10.1101_2020.03.10.985549.mdwn b/biblio/33906962.mdwn
similarity index 95%
rename from biblio/10.1101_2020.03.10.985549.mdwn
rename to biblio/33906962.mdwn
index 791bf8ac..5b9cb08c 100644
--- a/biblio/10.1101_2020.03.10.985549.mdwn
+++ b/biblio/33906962.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Third generation sequencing revises the molecular karyotype for Toxoplasma gondii and identifies emerging copy number variants in sexual recombinants"]]
-[[!tag bioRxiv genome]]
+[[!tag genome]]
 
 Jing Xia, Aarthi Venkat, Karine Le Roch, Ferhat Ay and Jon P. Boyle
 

diff --git a/biblio/10.1101_2023.07.18.549157v1.mdwn b/biblio/10.1101_2023.07.18.549157v1.mdwn
new file mode 100644
index 00000000..d46ce5e8
--- /dev/null
+++ b/biblio/10.1101_2023.07.18.549157v1.mdwn
@@ -0,0 +1,15 @@
+[[!meta title="Pax37 gene function in Oikopleura dioica supports a neuroepithelial-like origin for its house-making Fol territory"]]
+[[!tag Oikopleura bioRxiv]]
+
+David Lagman, Anthony Leon, Nadia Cieminska, Wei Deng, Marios Chatzigeorgiou, Simon Henriet, Daniel Chourrout
+
+bioRxiv 2023.07.18.549157; doi:10.1101/2023.07.18.549157
+
+Pax37 gene function in Oikopleura dioica supports a neuroepithelial-like origin for its house-making Fol territory
+
+[[!doi 2023.07.18.549157v1 desc="Knock-out of Pax37B and Pax37A using
+CRISPR-Cas9.  Pax37B is essential to the proper patterning of the oikoblastic
+epithelium but not Pax37A.  Based on the analysis of single-cell and
+transcriptomic data in Oikopleura and Ciona, the authors propose a parallel
+between oikoblastic cells in Oikopleura and the neuroepithelial cells that
+produce gluing collocytes in Ciona."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 774f1cac..fa7ea4e7 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -464,7 +464,8 @@ Development
  - Endocycling cells show no polytenisation nor _in loco_ amplifications.  Deep invaginations
    of the nuclear envelopper are shown by simultaneous staining of DNA, RNA and membranes
    ([[Spada and coll., 2007|biblio/17288541]]).
-
+ - Knock-out of _Pax37B_ shows it is essential to the proper patterning of the oikoblastic
+   epithelium ([[Langma an coll., 2023|biblio/10.1101_2023.07.18.549157v1]]). 
 
 Anatomy
 -------

diff --git a/biblio/29325078.mdwn b/biblio/29325078.mdwn
new file mode 100644
index 00000000..50ac319b
--- /dev/null
+++ b/biblio/29325078.mdwn
@@ -0,0 +1,21 @@
+[[!meta title="Genomic basis of recombination suppression in the hybrid between Caenorhabditis briggsae and C. nigoni."]]
+[[!tag nematode]]
+
+Ren X, Li R, Wei X, Bi Y, Ho VWS, Ding Q, Xu Z, Zhang Z, Hsieh CL, Young A, Zeng J, Liu X, Zhao Z.
+
+Nucleic Acids Res. 2018 Feb 16;46(3):1295-1307. doi:10.1093/nar/gkx1277
+
+Genomic basis of recombination suppression in the hybrid between _Caenorhabditis briggsae_ and _C. nigoni_.
+
+[[!pmid 29325078 desc="”the coding sequences of [the] one-to-one orthologs
+exhibited only around a 90% identity, and most of [the] introns and intergenic
+regions were not alignable” “we produced [15,157] one-to-one orthologous gene
+pairs between C. briggsae and C. nigoni.”  “we extracted all of the best hits
+between the two genomes that were >1 kb in size [and] observed over 400
+interchromosomal translocations”  “[we produced] produce homozygous viable
+introgressions representing ∼28% of the C. briggsae genome”   “We observed a
+significantly higher [alignment score] in recombination sites than in genomic
+background”  “Nearly half of the reduced genome in C. briggsae could be
+explained by its lost repeats relative to the C. nigoni genome. These
+differences in genome size and repeat content are expected to create gaps in
+the sequence alignment or make the syntenic sequences not alignable.”"]]
diff --git a/tags/nematode.mdwn b/tags/nematode.mdwn
index 626da130..6d3c50ef 100644
--- a/tags/nematode.mdwn
+++ b/tags/nematode.mdwn
@@ -65,4 +65,8 @@ Nematode chromosomes have been called “Nigon elements” by [[Tandonnet and co
    of neighboring genes are rearranged in the selfers compared with 15.0% in the
    outcrossers)” ([[Stevens and coll., 2022|biblio/35348662]]).
 
+ - When comparing _C. briggsae_ and _C. nigoni_, most of the introns and
+   intergenic regions are not alignable.  The aligned regions are ~90%
+   identical ([[Ren and coll., 2018|biblio/29325078]]).
+
 [[!inline pages="tagged(nematode)" limit=0]]

diff --git a/biblio/30770412.mdwn b/biblio/30770412.mdwn
new file mode 100644
index 00000000..5fe1c8e5
--- /dev/null
+++ b/biblio/30770412.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Chromosome-Wide Evolution and Sex Determination in the Three-Sexed Nematode Auanema rhodensis."]]
+[[!tag nematode]]
+
+Tandonnet S, Koutsovoulos GD, Adams S, Cloarec D, Parihar M, Blaxter ML, Pires-daSilva A.
+
+Chromosome-Wide Evolution and Sex Determination in the Three-Sexed Nematode Auanema rhodensis.
+
+G3 (Bethesda). 2019 Apr 9;9(4):1211-1230. doi: 10.1534/g3.119.0011
+
+[[!pmid 30770412 desc="Nigon elements"]]
diff --git a/tags/nematode.mdwn b/tags/nematode.mdwn
index d79694c9..626da130 100644
--- a/tags/nematode.mdwn
+++ b/tags/nematode.mdwn
@@ -2,6 +2,9 @@
 
 ... in progress ...
 
+Nematode chromosomes have been called “Nigon elements” by [[Tandonnet and coll,
+2019|biblio/30770412]].
+
 ### _C. inopinata_
 
  - _C. inopinata_ was discovered in 2018 to be the closest species to _C.