Dernières modifications :

Mdwn
diff --git "a/Debian/debi\303\242neries/initgr.en.po" "b/Debian/debi\303\242neries/initgr.en.po"
index b511c8ca..6dc5e6bb 100644
--- "a/Debian/debi\303\242neries/initgr.en.po"
+++ "b/Debian/debi\303\242neries/initgr.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2019-12-08 01:04+0000\n"
-"PO-Revision-Date: 2019-12-08 08:59+0900\n"
+"PO-Revision-Date: 2019-12-08 10:05+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -37,16 +37,6 @@ msgid "[[!meta title=\"A voté\"]]\n"
 msgstr "[[!meta title=\"I voted\"]]\n"
 
 #. type: Plain text
-#, fuzzy
-#| msgid ""
-#| "Lors de la préparation du vote sur les systèmes d'initialisation dans "
-#| "Debian, j'ai pensé proposer une option disant que ce vote n'est pas "
-#| "nécessaire et rappelant qu'il faut utiliser les résolutions générales "
-#| "avec parcimonie [comme en 2014|https://www.debian.org/vote/2014/vote_003."
-#| "fr.html#amendmenttextc].  Cependant je me suis souvenu que a) Sam a été "
-#| "élu DPL avec une plateforme proposant de lancer des votes plus souvent et "
-#| "que b) j'avais moi-même proposé quelque chose de similaire lors des "
-#| "[élections en 2010|https://www.debian.org/vote/2010/platforms/plessy]..."
 msgid ""
 "Lors de la préparation du vote sur les systèmes d'initialisation dans "
 "Debian, j'ai pensé proposer une option disant que ce vote n'est pas "
@@ -58,12 +48,12 @@ msgid ""
 "2010](https://www.debian.org/vote/2010/platforms/plessy)..."
 msgstr ""
 "While the vote on init systems was being prepared, I thought about proposing "
-"an option telling that this vote is not necessary, and reminding that genera "
-"resolutions should be used with parcimony, [like in 2014|https://www.debian."
-"org/vote/2014/vote_003.fr.html#amendmenttextc]. However, I then remembered "
-"that a) Sam was elected on a platform proposing more votes, and b) I "
-"proposed something similar in the [elections in 2010|https://www.debian.org/"
-"vote/2010/platforms/plessy]..."
+"an option telling that this vote is not necessary, and reminding that "
+"general resolutions should be used with parcimony, [like in 2014](https://"
+"www.debian.org/vote/2014/vote_003.fr.html#amendmenttextc). However, I then "
+"remembered that a) Sam was elected on a platform proposing more votes, and "
+"b) I proposed something similar in the [elections in 2010](https://www."
+"debian.org/vote/2010/platforms/plessy)..."
 
 #. type: Plain text
 msgid ""

updated PO files
diff --git "a/Debian/debi\303\242neries/initgr.en.po" "b/Debian/debi\303\242neries/initgr.en.po"
index a11e9f57..b511c8ca 100644
--- "a/Debian/debi\303\242neries/initgr.en.po"
+++ "b/Debian/debi\303\242neries/initgr.en.po"
@@ -6,7 +6,7 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2019-12-07 23:58+0000\n"
+"POT-Creation-Date: 2019-12-08 01:04+0000\n"
 "PO-Revision-Date: 2019-12-08 08:59+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
@@ -37,15 +37,25 @@ msgid "[[!meta title=\"A voté\"]]\n"
 msgstr "[[!meta title=\"I voted\"]]\n"
 
 #. type: Plain text
+#, fuzzy
+#| msgid ""
+#| "Lors de la préparation du vote sur les systèmes d'initialisation dans "
+#| "Debian, j'ai pensé proposer une option disant que ce vote n'est pas "
+#| "nécessaire et rappelant qu'il faut utiliser les résolutions générales "
+#| "avec parcimonie [comme en 2014|https://www.debian.org/vote/2014/vote_003."
+#| "fr.html#amendmenttextc].  Cependant je me suis souvenu que a) Sam a été "
+#| "élu DPL avec une plateforme proposant de lancer des votes plus souvent et "
+#| "que b) j'avais moi-même proposé quelque chose de similaire lors des "
+#| "[élections en 2010|https://www.debian.org/vote/2010/platforms/plessy]..."
 msgid ""
 "Lors de la préparation du vote sur les systèmes d'initialisation dans "
 "Debian, j'ai pensé proposer une option disant que ce vote n'est pas "
 "nécessaire et rappelant qu'il faut utiliser les résolutions générales avec "
-"parcimonie [comme en 2014|https://www.debian.org/vote/2014/vote_003.fr."
-"html#amendmenttextc].  Cependant je me suis souvenu que a) Sam a été élu DPL "
+"parcimonie [comme en 2014](https://www.debian.org/vote/2014/vote_003.fr."
+"html#amendmenttextc).  Cependant je me suis souvenu que a) Sam a été élu DPL "
 "avec une plateforme proposant de lancer des votes plus souvent et que b) "
 "j'avais moi-même proposé quelque chose de similaire lors des [élections en "
-"2010|https://www.debian.org/vote/2010/platforms/plessy]..."
+"2010](https://www.debian.org/vote/2010/platforms/plessy)..."
 msgstr ""
 "While the vote on init systems was being prepared, I thought about proposing "
 "an option telling that this vote is not necessary, and reminding that genera "

Mdwn
diff --git "a/Debian/debi\303\242neries/initgr.mdwn" "b/Debian/debi\303\242neries/initgr.mdwn"
index de6aba98..5770703f 100644
--- "a/Debian/debi\303\242neries/initgr.mdwn"
+++ "b/Debian/debi\303\242neries/initgr.mdwn"
@@ -7,11 +7,11 @@
 Lors de la préparation du vote sur les systèmes d'initialisation dans Debian,
 j'ai pensé proposer une option disant que ce vote n'est pas nécessaire et
 rappelant qu'il faut utiliser les résolutions générales avec parcimonie [comme
-en 2014|https://www.debian.org/vote/2014/vote_003.fr.html#amendmenttextc].
+en 2014](https://www.debian.org/vote/2014/vote_003.fr.html#amendmenttextc).
 Cependant je me suis souvenu que a) Sam a été élu DPL avec une plateforme
 proposant de lancer des votes plus souvent et que b) j'avais moi-même proposé
 quelque chose de similaire lors des [élections en
-2010|https://www.debian.org/vote/2010/platforms/plessy]...
+2010](https://www.debian.org/vote/2010/platforms/plessy)...
 
 Néanmoins je suis écrasé sous le nombre d'options.  Leurs textes sont longs,
 parfois très similaires, et ne séparent pas clairement le normatif du

Spelling and date
diff --git "a/Debian/debi\303\242neries/initgr.en.po" "b/Debian/debi\303\242neries/initgr.en.po"
index 4c042e3b..a11e9f57 100644
--- "a/Debian/debi\303\242neries/initgr.en.po"
+++ "b/Debian/debi\303\242neries/initgr.en.po"
@@ -7,7 +7,7 @@ msgid ""
 msgstr ""
 "Project-Id-Version: \n"
 "POT-Creation-Date: 2019-12-07 23:58+0000\n"
-"PO-Revision-Date: 2019-12-08 08:56+0900\n"
+"PO-Revision-Date: 2019-12-08 08:59+0900\n"
 "Last-Translator: Charles Plessy <toto@example.com>\n"
 "Language-Team: \n"
 "Language: en\n"
@@ -17,16 +17,14 @@ msgstr ""
 "X-Generator: Poedit 2.2.1\n"
 
 #. type: Plain text
-#, fuzzy, no-wrap
-#| msgid "[[!meta date=\"Sun, 08 Dec 2019 08:09:02 +0900\"]]\n"
+#, no-wrap
 msgid "[[!meta date=\"Sun, 08 Dec 2019 08:57:43 +0900\"]]\n"
-msgstr "[[!meta date=\"Sun, 08 Dec 2019 08:09:02 +0900\"]]\n"
+msgstr "[[!meta date=\"Sun, 08 Dec 2019 08:57:43 +0900\"]]\n"
 
 #. type: Plain text
-#, fuzzy, no-wrap
-#| msgid "[[!meta updated=\"Sun, 08 Dec 2019 08:09:02 +0900\"]]\n"
+#, no-wrap
 msgid "[[!meta updated=\"Sun, 08 Dec 2019 08:57:43 +0900\"]]\n"
-msgstr "[[!meta updated=\"Sun, 08 Dec 2019 08:09:02 +0900\"]]\n"
+msgstr "[[!meta updated=\"Sun, 08 Dec 2019 08:57:43 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
@@ -39,16 +37,6 @@ msgid "[[!meta title=\"A voté\"]]\n"
 msgstr "[[!meta title=\"I voted\"]]\n"
 
 #. type: Plain text
-#, fuzzy
-#| msgid ""
-#| "Lors de la préparation du vote sur les systèmes d'initialisation dans "
-#| "Debian, j'ai pensé proposer une option disant que ce vote n'est pas "
-#| "nécessaire et rappellant qu'il faut utiliser les résolutions générales "
-#| "avec parcimonie [comme en 2014|https://www.debian.org/vote/2014/vote_003."
-#| "fr.html#amendmenttextc].  Cependant je me suis souvenu que a) Sam a été "
-#| "élu DPL avec une plateforme proposant de lancer des votes plus souvent et "
-#| "que b) j'avais moi-même proposé quelque chose de similaire lors des "
-#| "[élections en 2010|https://www.debian.org/vote/2010/platforms/plessy]..."
 msgid ""
 "Lors de la préparation du vote sur les systèmes d'initialisation dans "
 "Debian, j'ai pensé proposer une option disant que ce vote n'est pas "
@@ -59,7 +47,7 @@ msgid ""
 "j'avais moi-même proposé quelque chose de similaire lors des [élections en "
 "2010|https://www.debian.org/vote/2010/platforms/plessy]..."
 msgstr ""
-"Whil the vote on init systems was being prepared, I thought about proposing "
+"While the vote on init systems was being prepared, I thought about proposing "
 "an option telling that this vote is not necessary, and reminding that genera "
 "resolutions should be used with parcimony, [like in 2014|https://www.debian."
 "org/vote/2014/vote_003.fr.html#amendmenttextc]. However, I then remembered "

updated PO files
diff --git "a/Debian/debi\303\242neries/initgr.en.po" "b/Debian/debi\303\242neries/initgr.en.po"
index a0676d6c..4c042e3b 100644
--- "a/Debian/debi\303\242neries/initgr.en.po"
+++ "b/Debian/debi\303\242neries/initgr.en.po"
@@ -6,24 +6,26 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2019-12-07 23:38+0000\n"
+"POT-Creation-Date: 2019-12-07 23:58+0000\n"
 "PO-Revision-Date: 2019-12-08 08:56+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
-#, no-wrap
-msgid "[[!meta date=\"Sun, 08 Dec 2019 08:09:02 +0900\"]]\n"
+#, fuzzy, no-wrap
+#| msgid "[[!meta date=\"Sun, 08 Dec 2019 08:09:02 +0900\"]]\n"
+msgid "[[!meta date=\"Sun, 08 Dec 2019 08:57:43 +0900\"]]\n"
 msgstr "[[!meta date=\"Sun, 08 Dec 2019 08:09:02 +0900\"]]\n"
 
 #. type: Plain text
-#, no-wrap
-msgid "[[!meta updated=\"Sun, 08 Dec 2019 08:09:02 +0900\"]]\n"
+#, fuzzy, no-wrap
+#| msgid "[[!meta updated=\"Sun, 08 Dec 2019 08:09:02 +0900\"]]\n"
+msgid "[[!meta updated=\"Sun, 08 Dec 2019 08:57:43 +0900\"]]\n"
 msgstr "[[!meta updated=\"Sun, 08 Dec 2019 08:09:02 +0900\"]]\n"
 
 #. type: Plain text
@@ -37,10 +39,20 @@ msgid "[[!meta title=\"A voté\"]]\n"
 msgstr "[[!meta title=\"I voted\"]]\n"
 
 #. type: Plain text
+#, fuzzy
+#| msgid ""
+#| "Lors de la préparation du vote sur les systèmes d'initialisation dans "
+#| "Debian, j'ai pensé proposer une option disant que ce vote n'est pas "
+#| "nécessaire et rappellant qu'il faut utiliser les résolutions générales "
+#| "avec parcimonie [comme en 2014|https://www.debian.org/vote/2014/vote_003."
+#| "fr.html#amendmenttextc].  Cependant je me suis souvenu que a) Sam a été "
+#| "élu DPL avec une plateforme proposant de lancer des votes plus souvent et "
+#| "que b) j'avais moi-même proposé quelque chose de similaire lors des "
+#| "[élections en 2010|https://www.debian.org/vote/2010/platforms/plessy]..."
 msgid ""
 "Lors de la préparation du vote sur les systèmes d'initialisation dans "
 "Debian, j'ai pensé proposer une option disant que ce vote n'est pas "
-"nécessaire et rappellant qu'il faut utiliser les résolutions générales avec "
+"nécessaire et rappelant qu'il faut utiliser les résolutions générales avec "
 "parcimonie [comme en 2014|https://www.debian.org/vote/2014/vote_003.fr."
 "html#amendmenttextc].  Cependant je me suis souvenu que a) Sam a été élu DPL "
 "avec une plateforme proposant de lancer des votes plus souvent et que b) "

date et orthographe
diff --git "a/Debian/debi\303\242neries/initgr.mdwn" "b/Debian/debi\303\242neries/initgr.mdwn"
index ea4d3ddc..de6aba98 100644
--- "a/Debian/debi\303\242neries/initgr.mdwn"
+++ "b/Debian/debi\303\242neries/initgr.mdwn"
@@ -1,12 +1,12 @@
-[[!meta date="Sun, 08 Dec 2019 08:09:02 +0900"]]
-[[!meta updated="Sun, 08 Dec 2019 08:09:02 +0900"]]
+[[!meta date="Sun, 08 Dec 2019 08:57:43 +0900"]]
+[[!meta updated="Sun, 08 Dec 2019 08:57:43 +0900"]]
 [[!tag Debian]]
 
 [[!meta title="A voté"]]
 
 Lors de la préparation du vote sur les systèmes d'initialisation dans Debian,
 j'ai pensé proposer une option disant que ce vote n'est pas nécessaire et
-rappellant qu'il faut utiliser les résolutions générales avec parcimonie [comme
+rappelant qu'il faut utiliser les résolutions générales avec parcimonie [comme
 en 2014|https://www.debian.org/vote/2014/vote_003.fr.html#amendmenttextc].
 Cependant je me suis souvenu que a) Sam a été élu DPL avec une plateforme
 proposant de lancer des votes plus souvent et que b) j'avais moi-même proposé

I voted
diff --git "a/Debian/debi\303\242neries/initgr.en.po" "b/Debian/debi\303\242neries/initgr.en.po"
index dc8ba203..a0676d6c 100644
--- "a/Debian/debi\303\242neries/initgr.en.po"
+++ "b/Debian/debi\303\242neries/initgr.en.po"
@@ -3,51 +3,57 @@
 # This file is distributed under the same license as the PACKAGE package.
 # FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
 #
-#, fuzzy
 msgid ""
 msgstr ""
-"Project-Id-Version: PACKAGE VERSION\n"
+"Project-Id-Version: \n"
 "POT-Creation-Date: 2019-12-07 23:38+0000\n"
-"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
-"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
-"Language-Team: LANGUAGE <LL@li.org>\n"
-"Language: \n"
+"PO-Revision-Date: 2019-12-08 08:56+0900\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
 #, no-wrap
 msgid "[[!meta date=\"Sun, 08 Dec 2019 08:09:02 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Sun, 08 Dec 2019 08:09:02 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Sun, 08 Dec 2019 08:09:02 +0900\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Sun, 08 Dec 2019 08:09:02 +0900\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta title=\"A voté\"]]\n"
-msgstr ""
+msgstr "[[!meta title=\"I voted\"]]\n"
 
 #. type: Plain text
 msgid ""
 "Lors de la préparation du vote sur les systèmes d'initialisation dans "
 "Debian, j'ai pensé proposer une option disant que ce vote n'est pas "
 "nécessaire et rappellant qu'il faut utiliser les résolutions générales avec "
-"parcimonie [comme en "
-"2014|https://www.debian.org/vote/2014/vote_003.fr.html#amendmenttextc].  "
-"Cependant je me suis souvenu que a) Sam a été élu DPL avec une plateforme "
-"proposant de lancer des votes plus souvent et que b) j'avais moi-même "
-"proposé quelque chose de similaire lors des [élections en "
+"parcimonie [comme en 2014|https://www.debian.org/vote/2014/vote_003.fr."
+"html#amendmenttextc].  Cependant je me suis souvenu que a) Sam a été élu DPL "
+"avec une plateforme proposant de lancer des votes plus souvent et que b) "
+"j'avais moi-même proposé quelque chose de similaire lors des [élections en "
 "2010|https://www.debian.org/vote/2010/platforms/plessy]..."
 msgstr ""
+"Whil the vote on init systems was being prepared, I thought about proposing "
+"an option telling that this vote is not necessary, and reminding that genera "
+"resolutions should be used with parcimony, [like in 2014|https://www.debian."
+"org/vote/2014/vote_003.fr.html#amendmenttextc]. However, I then remembered "
+"that a) Sam was elected on a platform proposing more votes, and b) I "
+"proposed something similar in the [elections in 2010|https://www.debian.org/"
+"vote/2010/platforms/plessy]..."
 
 #. type: Plain text
 msgid ""
@@ -59,3 +65,9 @@ msgid ""
 "phase.  Je n'ai pas voté pour les autres, ce qui les place indistinctement "
 "sous le niveau « discussion supplémentaire »."
 msgstr ""
+"Nevertheless, I am crushed under the number of options. Their texts are "
+"long, sometimes very similar, and do not separate clearly the normative from "
+"the preambles. Like in a parody of the dysfunctions of modern democracies, I "
+"ended up considering only the proposals written or seconded by people with "
+"whom I feel in phase. I have not voted for the others, which ranks them "
+"equally under « further discussion »."

updated PO files
diff --git "a/Debian/debi\303\242neries/initgr.en.po" "b/Debian/debi\303\242neries/initgr.en.po"
new file mode 100644
index 00000000..dc8ba203
--- /dev/null
+++ "b/Debian/debi\303\242neries/initgr.en.po"
@@ -0,0 +1,61 @@
+# SOME DESCRIPTIVE TITLE
+# Copyright (C) YEAR Free Software Foundation, Inc.
+# This file is distributed under the same license as the PACKAGE package.
+# FIRST AUTHOR <EMAIL@ADDRESS>, YEAR.
+#
+#, fuzzy
+msgid ""
+msgstr ""
+"Project-Id-Version: PACKAGE VERSION\n"
+"POT-Creation-Date: 2019-12-07 23:38+0000\n"
+"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n"
+"Last-Translator: FULL NAME <EMAIL@ADDRESS>\n"
+"Language-Team: LANGUAGE <LL@li.org>\n"
+"Language: \n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta date=\"Sun, 08 Dec 2019 08:09:02 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Sun, 08 Dec 2019 08:09:02 +0900\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"A voté\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Lors de la préparation du vote sur les systèmes d'initialisation dans "
+"Debian, j'ai pensé proposer une option disant que ce vote n'est pas "
+"nécessaire et rappellant qu'il faut utiliser les résolutions générales avec "
+"parcimonie [comme en "
+"2014|https://www.debian.org/vote/2014/vote_003.fr.html#amendmenttextc].  "
+"Cependant je me suis souvenu que a) Sam a été élu DPL avec une plateforme "
+"proposant de lancer des votes plus souvent et que b) j'avais moi-même "
+"proposé quelque chose de similaire lors des [élections en "
+"2010|https://www.debian.org/vote/2010/platforms/plessy]..."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Néanmoins je suis écrasé sous le nombre d'options.  Leurs textes sont longs, "
+"parfois très similaires, et ne séparent pas clairement le normatif du "
+"préambule.  Comme dans une parodie des dysfonctionnements des démocraties "
+"modernes, j'en suis réduit à ne prendre en considération que les "
+"propositions écrites ou parrainées par des personnes avec qui je me sens en "
+"phase.  Je n'ai pas voté pour les autres, ce qui les place indistinctement "
+"sous le niveau « discussion supplémentaire »."
+msgstr ""

A voté
diff --git "a/Debian/debi\303\242neries/initgr.mdwn" "b/Debian/debi\303\242neries/initgr.mdwn"
new file mode 100644
index 00000000..ea4d3ddc
--- /dev/null
+++ "b/Debian/debi\303\242neries/initgr.mdwn"
@@ -0,0 +1,22 @@
+[[!meta date="Sun, 08 Dec 2019 08:09:02 +0900"]]
+[[!meta updated="Sun, 08 Dec 2019 08:09:02 +0900"]]
+[[!tag Debian]]
+
+[[!meta title="A voté"]]
+
+Lors de la préparation du vote sur les systèmes d'initialisation dans Debian,
+j'ai pensé proposer une option disant que ce vote n'est pas nécessaire et
+rappellant qu'il faut utiliser les résolutions générales avec parcimonie [comme
+en 2014|https://www.debian.org/vote/2014/vote_003.fr.html#amendmenttextc].
+Cependant je me suis souvenu que a) Sam a été élu DPL avec une plateforme
+proposant de lancer des votes plus souvent et que b) j'avais moi-même proposé
+quelque chose de similaire lors des [élections en
+2010|https://www.debian.org/vote/2010/platforms/plessy]...
+
+Néanmoins je suis écrasé sous le nombre d'options.  Leurs textes sont longs,
+parfois très similaires, et ne séparent pas clairement le normatif du
+préambule.  Comme dans une parodie des dysfonctionnements des démocraties
+modernes, j'en suis réduit à ne prendre en considération que les propositions
+écrites ou parrainées par des personnes avec qui je me sens en phase.  Je n'ai
+pas voté pour les autres, ce qui les place indistinctement sous le niveau
+« discussion supplémentaire ».

nematode
diff --git a/tags/nematode.mdwn b/tags/nematode.mdwn
index ad53c985..fb04f59e 100644
--- a/tags/nematode.mdwn
+++ b/tags/nematode.mdwn
@@ -12,4 +12,8 @@
    according to BUSCO and CEGMA) ([[Weinstein and coll.,
    2019|biblio/31754114]]).
 
+ - The whipworms _Trichuris trichiura_ and _Trichuris muris_ have 3
+   chromosomes, as determined by a synteny comparison between two related
+   species ([[Foth and coll., 2014|biblio/24929830]]).
+
 [[!inline pages="tagged(nematode)" limit=0]]

nematode
diff --git a/tags/nematode.mdwn b/tags/nematode.mdwn
index d7606f40..ad53c985 100644
--- a/tags/nematode.mdwn
+++ b/tags/nematode.mdwn
@@ -4,5 +4,12 @@
    is specialised on both its prefered fig and wasp [[(Woodruff and Phillips,
    2018)|biblio/30129423]].
 
-[[!inline pages="tagged(nematode)" actions="no" archive="yes"
-feedshow=10]]
+ - _Diploscapter pachys_ has a single chromosome, that is still organised in
+   ancestral domains homologous to the ones of other nematodes ([[Fradin and
+   coll., 2019|biblio/28943090]]).
+
+ - The genome of _Halicephalobus mephisto_ is only 61.4 Mb (95% complete
+   according to BUSCO and CEGMA) ([[Weinstein and coll.,
+   2019|biblio/31754114]]).
+
+[[!inline pages="tagged(nematode)" limit=0]]

nematode
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index dd41624c..293c0f7a 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -82,7 +82,9 @@ Genome
    2001|biblio/11752568]].  A 70.4 Mb genome "reference assembly" was later
    produced from the shotgun sequencing of sperm DNA from ~200 partially inbred
    males (11 successive sib-matings).  Two distinct haplotypes were found
-   ([[Denoeud et al., 2010|biblio/21097902]]).
+   ([[Denoeud et al., 2010|biblio/21097902]]).  In 2019, it is the smallest
+   sequenced chordate genome, but some [[nematodes|nematode]] have been found
+   with smaller genomes.
  - Other oikopleuid genomes have been sequenced by [[Naville and coll. (2019)|biblio/30880010]]:
    small genomes are also found in _O. longicauda_ (131 Mbp) and _F. borealis_ (91 Mbp).
    There is an apparent correlation between organism size and genome size:

inopinata
diff --git a/tags/nematode.mdwn b/tags/nematode.mdwn
index 1e99f97b..d7606f40 100644
--- a/tags/nematode.mdwn
+++ b/tags/nematode.mdwn
@@ -1,4 +1,8 @@
 [[!meta title="pages tagged nematode"]]
 
+ - _C. inopinata_ travels from fig to fig on Ceratosolen pollinating wasps and
+   is specialised on both its prefered fig and wasp [[(Woodruff and Phillips,
+   2018)|biblio/30129423]].
+
 [[!inline pages="tagged(nematode)" actions="no" archive="yes"
 feedshow=10]]

creating tag page tags/nematode
diff --git a/tags/nematode.mdwn b/tags/nematode.mdwn
new file mode 100644
index 00000000..1e99f97b
--- /dev/null
+++ b/tags/nematode.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged nematode"]]
+
+[[!inline pages="tagged(nematode)" actions="no" archive="yes"
+feedshow=10]]

nematode
diff --git a/biblio/30129423.mdwn b/biblio/30129423.mdwn
new file mode 100644
index 00000000..69f3fea7
--- /dev/null
+++ b/biblio/30129423.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Field studies reveal a close relative of C. elegans thrives in the fresh figs of Ficus septica and disperses on its Ceratosolen pollinating wasps."]]
+[[!tag nematode]]
+
+Woodruff GC, Phillips PC.
+
+BMC Ecol. 2018 Aug 21;18(1):26. doi: 10.1186/s12898-018-0182-z.
+
+Field studies reveal a close relative of C. elegans thrives in the fresh figs of Ficus septica and disperses on its Ceratosolen pollinating wasps.
+
+[[!pmid 30129423 desc="C. inopinata is travelling from fig to fig on Ceratosolen pollinating fig wasps.  It appears to be very specialised in both the fig species and the wasp species."]]

Formatting.
diff --git a/biblio/30166445.mdwn b/biblio/30166445.mdwn
index 320f0bb1..e7ecad1d 100644
--- a/biblio/30166445.mdwn
+++ b/biblio/30166445.mdwn
@@ -1,4 +1,4 @@
-[[!meta title="Muller "Elements" in Drosophila: How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics."]]
+[[!meta title="Muller “Elements” in Drosophila: How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics."]]
 [[!tag Drosophila chromosome variants review]]
 
 Schaeffer SW

Dans l'avion et le bus
diff --git a/biblio/30166445.mdwn b/biblio/30166445.mdwn
new file mode 100644
index 00000000..320f0bb1
--- /dev/null
+++ b/biblio/30166445.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Muller "Elements" in Drosophila: How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics."]]
+[[!tag Drosophila chromosome variants review]]
+
+Schaeffer SW
+
+Genetics. 2018 Sep;210(1):3-13. doi:10.1534/genetics.118.301084
+
+Muller "Elements" in Drosophila: How the Search for the Genetic Basis for Speciation Led to the Birth of Comparative Genomics.
+
+[[!pmid 30166445 desc="Review"]]

Dans l'avion
diff --git a/biblio/28943090.mdwn b/biblio/28943090.mdwn
new file mode 100644
index 00000000..5298cf05
--- /dev/null
+++ b/biblio/28943090.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genome Architecture and Evolution of a Unichromosomal Asexual Nematode."]]
+[[!tag genome chromosome]]
+
+Fradin H, Kiontke K, Zegar C, Gutwein M, Lucas J, Kovtun M, Corcoran DL, Baugh LR, Fitch DHA, Piano F, Gunsalus KC.
+
+Curr Biol. 2017 Oct 9;27(19):2928-2939.e6. doi:10.1016/j.cub.2017.08.038
+
+Genome Architecture and Evolution of a Unichromosomal Asexual Nematode.
+
+[[!pmid 28943090 desc="“By comparing divergence rates with those of Caenorhabditis, we estimate that the asexual clade originated ca. 18 mya”.  “We obtained a genome assembly of 158 Mb with an N50 of 124 kb”.  “the haploid size [...] is ~88 Mb”.  “~4% average difference between [heterozygous] alleles.”  “Genomic regions in D. pachys have generally maintained the same chro- mosomal identity since diverging from Caenorhabditis”.  “ we used macro- synteny with C. elegans to infer an ancestral chromosome iden- tity (ACD) for each D. pachys scaffold.”  “We identified specific patterns of rearrangements consistent with an order of ACD fusions.”  “The data [of reciprocal reaggangements between ACDs] thus allow us to propose that four ancestral chromosomes became fused in the order I-X-III-II”  “Telomeres are either absent from the D. pachys genome or are highly divergent from the ancestral telomeric sequence.”  “The combined absence of telomere sequences and mainte- nance proteins suggests a connection between chromosome fusion and loss of telomeres”.  “84% of homozygous regions localize to ACDs I and X, which are neighbors in the inferred chromosomal fusion”.  ”The reductional division during meiosis I is skipped; the two chromosomes condense but do not pair or synapse.”  “The phenotype of C. elegans rec-8 mutants is reminiscent of the modified meiosis in D. pachys. [...] rec-8 is one of the conserved meiosis genes that was not detected in the D. pachys and D. coronatus genomes”"]]

dessert
diff --git a/biblio/31754114.mdwn b/biblio/31754114.mdwn
new file mode 100644
index 00000000..e421c3cb
--- /dev/null
+++ b/biblio/31754114.mdwn
@@ -0,0 +1,11 @@
+[[!meta title="The genome of a subterrestrial nematode reveals adaptations to heat"]]
+[[!tag genome]]
+
+Weinstein DJ, Allen SE, Lau MCY, Erasmus M, Asalone KC, Walters-Conte K,
+Deikus G, Sebra R, Borgonie G, van Heerden E, Onstott TC, Bracht JR.
+
+Nat Commun. 2019 Nov 21;10(1):5268. doi:10.1038/s41467-019-13245-8
+
+The genome of a subterrestrial nematode reveals adaptations to heat
+
+[[!pmid 31754114 desc="“61.4 Mb comprising 880 scaffolds with N50 of 313 kb, though 90% of the sequence is encoded on just 193 scaffolds. ~95% complete according to BUSCO and CEGMA.”"]]

Café
diff --git a/biblio/24929830.mdwn b/biblio/24929830.mdwn
new file mode 100644
index 00000000..301feb8d
--- /dev/null
+++ b/biblio/24929830.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction."]]
+[[!tag genome chromosome]]
+
+Nat Genet. 2014 Jul;46(7):693-700. doi:10.1038/ng.3010
+
+Foth BJ, Tsai IJ, Reid AJ, Bancroft AJ, Nichol S, Tracey A, Holroyd N, Cotton 
+JA, Stanley EJ, Zarowiecki M, Liu JZ, Huckvale T, Cooper PJ, Grencis RK, Berriman
+M.
+
+Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction.
+
+[[!pmid 24929830 desc="Clustering scaffolds on the number of shared orthologs they have with scaffolds of a related species' genome identifies three chromosomes."]]

Avion
diff --git a/biblio/16586749.mdwn b/biblio/16586749.mdwn
new file mode 100644
index 00000000..db424b23
--- /dev/null
+++ b/biblio/16586749.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genetic Factors Affecting the Strength of Linkage in Drosophila."]]
+[[!tag Drosophila chromosome variants]]
+
+Proc Natl Acad Sci U S A. 1917 Sep;3(9):555-8 doi:10.1073/pnas.3.9.555
+
+Sturtevant AH
+
+Genetic Factors Affecting the Strength of Linkage in Drosophila.
+
+[[!pmid 16586749 desc="Chromosomal inversions (not recognised as such at the time) strongly reduce crossing overs in their vicinity."]]

LAVA elements.
diff --git a/biblio/25209798.mdwn b/biblio/25209798.mdwn
index 0c95e810..487e4faf 100644
--- a/biblio/25209798.mdwn
+++ b/biblio/25209798.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Gibbon genome and the fast karyotype evolution of small apes."]]
-[[!tag chromosome synteny evolution]]
+[[!tag chromosome synteny evolution repeat]]
 
 Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J,
 Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C,
@@ -20,4 +20,4 @@ Nature. 2014 Sep 11;513(7517):195-201. doi:10.1038/nature13679
 
 Gibbon genome and the fast karyotype evolution of small apes.
 
-[[!pmid 25209798 desc="“We identified 96 gibbon–human synteny breakpoints in Nleu1.0.”  “Segmental duplication enrichment was the best predictor of gibbon–human synteny breakpoints,[...] however, breakpoints were also enriched for Alu elements.”  “ The majority of gibbon chromosomal breakpoints bore signatures of non-homology based mechanisms.” “We observed an enrichment of gibbon–human breakpoints in CTCF-binding events.”"]]
+[[!pmid 25209798 desc="“We identified 96 gibbon–human synteny breakpoints in Nleu1.0.”  “Segmental duplication enrichment was the best predictor of gibbon–human synteny breakpoints,[...] however, breakpoints were also enriched for Alu elements.”  “ The majority of gibbon chromosomal breakpoints bore signatures of non-homology based mechanisms.” “We observed an enrichment of gibbon–human breakpoints in CTCF-binding events.”  Insertion of LAVA (3'-L1-AluS-VNTR-Alu-like-5') elements in genes related to cell division might have caused the accelerated evolution of the karyotype in gibbons."]]

OIST
diff --git a/biblio/31386470.mdwn b/biblio/31386470.mdwn
new file mode 100644
index 00000000..c90f5ec4
--- /dev/null
+++ b/biblio/31386470.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Error-Speed Correlations in Biopolymer Synthesis."]]
+[[!tag enzyme]]
+
+Chiuchiú D, Tu Y, Pigolotti S.
+
+Phys Rev Lett. 2019 Jul 19;123(3):038101. doi:10.1103/PhysRevLett.123.038101
+
+Error-Speed Correlations in Biopolymer Synthesis.
+
+[[!pmid 31386470 desc="The sign of the correlation can provide insight in the mechanism of the polymerisation.  Proofreading suppresses the speed-error correlation."]]

U12 not found in F. borealis either.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 16286552..dd41624c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -214,7 +214,8 @@ Genes and pathways
  - In line with the above, “There is no H2AX homolog in O. dioica.” (H2AX is
    implicated in DNA repair).  [[Moosmann and coll., 2011|biblio/21756361]]
  - The minor spliceosome could not be found in _Oikopleura_'s genome ([[Marz
-   et al., 2008|biblio/19030770]]), [[Denoeud et al., 2010|biblio/21097902]]).
+   et al., 2008|biblio/19030770]]), [[Denoeud et al., 2010|biblio/21097902]]),
+   nor in _F. borealis_ ([[Henriet and coll., 2019|biblio/31543449]]).
    It is found in _Ciona_ but not in _C. elegans_ ([[Marz et al.,
    2008|biblio/19030770]]).
  - More than 50 % of the Rab family is lost ([[Coppola and coll., 2019|biblio/31028425]]):

Typo
diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn
index 606174ae..f02c8785 100644
--- a/tags/LAST.mdwn
+++ b/tags/LAST.mdwn
@@ -5,7 +5,7 @@ _bibliography in progress..._
  - `last-postmask` ([[Frith, 2011|biblio/22205972]]): discards alignments that
    contain a significant amount of lower-case-masked sequences.
 
- - `last-split` ([[Frith and Kawaguchi, 2017|biblio/25994148]]): heuristic
+ - `last-split` ([[Frith and Kawaguchi, 2015|biblio/25994148]]): heuristic
    algorithm inspired by the “repeated matches algorithm” of Durbin and coll.
    (1998).  It searchs for an optimal set of local alignments (as opposed to a set
    of optimal local alignments).   Its output is also used by third-party tool

Caf∂e
diff --git a/biblio/10.1101_831495.mdwn b/biblio/10.1101_831495.mdwn
new file mode 100644
index 00000000..b21a6829
--- /dev/null
+++ b/biblio/10.1101_831495.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="High throughput, error corrected Nanopore single cell transcriptome sequencing"]]
+[[!tag bioRxiv Nanopore single_cell]]
+
+Kevin Lebrigand, Virginie Magnone, Pascal Barbry and Rainer Waldmann
+
+Posted November 05, 2019
+
+High throughput, error corrected Nanopore single cell transcriptome sequencing
+
+[[!doi 10.1101/831495 desc="Sequences libraries with Illumina first, to find UMI and cell barcode sequences, and then sequences again with Nanopore."]]

scaffolders...
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 450bf877..9f9bd5b6 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -21,13 +21,13 @@ Nagarajan and Šikić, 2017|biblio/28100585]]).
 When coverage is too low for efficient reference-free assembly, related
 references can be used as a guide.  The Ragout software ([[Kolmogorov and
 coll., 2014|biblio/24931998]], [[Kolmogorov and coll., 2018|biblio/30341161]])
-can take multiple reference genomes to guide the assembly of one target.
-Polymorphisms unique to the target genome can be recovered, but chromosome
-fusions are typically hard to detect.  Compared to version 1, version 2 infers
-phylogenetic relationships between the reference genomes automatically.  An
-alterative reference-guided assembler, RagOO ([[Alonge and coll.,
-2019|biblio/31661016]]) is reported to be faster, but can only take a single
-reference.
+can take multiple reference genomes to guide the scaffolding of a target
+assembly.  Polymorphisms unique to the target genome can be recovered, but
+chromosome fusions are typically hard to detect.  Compared to version 1,
+version 2 infers phylogenetic relationships between the reference genomes
+automatically.  An alterative reference-guided scaffolder, RagOO ([[Alonge and
+coll., 2019|biblio/31661016]]) is reported to be faster, but can only take a
+single reference.
 
 The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a
 diploid assembly and outputs a reference and an alternative sub-assembly for

Café
diff --git a/biblio/31661016.mdwn b/biblio/31661016.mdwn
new file mode 100644
index 00000000..b5641dba
--- /dev/null
+++ b/biblio/31661016.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="RaGOO: fast and accurate reference-guided scaffolding of draft genomes."]]
+[[!tag assembly software]]
+
+Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC.
+
+Genome Biol. 2019 Oct 28;20(1):224. doi:10.1186/s13059-019-1829-6
+
+RaGOO: fast and accurate reference-guided scaffolding of draft genomes.
+
+[[!pmid 31661016 desc="Aligns contigs to a reference genome with minimap2, and resolves structural variants with a modified version of Assemblytics that uses minimap2."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index d58f2667..450bf877 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -24,7 +24,10 @@ coll., 2014|biblio/24931998]], [[Kolmogorov and coll., 2018|biblio/30341161]])
 can take multiple reference genomes to guide the assembly of one target.
 Polymorphisms unique to the target genome can be recovered, but chromosome
 fusions are typically hard to detect.  Compared to version 1, version 2 infers
-phylogenetic relationships between the reference genomes automatically.
+phylogenetic relationships between the reference genomes automatically.  An
+alterative reference-guided assembler, RagOO ([[Alonge and coll.,
+2019|biblio/31661016]]) is reported to be faster, but can only take a single
+reference.
 
 The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a
 diploid assembly and outputs a reference and an alternative sub-assembly for

Café
diff --git a/biblio/22265598.mdwn b/biblio/22265598.mdwn
new file mode 100644
index 00000000..313c6e8d
--- /dev/null
+++ b/biblio/22265598.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Three-dimensional folding and functional organization principles of the Drosophila genome."]]
+[[!tag Drosophila chromosome structure]]
+
+Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, Parrinello H, Tanay A, Cavalli G.
+
+Cell. 2012 Feb 3;148(3):458-72. doi:10.1016/j.cell.2012.01.010
+
+Three-dimensional folding and functional organization principles of the Drosophila genome.
+
+[[!pmid 22265598 desc="Co-clustering of the centromeres."]]

Café
diff --git a/biblio/29148971.mdwn b/biblio/29148971.mdwn
new file mode 100644
index 00000000..eedf8dbb
--- /dev/null
+++ b/biblio/29148971.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo."]]
+[[!tag Drosophila chromosome structure]]
+
+Stadler MR, Haines JE, Eisen MB.
+
+Elife. 2017 Nov 17;6. pii: e29550. doi:10.7554/eLife.29550
+
+Convergence of topological domain boundaries, insulators, and polytene interbands revealed by high-resolution mapping of chromatin contacts in the early Drosophila melanogaster embryo.
+
+[[!pmid 29148971 desc="High-resolution Hi-C analysis of Drosophila chromosomes in Rabl conformation during embryogenesis.  “We propose a model in which insulators achieve domain separation by lowering the compaction ratio of bound chromatin, thereby converting the short lengths of insulator DNA (measured in base pairs) into large relative physical distances.”"]]

Simplification
diff --git a/biblio/16600568.mdwn b/biblio/16600568.mdwn
index 66893fe2..64e74f53 100644
--- a/biblio/16600568.mdwn
+++ b/biblio/16600568.mdwn
@@ -1,3 +1,3 @@
 [[!meta title="Differentially expressed transcripts from phenotypically identified olfactory sensory neurons."]]
-[[!tag olfaction promoter gene-structure]]
+[[!tag olfaction promoter]]
 [[!pmid 15682396 desc="Related OR genes can have a different intron-exon structure and even share promoters."]]
diff --git a/tags/gene-structure.mdwn b/tags/gene-structure.mdwn
deleted file mode 100644
index 54b2b35f..00000000
--- a/tags/gene-structure.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged gene-structure"]]
-
-[[!inline pages="tagged(gene-structure)" actions="no" archive="yes"
-feedshow=10]]

Café
diff --git a/biblio/29776991.mdwn b/biblio/29776991.mdwn
new file mode 100644
index 00000000..19643891
--- /dev/null
+++ b/biblio/29776991.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Inversion variants in human and primate genomes."]]
+[[!tag chromosome variants]]
+
+Catacchio CR, Maggiolini FAM, D'Addabbo P, Bitonto M, Capozzi O, Lepore Signorile M, Miroballo M, Archidiacono N, Eichler EE, Ventura M, Antonacci F.
+
+Genome Res. 2018 Jun;28(6):910-920. doi:10.1101/gr.234831.118
+
+Inversion variants in human and primate genomes.
+
+[[!pmid 29776991 desc="105 validation inversions between human and either chimpanzee, gorilla, orangutan, or macaque genomes, that range in size from 103 kb to 91 Mb."]]

Dans l'avion
diff --git a/biblio/30497373.mdwn b/biblio/30497373.mdwn
new file mode 100644
index 00000000..ed899729
--- /dev/null
+++ b/biblio/30497373.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies."]]
+[[!tag assembly software]]
+
+Roach MJ, Schmidt SA, Borneman AR.
+
+BMC Bioinformatics. 2018 Nov 29;19(1):460. doi:10.1186/s12859-018-2485-7
+
+Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies.
+
+[[!pmid 30497373 desc="Aligns the reads to the draft genome in order to estimate coverage.  A bimodal distribution is expected: the 0.5× peak represents areas where both alleles are present in the assembly."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 9d5a0012..d58f2667 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -38,6 +38,10 @@ Relase notes of HM2 version 20180603 suggest to use “_HapCUT2 or other phasing
 tools to get the high-quality haplotype assembly based on the reference haploid
 assembly_”.
 
+Purge Haplotigs ([[Roach, Schmidt and Borneman (2018) |biblio/30497373]]) is an
+alternative to HaploMerger that takes read coverage into account when detecting
+potential haplotigs.
+
 SALSA (Simple AssembLy ScAffolder, [[Ghurye and coll., 2017|biblio/28701198]])
 takes Hi-C data and contigs as input and scaffolds them under the hypothesis
 that most contact points are due to local (same-chromosome) proximity.  Version

normalisation
diff --git a/biblio/19624849.mdwn b/biblio/19624849.mdwn
index ad1cce3e..e539fa92 100644
--- a/biblio/19624849.mdwn
+++ b/biblio/19624849.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data."]]
-[[!tag tags CAGE power_law normalisation]]
+[[!tag sequence_tags CAGE power_law normalisation]]
 
 Balwierz PJ, Carninci P, Daub CO, Kawai J, Hayashizaki Y, Van Belle W, Beisel C, van Nimwegen E.
 
diff --git a/biblio/21543516.mdwn b/biblio/21543516.mdwn
index 15b323b6..fb31aac7 100644
--- a/biblio/21543516.mdwn
+++ b/biblio/21543516.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq."]]
-[[!tag STRT template_switching single_cell method transcriptome tags]]
+[[!tag STRT template_switching single_cell method transcriptome sequence_tags]]
 
 Islam S, Kjällquist U, Moliner A, Zajac P, Fan JB, Lönnerberg P, Linnarsson S.
 
diff --git a/tags/tags.mdwn b/tags/tags.mdwn
deleted file mode 100644
index 1b8430b8..00000000
--- a/tags/tags.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged tags"]]
-
-[[!inline pages="tagged(tags)" actions="no" archive="yes"
-feedshow=10]]

More tags.
diff --git a/biblio/31649060.mdwn b/biblio/31649060.mdwn
index a38b3e53..bdaf0105 100644
--- a/biblio/31649060.mdwn
+++ b/biblio/31649060.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection."]]
-[[!tag variants]]
+[[!tag chromosome assembly variants]]
 
 Pettersson ME, Rochus CM, Han F, Chen J, Hill J, Wallerman O, Fan G, Hong X, Xu Q, Zhang H, Liu S, Liu X, Haggerty L, Hunt T, Martin FJ, Flicek P, Bunikis I, Folkvord A, Andersson L.
 

Normalise
diff --git a/biblio/16136133.mdwn b/biblio/16136133.mdwn
index aa16959c..85ee4448 100644
--- a/biblio/16136133.mdwn
+++ b/biblio/16136133.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication."]]
-[[!tag chromosome variations]]
+[[!tag chromosome variants]]
 
 Linardopoulou EV, Williams EM, Fan Y, Friedman C, Young JM, Trask BJ.
 
diff --git a/tags/variations.mdwn b/tags/variations.mdwn
deleted file mode 100644
index 47fe6435..00000000
--- a/tags/variations.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged variations"]]
-
-[[!inline pages="tagged(variations)" actions="no" archive="yes"
-feedshow=10]]

In the bus.
diff --git a/biblio/31649060.mdwn b/biblio/31649060.mdwn
new file mode 100644
index 00000000..a38b3e53
--- /dev/null
+++ b/biblio/31649060.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection."]]
+[[!tag variants]]
+
+Pettersson ME, Rochus CM, Han F, Chen J, Hill J, Wallerman O, Fan G, Hong X, Xu Q, Zhang H, Liu S, Liu X, Haggerty L, Hunt T, Martin FJ, Flicek P, Bunikis I, Folkvord A, Andersson L.
+
+Genome Res. 2019 Nov;29(11):1919-1928. doi:10.1101/gr.253435.119
+
+A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection.
+
+[[!pmid 31649060 desc="Linkage analysis of 45,000 markers from 2 crosses with ~50 offsprings each confirmed that there are 26 linkage groups, and suggests ~1 recombination per chromosome pair at meiosis.  Recombination rate is lower towards centromeres.  This is in line with the known fact that 3 chromosomes are metacentric and the other are acrocentric.  When comparing with other fish species, genes tend to stay on the same chromosomes, but move within (like birds and invertebrates, but unlike mammals).  A 7.8-Mb region on chr12 with strange linkage desequilibrium pattern was shown to be an inversion between southern and northern individuals.  It may act as a supergene.  Genetic exchanges between both haplotypes is reduced by the inversion."]]

last-split
diff --git a/tags/LAST.mdwn b/tags/LAST.mdwn
index b0cb4e60..606174ae 100644
--- a/tags/LAST.mdwn
+++ b/tags/LAST.mdwn
@@ -7,8 +7,9 @@ _bibliography in progress..._
 
  - `last-split` ([[Frith and Kawaguchi, 2017|biblio/25994148]]): heuristic
    algorithm inspired by the “repeated matches algorithm” of Durbin and coll.
-   (1998).  Its output is also used by third-party tool NanoSV ([[Cretu and
-   coll., 2017|biblio/29109544]].
+   (1998).  It searchs for an optimal set of local alignments (as opposed to a set
+   of optimal local alignments).   Its output is also used by third-party tool
+   NanoSV ([[Cretu and coll., 2017|biblio/29109544]]).
 
  - `last-train` ([[Hamada, Ono, Asai and Frith, 2017|biblio/28039163]]):
    estimation of alignment parameters.

To read
diff --git a/biblio/31504804.mdwn b/biblio/31504804.mdwn
new file mode 100644
index 00000000..1a6c464e
--- /dev/null
+++ b/biblio/31504804.mdwn
@@ -0,0 +1,11 @@
+[[!meta title="Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA."]]
+[[!tag cap to_read]]
+
+Nucleic Acids Res. 2019 Nov 18;47(20):e130. doi:10.1093/nar/gkz751
+
+Wang J, Alvin Chew BL, Lai Y, Dong H, Xu L, Balamkundu S, Cai WM, Cui L, Liu
+CF, Fu XY, Lin Z, Shi PY, Lu TK, Luo D, Jaffrey SR, Dedon PC.
+
+Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA.
+
+[[!pmid 31504804 desc="CapQuant, to read"]]

One more phylogeny.
diff --git a/biblio/12116483.mdwn b/biblio/12116483.mdwn
new file mode 100644
index 00000000..c1c7457f
--- /dev/null
+++ b/biblio/12116483.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Urochordates are monophyletic within the deuterostomes."]]
+[[!tag Oikopleura tunicate]]
+
+Syst Biol. 2000 Mar;49(1):52-64 doi:10.1080/10635150050207384
+
+Swalla BJ, Cameron CB, Corley LS, Garey JR.
+
+Urochordates are monophyletic within the deuterostomes.
+
+[[!pmid 12116483 desc="Places appendicularians as sister to all other tunicates, but notes that long branches raise uncertaincies."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index c717b238..16286552 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -39,13 +39,15 @@ Parasites: _Oodinium pouchetii_ and others.
 Phylogeny
 ---------
 
+ - 18S rDNA phylogeny of [[Swalla and coll., 2000|biblio/12116483]] places
+   larvaceans sister to all tunicates.
  - Based on 18S rRNA sequences from 110 species including 4 Oikopleuridae, this
    clade is sister of Stolidobranchia (that is, not basal in Tunicates).
    Stolidobranchia.  Nevertheless, it might be an artefact of AT-richness or
    long-branch attraction ([[Tsagkogeorga et al, 2009|biblio/19656395]]).
  - Studies based on 146 genes in 28 species ([[Delsuc et al., 2006|biblio/16495997]])
    and then 258 orthologous proteins from 63 species ([[Delsuc et al., 2018|biblio/29653534]])
-   show that Oikopleuridae is basal to all other tunicates.
+   show that Oikopleuridae is sister to all other tunicates.
  - “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

Typo.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 9103cbcd..c717b238 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -21,7 +21,7 @@ Some links:
  - Études sur les Appendiculaires du Détroit de Messine, Hermann Fol, 1872
    ([[ark:/13960/t7fr0vj77|https://archive.org/details/cbarchive_100233_etudessurlesappendiculairesdud1821]]).
  - [A day in the life of an Oikopleura lab](http://thenode.biologists.com/day-life-oikopleura-lab/).
- - OSA2016 genome on aniseed: <https://www.aniseed.cnrs.fr/aniseed/species/show_species?unique_name=Oikopleura_dioica>
+ - OSAKA2016 genome on aniseed: <https://www.aniseed.cnrs.fr/aniseed/species/show_species?unique_name=Oikopleura_dioica>
 
 Food tested in laboratory (totally incomplete list): _Isochrysis galbana_ (5.5
 µm in size), _Tetraselmis suecica_ (9.5 µm), and the chlorophyte _Chlorella

creating tag page tags/experiment_design
diff --git a/tags/experiment_design.mdwn b/tags/experiment_design.mdwn
new file mode 100644
index 00000000..ae7a5322
--- /dev/null
+++ b/tags/experiment_design.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged experiment design"]]
+
+[[!inline pages="tagged(experiment_design)" actions="no" archive="yes"
+feedshow=10]]

Heard of at the ICSB2019
diff --git a/biblio/27180805.mdwn b/biblio/27180805.mdwn
new file mode 100644
index 00000000..f54dc076
--- /dev/null
+++ b/biblio/27180805.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="Fast machine-learning online optimization of ultra-cold-atom experiments."]]
+[[!tag machine_learning experiment_design]]
+
+Sci Rep. 2016 May 16;6:25890. doi:10.1038/srep25890
+
+Wigley PB, Everitt PJ, van den Hengel A, Bastian JW, Sooriyabandara MA,
+McDonald GD, Hardman KS, Quinlivan CD, Manju P, Kuhn CC, Petersen IR, Luiten AN, 
+Hope JJ, Robins NP, Hush MR.
+
+Fast machine-learning online optimization of ultra-cold-atom experiments.
+
+[[!pmid desc="Primary paper for https://github.com/michaelhush/M-LOOP (Machine-learning online optimization package)"]]

Café
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 1259ee44..9103cbcd 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -211,9 +211,9 @@ Genes and pathways
    and triggers microdeletions at the joining site ([[Deng, Henriet and Chourrout, 2018|biblio/30293719]]).
  - In line with the above, “There is no H2AX homolog in O. dioica.” (H2AX is
    implicated in DNA repair).  [[Moosmann and coll., 2011|biblio/21756361]]
- - The minor spliceosome could not be found in _Oikopleura_'s genome ([[Martz
+ - The minor spliceosome could not be found in _Oikopleura_'s genome ([[Marz
    et al., 2008|biblio/19030770]]), [[Denoeud et al., 2010|biblio/21097902]]).
-   It is found in _Ciona_ but not in _C. elegans_ ([[Martz et al.,
+   It is found in _Ciona_ but not in _C. elegans_ ([[Marz et al.,
    2008|biblio/19030770]]).
  - More than 50 % of the Rab family is lost ([[Coppola and coll., 2019|biblio/31028425]]):
    Rab4, Rab7L1, Rab9, Rab19/43, Rab21 Rab26/37, Rab28, Ift27, RabX1 and the

Tyop
diff --git a/biblio/19030770.mdwn b/biblio/19030770.mdwn
index 0d62fc19..bb0f49be 100644
--- a/biblio/19030770.mdwn
+++ b/biblio/19030770.mdwn
@@ -1,4 +1,4 @@
-[[!meta title=""Evolution of spliceosomal snRNA genes in metazoan animals.]]
+[[!meta title="Evolution of spliceosomal snRNA genes in metazoan animals."]]
 [[!tag Oikopleura splicing]]
 
 J Mol Evol. 2008 Dec;67(6):594-607. doi:10.1007/s00239-008-9149-6

Café
diff --git a/biblio/19030770.mdwn b/biblio/19030770.mdwn
new file mode 100644
index 00000000..0d62fc19
--- /dev/null
+++ b/biblio/19030770.mdwn
@@ -0,0 +1,10 @@
+[[!meta title=""Evolution of spliceosomal snRNA genes in metazoan animals.]]
+[[!tag Oikopleura splicing]]
+
+J Mol Evol. 2008 Dec;67(6):594-607. doi:10.1007/s00239-008-9149-6
+
+Marz M, Kirsten T, Stadler PF.
+
+Evolution of spliceosomal snRNA genes in metazoan animals.
+
+[[!pmid 19030770 desc="”The snRNAs of the minor spliceosome were in most cases single-copy genes.”  The minor spliceosome was not found in Oikopleura dioica, but it was found in Ciona. “SnRNA locations are not syntenically conserved, i.e., snRNA behave like mobile elements in their genomic context.” "]]

Café
diff --git a/biblio/31543449.mdwn b/biblio/31543449.mdwn
new file mode 100644
index 00000000..396eb71a
--- /dev/null
+++ b/biblio/31543449.mdwn
@@ -0,0 +1,17 @@
+[[!meta title="Evolution of the U2 Spliceosome for Processing Numerous and Highly Diverse Non-canonical Introns in the Chordate Fritillaria borealis."]]
+[[!tag Oikopleura intron]]
+
+Curr Biol. 2019 Oct 7;29(19):3193-3199.e4. doi:10.1016/j.cub.2019.07.092
+
+Henriet S, Colom Sanmartí B, Sumic S, Chourrout D.
+
+Evolution of the U2 Spliceosome for Processing Numerous and Highly Diverse Non-canonical Introns in the Chordate Fritillaria borealis.
+
+[[!pmid 31543449 desc="In Fritillaria borealis, most ancestral canonical
+introns were lost.  New introns with non-canonical splice sites were created by
+the insertion of MITEs (miniature inverted-repeat transposable elements) after
+TA sites.  Splicing of non-canonical introns can be inhibited with Pladienolide
+B.  Non-canonical introns of F. bor and O. dioica genes can not be spliced in
+HEK293T cells, but canonical introns can.  In ~90% of lariats from F. bor or O.
+dio, the branchpoint is an A.  Distance to 3′ splice site is similar in both
+species.  A single U2 spliceosome was found in F. bor."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 752a59d6..1259ee44 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -255,12 +255,17 @@ Transcriptome
  - “Maternal promoters in O. dioica were located on the X-chromosome more
    frequently than expected” ([[Danks et al, 2018|biblio/29482522]]).
  - Introns are very small (peak at 47 base pairs, 2.4% > 1 kb, [[Denoeud et
-   al., 2010|biblio/21097902]]) and subjected to a large turnover: many ancestral
-   introns are lost, and many new species-specific introns found ([[Edvarsen et
-   al., 2004|biblio/15638456]]).  Introns are gained by insertion of transposon-like elements and
-   by reverse splicing, ([[Denoeud et al., 2010|biblio/21097902]]).  Larger introns tend
-   to be older, and among the large introns, the older contain repeat elements less frequently
-   than the newer ([[Denoeud et al., 2010|biblio/21097902]]). 
+   al., 2010|biblio/21097902]]) and subjected to a large turnover: many
+   ancestral introns are lost, and many new species-specific introns found
+   ([[Edvarsen et al., 2004|biblio/15638456]]).  Introns are gained by insertion
+   of transposon-like elements and by reverse splicing, ([[Denoeud et al.,
+   2010|biblio/21097902]]).  Larger introns tend to be older, and among the large
+   introns, the older contain repeat elements less frequently than the newer
+   ([[Denoeud et al., 2010|biblio/21097902]]).  In _Fritilaria borealis_, most
+   introns are derived from the insertion of MITE elements and are non-canonical
+   ([[Henriet and coll., 2019|biblio/31543449]]).
+ - HEK293T cells can only splice canonical _O. dioica_ (and _F. borealis_) introns,
+   but not the non-canonical ones ([[Henriet and coll., 2019|biblio/31543449]]).
  - 12 developmental stages were studied with tiling arrays by [[Danks et al., 2013|biblio/23185044]].
  - On the histone mRNAs, no purine-rich histone downstream element (HDE) was found
    by [[Chioda, Eskeland and Thompson in 2002|biblio/12446815]].

Typo
diff --git a/tags/microplastic.mdwn b/tags/microplastic.mdwn
index 7c171678..b94dae10 100644
--- a/tags/microplastic.mdwn
+++ b/tags/microplastic.mdwn
@@ -1,7 +1,7 @@
 [[!meta title="pages tagged microplastic"]]
 
 [[Oikopleura]] can ingest microplastics and participate to their sedimentation
-([[Katija and coll., 2017|28835922]], [[Choy and coll., 2019|biblio/31171833]]).
+([[Katija and coll., 2017|biblio/28835922]], [[Choy and coll., 2019|biblio/31171833]]).
 
 To do: read Furukawa M, Kawakami N, Oda K, Miyamoto K (2018) Acceleration of
 enzymatic degradation of poly(ethylene terephthalate) by surface coating with

Café sans café
diff --git a/biblio/31646721.mdwn b/biblio/31646721.mdwn
new file mode 100644
index 00000000..417a63bc
--- /dev/null
+++ b/biblio/31646721.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="Biodegradation of waste PET: A sustainable solution for dealing with plastic pollution."]]
+[[!tag microplastic enzyme]]
+
+EMBO Rep. 2019 Nov 5;20(11):e49365. doi:10.15252/embr.201949365
+
+Hiraga K, Taniguchi I, Yoshida S, Kimura Y, Oda K
+
+Biodegradation of waste PET: A sustainable solution for dealing with plastic pollution.
+
+[[!pmid 31646721 desc="Cites that “the use of surfactants can enhance PET
+degradation at least by a factor of 120”.  Points that “isolation and analysis
+of other PET‐degrading organisms and enzymes from high‐salt environment are
+also important for the biodegradation of waste PET directly in the ocean”."]]
diff --git a/tags/microplastic.mdwn b/tags/microplastic.mdwn
index e43c1695..7c171678 100644
--- a/tags/microplastic.mdwn
+++ b/tags/microplastic.mdwn
@@ -1,4 +1,15 @@
 [[!meta title="pages tagged microplastic"]]
 
-[[!inline pages="tagged(microplastic)" actions="no" archive="yes"
-feedshow=10]]
+[[Oikopleura]] can ingest microplastics and participate to their sedimentation
+([[Katija and coll., 2017|28835922]], [[Choy and coll., 2019|biblio/31171833]]).
+
+To do: read Furukawa M, Kawakami N, Oda K, Miyamoto K (2018) Acceleration of
+enzymatic degradation of poly(ethylene terephthalate) by surface coating with
+anionic surfactants. Chem Sus Chem 11: 4018–4025
+
+Hiraga, Taniguchi, Yoshida, Kimura and Oda K proposed in
+[[2019|biblio/31646721]] that PET-degrading organisms can be the foundation for
+a biological recycling of plastic.  They also underlined that salt-tolerating
+enzymes would be needed for bioremediation of oceans.
+
+[[!inline pages="tagged(microplastic)" limit=0]]

Lu il y a longtemps.
diff --git a/biblio/25079858.mdwn b/biblio/25079858.mdwn
new file mode 100644
index 00000000..3f8da97d
--- /dev/null
+++ b/biblio/25079858.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Tn5 transposase and tagmentation procedures for massively scaled sequencing projects."]]
+[[!tag transposase enzyme method]]
+
+Picelli S, Björklund AK, Reinius B, Sagasser S, Winberg G, Sandberg R.
+
+Genome Res. 2014 Dec;24(12):2033-40. doi:10.1101/gr.177881.114
+
+Tn5 transposase and tagmentation procedures for massively scaled sequencing projects.
+
+[[!pmid 25079858 desc="Production and purification of the Tn5 transposase."]]

syntaxerror
diff --git a/biblio/29914971.mdwn b/biblio/29914971.mdwn
index 0405ef44..4d085a8e 100644
--- a/biblio/29914971.mdwn
+++ b/biblio/29914971.mdwn
@@ -1,4 +1,4 @@
-[[!meta title=""Epigenetic maintenance of topological domains in the highly rearranged gibbon genome.]]
+[[!meta title="Epigenetic maintenance of topological domains in the highly rearranged gibbon genome."]]
 [[!tag to_read synteny]]
 
 Lazar NH, Nevonen KA, O'Connell B, McCann C, O'Neill RJ, Green RE, Meyer TJ, Okhovat M, Carbone L.

syntaxerror
diff --git a/biblio/25209798.mdwn b/biblio/25209798.mdwn
index f95f9b7a..0c95e810 100644
--- a/biblio/25209798.mdwn
+++ b/biblio/25209798.mdwn
@@ -20,4 +20,4 @@ Nature. 2014 Sep 11;513(7517):195-201. doi:10.1038/nature13679
 
 Gibbon genome and the fast karyotype evolution of small apes.
 
-[[!pmid 25209798 desc=""“We identified 96 gibbon–human synteny breakpoints in Nleu1.0.”  “Segmental duplication enrichment was the best predictor of gibbon–human synteny breakpoints,[...] however, breakpoints were also enriched for Alu elements.”  “ The majority of gibbon chromosomal breakpoints bore signatures of non-homology based mechanisms.” “We observed an enrichment of gibbon–human breakpoints in CTCF-binding events.”]]
+[[!pmid 25209798 desc="“We identified 96 gibbon–human synteny breakpoints in Nleu1.0.”  “Segmental duplication enrichment was the best predictor of gibbon–human synteny breakpoints,[...] however, breakpoints were also enriched for Alu elements.”  “ The majority of gibbon chromosomal breakpoints bore signatures of non-homology based mechanisms.” “We observed an enrichment of gibbon–human breakpoints in CTCF-binding events.”"]]

FFPE-seq
diff --git a/biblio/31649055.mdwn b/biblio/31649055.mdwn
new file mode 100644
index 00000000..23854b46
--- /dev/null
+++ b/biblio/31649055.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples."]]
+[[!tag nanoCAGE method template_switching manganese]]
+
+Genome Res. 2019 Oct 24. doi:10.1101/gr.249656.119
+
+Vahrenkamp JM, Szczotka K, Dodson MK, Jarboe EA, Soisson AP, Gertz J.
+
+FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples.
+
+[[!pmid 31649055 desc="Terminator, concatenation blocker, no manganese, indexes. Fails to cite our latest protocol."]]
diff --git a/tags/manganese.mdwn b/tags/manganese.mdwn
index 5aec4360..7b7ff5a9 100644
--- a/tags/manganese.mdwn
+++ b/tags/manganese.mdwn
@@ -1,4 +1,6 @@
 [[!meta title="pages tagged manganese"]]
 
-[[!inline pages="tagged(manganese)" actions="no" archive="yes"
-feedshow=10]]
+See [[template_switching]] for the effect of manganese addition on cap
+specificity of transcriptome methods.
+
+[[!inline pages="tagged(manganese)" limit=0]]
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index ece27413..351d4908 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -57,7 +57,8 @@ as a replacement for RNA.
 
  - 5′ iso-dC and iso-dG prevents reverse-transcriptase to reach the end
    of the TSO, and therefore blocks concatenation
-   ([[Kapteyn et al., 2010|biblio/20598146]]).
+   ([[Kapteyn et al., 2010|biblio/20598146]]).  This was also used in
+   FFPEcap-seq ([[Vahrenkamp and coll., 2019|biblio/31649055]]).
 
 ### Effect of TSO concentration
 
@@ -73,9 +74,12 @@ as a replacement for RNA.
    concentration: 1 mM each.  [[Pinto & Lindblad (2010)|biblio/19837043]] also
    used manganese.
 
- - [[Lee et al (2017)|biblio/28327113]] increased the efficiency of template
+ - [[Lee and coll. (2017)|biblio/28327113]] increased the efficiency of template
    switching non-capped molecules by increasing dNTPs to 2 mM and
    Mg<sup>2+</sup> to 9 mM.
 
+ - [[Vahrenkamp and coll. (2019)|biblio/31649055]] reported that addition of
+   1 mM manganese increases the formation of TSO concatenates and the fraction
+   of reads aliging to ribosomal sequences.
 
 [[!inline pages="tagged(template_switching)" limit=0]]

Café
diff --git a/biblio/25209798.mdwn b/biblio/25209798.mdwn
new file mode 100644
index 00000000..f95f9b7a
--- /dev/null
+++ b/biblio/25209798.mdwn
@@ -0,0 +1,23 @@
+[[!meta title="Gibbon genome and the fast karyotype evolution of small apes."]]
+[[!tag chromosome synteny evolution]]
+
+Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J,
+Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C,
+Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS,
+Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L,
+Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW,
+Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG,
+Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, 
+Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA,
+O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann 
+GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E,
+Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan
+SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF,
+Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC,
+Rogers J, Wilson RK, Gibbs RA.
+
+Nature. 2014 Sep 11;513(7517):195-201. doi:10.1038/nature13679
+
+Gibbon genome and the fast karyotype evolution of small apes.
+
+[[!pmid 25209798 desc=""“We identified 96 gibbon–human synteny breakpoints in Nleu1.0.”  “Segmental duplication enrichment was the best predictor of gibbon–human synteny breakpoints,[...] however, breakpoints were also enriched for Alu elements.”  “ The majority of gibbon chromosomal breakpoints bore signatures of non-homology based mechanisms.” “We observed an enrichment of gibbon–human breakpoints in CTCF-binding events.”]]
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index 6dd88e5b..4ece1256 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -1,6 +1,11 @@
 [[!meta title="pages tagged synteny"]]
 
-[[Renschler and coll, (2019)|biblio/31601616]] found 20 synteny breakpoints
+[[Carbone and coll. (2014)|biblio/25209798]] found 96 gibbon–human synteny
+breakpoints (~30 per Gb), associated with segmental duplication or Alu element
+enrichment.  They often bore signatures of non-homology based mechanisms, and
+were enriched near CTCF-binding events.
+
+[[Renschler and coll. (2019)|biblio/31601616]] found 20 synteny breakpoints
 (SB) per Mb on average. “Approximately 75% of SBs stay within the A or B
 compartment”  “Overlaps of TAD boundaries and SB breakpoints in all comparisons
 are highly significant”

To read
diff --git a/biblio/29914971.mdwn b/biblio/29914971.mdwn
new file mode 100644
index 00000000..0405ef44
--- /dev/null
+++ b/biblio/29914971.mdwn
@@ -0,0 +1,10 @@
+[[!meta title=""Epigenetic maintenance of topological domains in the highly rearranged gibbon genome.]]
+[[!tag to_read synteny]]
+
+Lazar NH, Nevonen KA, O'Connell B, McCann C, O'Neill RJ, Green RE, Meyer TJ, Okhovat M, Carbone L.
+
+Genome Res. 2018 Jul;28(7):983-997. doi:10.1101/gr.233874.117
+
+Epigenetic maintenance of topological domains in the highly rearranged gibbon genome.
+
+[[!pmid desc="to read"]]

Café
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
index ce49564f..6dd88e5b 100644
--- a/tags/synteny.mdwn
+++ b/tags/synteny.mdwn
@@ -1,4 +1,8 @@
 [[!meta title="pages tagged synteny"]]
 
-[[!inline pages="tagged(synteny)" actions="no" archive="yes"
-feedshow=10]]
+[[Renschler and coll, (2019)|biblio/31601616]] found 20 synteny breakpoints
+(SB) per Mb on average. “Approximately 75% of SBs stay within the A or B
+compartment”  “Overlaps of TAD boundaries and SB breakpoints in all comparisons
+are highly significant”
+
+[[!inline pages="tagged(synteny)" limit=0]]

creating tag page tags/synteny
diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn
new file mode 100644
index 00000000..ce49564f
--- /dev/null
+++ b/tags/synteny.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged synteny"]]
+
+[[!inline pages="tagged(synteny)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/31601616.mdwn b/biblio/31601616.mdwn
new file mode 100644
index 00000000..a96cc4fe
--- /dev/null
+++ b/biblio/31601616.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling."]]
+[[!tag chromosome evolution synteny]]
+
+Renschler G, Richard G, Valsecchi CIK, Toscano S, Arrigoni L, Ramírez F, Akhtar A.
+
+Genes Dev. 2019 Oct 10. doi: 10.1101/gad.328971.119
+
+Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling.
+
+[[!pmid 31601616 desc="Found 20 synteny breakpoints (SB) per Mb on average. “Approximately 75% of SBs stay within the A or B compartment”  “Overlaps of TAD boundaries and SB breakpoints in all comparisons are highly significant”"]]

Encore au café
diff --git a/biblio/7739381.mdwn b/biblio/7739381.mdwn
new file mode 100644
index 00000000..e203d9b0
--- /dev/null
+++ b/biblio/7739381.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="Molecular phylogeny and divergence times of drosophilid species."]]
+[[!tag Drosophila speciation]]
+
+Russo CA, Takezaki N, Nei M.
+
+Mol Biol Evol. 1995 May;12(3):391-404 doi:10.1093/oxfordjournals.molbev.a040214
+
+Molecular phylogeny and divergence times of drosophilid species.
+
+[[!pmid 7739381 desc="Study of Adh genes, nuclear 18S rRNA and mitochondrial
+DNA suggests that D. mel and D. pseudoobscura diverged 24.9 +/- 2.88 My ago,
+based on the assumption that D. picticornis and D. silvestris diverged 5.1 My
+ago."]]
diff --git a/tags/Drosophila.mdwn b/tags/Drosophila.mdwn
index 5ff9700f..5d7fe7f3 100644
--- a/tags/Drosophila.mdwn
+++ b/tags/Drosophila.mdwn
@@ -7,5 +7,9 @@ Analysis of Cox2 sequences of _Drosophila_ species by [[Beckenbach, Wei and Liu
 melanogaster_ and _D. pseudoobscura_ ~35 My ago.  Sequence divergence between
 _D. mel._ and members of the _D. obscura_ species group is in average of 11.4 %.
 
-[[!inline pages="tagged(Drosophila)" actions="no" archive="yes"
-feedshow=10]]
+A study of Adh genes, nuclear 18S rRNA and mitochondrial DNA ([[Russo, Takezaki
+and Nei  (1995)|biblio/7739381]]) suggests that D. mel and D. pseudoobscura
+diverged 24.9 +/- 2.88 My ago, based on the assumption that D. picticornis and
+D. silvestris diverged 5.1 My ago.
+
+[[!inline pages="tagged(Drosophila)" limit=0]]

Normalise tags.
diff --git a/biblio/10.1111_jzs.12101.mdwn b/biblio/10.1111_jzs.12101.mdwn
index 51518745..22419adf 100644
--- a/biblio/10.1111_jzs.12101.mdwn
+++ b/biblio/10.1111_jzs.12101.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Morphological evidence that the molecularly determined Ciona intestinalis type A and type B are different species: Ciona robusta and Ciona intestinalis."]]
-[[!tag Ciona species]]
+[[!tag Ciona speciation]]
 
 Brunetti, R. , Gissi, C. , Pennati, R. , Caicci, F. , Gasparini, F. and Manni, L. 
 
diff --git a/tags/species.mdwn b/tags/species.mdwn
deleted file mode 100644
index 99f657ba..00000000
--- a/tags/species.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged species"]]
-
-[[!inline pages="tagged(species)" actions="no" archive="yes"
-feedshow=10]]

Café
diff --git a/biblio/8393127.mdwn b/biblio/8393127.mdwn
new file mode 100644
index 00000000..32432c8b
--- /dev/null
+++ b/biblio/8393127.mdwn
@@ -0,0 +1,13 @@
+[[!meta title="Relationships in the Drosophila obscura species group, inferred from mitochondrial cytochrome oxidase II sequences."]]
+[[!tag Drosophila speciation]]
+
+Beckenbach AT, Wei YW, Liu H.
+
+Mol Biol Evol. 1993 May;10(3):619-34 doi:10.1093/oxfordjournals.molbev.a040034
+
+Relationships in the Drosophila obscura species group, inferred from mitochondrial cytochrome oxidase II sequences.
+
+[[!pmid 8393127 desc="Analysis of Cox2 sequences of _Drosophila_ species is
+most compatible with a speciation of _D.  melanogaster_ and _D. pseudoobscura_
+~35 My ago.  Sequence divergence between _D. mel._ and members of the _D.
+obscura_ species group is in average of 11.4 %."]]
diff --git a/tags/Drosophila.mdwn b/tags/Drosophila.mdwn
index 14d9883b..5ff9700f 100644
--- a/tags/Drosophila.mdwn
+++ b/tags/Drosophila.mdwn
@@ -1,4 +1,11 @@
 [[!meta title="pages tagged Drosophila"]]
 
+**  Work in progress **
+
+Analysis of Cox2 sequences of _Drosophila_ species by [[Beckenbach, Wei and Liu
+(1993)|biblio/8393127]] are most compatible with a speciation of _D.
+melanogaster_ and _D. pseudoobscura_ ~35 My ago.  Sequence divergence between
+_D. mel._ and members of the _D. obscura_ species group is in average of 11.4 %.
+
 [[!inline pages="tagged(Drosophila)" actions="no" archive="yes"
 feedshow=10]]

creating tag page tags/bioRxiv
diff --git a/tags/bioRxiv.mdwn b/tags/bioRxiv.mdwn
new file mode 100644
index 00000000..0a5a5463
--- /dev/null
+++ b/tags/bioRxiv.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged bioRxiv"]]
+
+[[!inline pages="tagged(bioRxiv)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/10.1101_817783.mdwn b/biblio/10.1101_817783.mdwn
new file mode 100644
index 00000000..19aeb21e
--- /dev/null
+++ b/biblio/10.1101_817783.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evolution of multiple CDK1 paralogs towards specializations in late cell cycle events in a lineage with fast developing planktonic embryos."]]
+[[!tag Oikopleura bioRxiv]]
+
+bioRxiv 817783; doi: https://doi.org/10.1101/817783 
+
+Xiaofei Ma. Jan Inge Øvrebø, Eric M Thompson.
+
+Evolution of multiple CDK1 paralogs towards specializations in late cell cycle events in a lineage with fast developing planktonic embryos.
+
+[[!doi 10.1101/817783 desc="“Interspecies clustering of CDK1 paralogs [show] conservation of their intron-exon structures”  “_O. dioica_ CDK1a and b locate on the same autosome whereas CDK1c is present on a different autosome that also contains CDK1e. CDK1d is found on the X chromosome where, at a distance of 5 MB, the CycBa locus is also located.”  “The PSTAIRE helix is modified in all Oikopleura CDK1 paralogs whereas Oikopleura CDK2s retain the canonical PSTAIRE sequence. All of the 17 identified Oikopleura CDK1 sequences share the A48S substitution.”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 2e2b9b02..752a59d6 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -166,6 +166,9 @@ Genes and pathways
    intestinalis_ ([[Matthysse and coll., 2004|biblio/14722352]]).
  - _O. dioica_ has multiple CDK1 and Cyclin B paraplogs, some of which are
    implicated in oogenesis ([[Feng & Thompson, 2018|biblio/29969934]]).
+ - _O. dioica_ CDK1a and b locate on LG2; CDK1c and is CDK1e on LG1.
+   CDK1d is on the X chromosome near CycBa.  In _O. albicans_, CDK1a,b and c are
+   on the same chromosome ([[Ma, Øvrebø and Thompson, 2019|biblio/10.1101_817783]]).
  - _O. dioica_, like other deuterostomes, has acid-sensing ion channels (ASICs).
    They are expressed in the nervous system ([[Lynagh et al., 2018|biblio/30061402]]).
  - Some muscle genes were duplicated in the _Oikopleura_ stem lineage
@@ -249,6 +252,8 @@ Transcriptome
    [[Wang and coll., 2015|biblio/26032664]]).
  - A `TCTAGA` promoter element is found in 73.5% of the non-trans-spliced genes detected with
    CAGE in testis ([[Danks et al, 2018|biblio/29482522]]).
+ - “Maternal promoters in O. dioica were located on the X-chromosome more
+   frequently than expected” ([[Danks et al, 2018|biblio/29482522]]).
  - Introns are very small (peak at 47 base pairs, 2.4% > 1 kb, [[Denoeud et
    al., 2010|biblio/21097902]]) and subjected to a large turnover: many ancestral
    introns are lost, and many new species-specific introns found ([[Edvarsen et

X-linked maternal promoters.
diff --git a/biblio/29482522.mdwn b/biblio/29482522.mdwn
index 1b0cdc83..7f6ff364 100644
--- a/biblio/29482522.mdwn
+++ b/biblio/29482522.mdwn
@@ -7,4 +7,4 @@ BMC Genomics. 2018 Feb 26;19(1):164. doi:10.1186/s12864-018-4504-5
 
 Distinct core promoter codes drive transcription initiation at key developmental transitions in a marine chordate.
 
-[[!pmid 29482522 desc="“369/502 (73.5%) of genes that are specifically expressed in the testis are associated with a TCTAGA promoter element, compared to 100/906 (11.0%) that are specific to the ovary and 7/275 (2.5%) that are specific to the trunk.” “Strong association of gene body DNA methylation with TATA-dependent promoters in O. dioica.” "]]
+[[!pmid 29482522 desc="“369/502 (73.5%) of genes that are specifically expressed in the testis are associated with a TCTAGA promoter element, compared to 100/906 (11.0%) that are specific to the ovary and 7/275 (2.5%) that are specific to the trunk.” “Strong association of gene body DNA methylation with TATA-dependent promoters in O. dioica.” “Maternal promoters in O. dioica were located on the X-chromosome more frequently than expected.” "]]

Published in PLoS Comput Biol.
diff --git a/biblio/10.1101_261149.mdwn b/biblio/31433799.mdwn
similarity index 68%
rename from biblio/10.1101_261149.mdwn
rename to biblio/31433799.mdwn
index cf7b5e55..2955057e 100644
--- a/biblio/10.1101_261149.mdwn
+++ b/biblio/31433799.mdwn
@@ -1,10 +1,10 @@
 [[!meta title="Integrating Hi-C links with assembly graphs for chromosome-scale assembly"]]
 [[!tag genome assembly method]]
 
-Jay Ghurye, Arang Rhie, Brian P. Walenz, Anthony Schmitt, Siddarth Selvaraj, Mihai Pop, Adam M. Phillippy, Sergey Koren
+PLoS Comput Biol. 2019 Aug 21;15(8):e1007273. doi:10.1371/journal.pcbi.1007273
 
-bioRxiv, first February 07, 2018.
+Jay Ghurye, Arang Rhie, Brian P. Walenz, Anthony Schmitt, Siddarth Selvaraj, Mihai Pop, Adam M. Phillippy, Sergey Koren
 
 Integrating Hi-C links with assembly graphs for chromosome-scale assembly
 
-[[!doi 10.1101/261149 desc="Uses unitigs and the assembly graph as input."]]
+[[!pmid 31433799 desc="Uses unitigs and the assembly graph as input."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index b9f86208..9d5a0012 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -42,7 +42,7 @@ SALSA (Simple AssembLy ScAffolder, [[Ghurye and coll., 2017|biblio/28701198]])
 takes Hi-C data and contigs as input and scaffolds them under the hypothesis
 that most contact points are due to local (same-chromosome) proximity.  Version
 2 of SALSA uses unitigs and the assembly graph as input ([[Ghurye and coll.,
-2018|biblio/10.1101_261149]]).
+2019|biblio/31433799]]).
 
 BUSCO ([[Simão and coll., 2015|biblio/26059717]], [[Waterhouse and coll.,
 2017|biblio/29220515]]) assesses the presence of evolutionary conserved single-copy

Now in Science.
diff --git a/biblio/10.1101-104844.mdwn b/biblio/28818938.mdwn
similarity index 82%
rename from biblio/10.1101-104844.mdwn
rename to biblio/28818938.mdwn
index 608ffba9..b269fd02 100644
--- a/biblio/10.1101-104844.mdwn
+++ b/biblio/28818938.mdwn
@@ -1,10 +1,10 @@
 [[!meta title="Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing"]]
 [[!tag single_cell transcriptome methanol fixation method journal_club]]
 
-bioRxiv, posted February 2, 2017.
+Science. 2017 Aug 18;357(6352):661-667. doi:10.1126/science.aam8940
 
 Junyue Cao, Jonathan S. Packer, Vijay Ramani, Darren A. Cusanovich, Chau Huynh, Riza Daza, Xiaojie Qiu, Choli Lee, Scott N. Furlan, Frank J. Steemers, Andrew Adey, Robert H. Waterston, Cole Trapnell, Jay Shendure
 
 Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing
 
-[[!doi 10.1101/104844 desc="Methanol fixation."]]
+[[!pmid 28818938 desc="Methanol fixation."]]

creating tag page tags/chromothripsis
diff --git a/tags/chromothripsis.mdwn b/tags/chromothripsis.mdwn
new file mode 100644
index 00000000..417caf6a
--- /dev/null
+++ b/tags/chromothripsis.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged chromothripsis"]]
+
+[[!inline pages="tagged(chromothripsis)" actions="no" archive="yes"
+feedshow=10]]

To read.
diff --git a/biblio/10.3354_meps08923.mdwn b/biblio/10.3354_meps08923.mdwn
new file mode 100644
index 00000000..fc53ebec
--- /dev/null
+++ b/biblio/10.3354_meps08923.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Heritability of morphological and life history traits in a pelagic tunicate"]]
+[[!tag to_read]]
+
+Carla M. Lobón, José L. Acuña, Marcos López-Álvarez, Fabiana L. Capitanio
+
+Mar Ecol Prog Ser 422:145-154. doi:10.3354/meps08923
+
+Heritability of morphological and life history traits in a pelagic tunicate 
+
+[[!doi 10.3354/meps08923 desc="to read"]]

to read
diff --git a/biblio/24298051.mdwn b/biblio/24298051.mdwn
new file mode 100644
index 00000000..404acb1a
--- /dev/null
+++ b/biblio/24298051.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements"]]
+[[!tag to_read chromothripsis]]
+
+Zhang CZ, Leibowitz ML, Pellman D.
+
+Genes Dev. 2013 Dec 1;27(23):2513-30. doi:10.1101/gad.229559.113
+
+Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements.
+
+[[!pmid 24298051 desc="To read"]]

Papers using H3S28p antibodies.
diff --git a/tags/H3S28p.mdwn b/tags/H3S28p.mdwn
index 53ccd421..4764bf06 100644
--- a/tags/H3S28p.mdwn
+++ b/tags/H3S28p.mdwn
@@ -1,4 +1,31 @@
 [[!meta title="pages tagged H3S28p"]]
 
-[[!inline pages="tagged(H3S28p)" actions="no" archive="yes"
-feedshow=10]]
+In [[Spada and coll., 2005|biblio/15937898]], H3S28p was a rabbit polyclonal
+from Upstate (#07‐145).  It strongly stains mitotic cells, but also interphase
+endothelial cells (Figure 6E).  Fig 3C shows a staining of day3 cells with no
+signal in interphase.
+
+In [[Schulmeister and coll., 2007|biblio/17333540]], H3S28p (Abcam ab10543
+1:100) is shown to label sub-telomeric regions in Figure 3D!  On Figure 3C, the
+staining is more familiar to the ones described as centromeric in other
+publications.
+
+In [[Olsen and coll., 2018|biblio/29486709]], Figure 5e shows H3S28p staining
+(Abcam ab10543  1:100) of whole chromosomes in most cells, and a more punctate
+staining in other cells.  Figure 5f also shows extrachromosomal staining.
+
+In [[Feng and coll., 2019|biblio/31306061]], Figure 3A, Figure 4, Figure S1
+(https://doi.org/10.1080/15384101.2019.1634954) gives a timecourse showing
+punctate centromere staining at ”late prophase“, a stronger signal (but harder
+to resolve) at metaphase, a weaker signal at anaphase and a weaker or no signal
+at telophase.  Table S1, listing the antibodies used, is missing.
+
+In [[Campsteijn and coll, 2012|biblio/21734012]], the H3S28p antibody is reported to
+be from Abcam, with no catalog number.  Figure 1 shows centromere staining in some cells,
+broader staining in other cells and no staining in most cells in tadpoles (6 h p.f.).
+
+In [[Subramaniam and coll., 2014|biblio/24695788]], the H3S28p antibody is
+reported to be from Abcam; no catalog number.  Figure 4 shows mitotic and meiotic
+cells stained.
+
+[[!inline pages="tagged(H3S28p)" limit=0]]

In PNAS today.
diff --git a/biblio/31591214.mdwn b/biblio/31591214.mdwn
new file mode 100644
index 00000000..d83566e2
--- /dev/null
+++ b/biblio/31591214.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Human papillomavirus 16 promotes microhomology-mediated end-joining."]]
+[[!tag HPV not_read]]
+
+Proc Natl Acad Sci U S A. 2019 Oct 7. pii: 201906120. doi:10.1073/pnas.1906120116
+
+Leeman JE, Li Y, Bell A, Hussain SS, Majumdar R, Rong-Mullins X, Blecua P, Damerla R, Narang H, Ravindran PT, Lee NY, Riaz N, Powell SN, Higginson DS.
+
+Human papillomavirus 16 promotes microhomology-mediated end-joining.
+
+[[!31591214 desc="“Compared to HPV-negative HNSCC genomes, HPV+ cases demonstrated a marked increase in the proportion of deletions with flanking microhomology, a signature associated with a backup, error-prone double-strand break repair pathway known as microhomology-mediated end-joining (MMEJ). Then, using 3 different methodologies to comprehensively profile double-strand break repair pathways in isogenic paired cell lines, we demonstrate that the HPV16 E7 oncoprotein suppresses canonical nonhomologous end-joining (NHEJ) and promotes error-prone MMEJ, providing a mechanistic rationale for the clinical radiosensitivity of these cancers.”"]]

Dans l'avion.
diff --git a/biblio/31621849.mdwn b/biblio/31621849.mdwn
new file mode 100644
index 00000000..d97868b2
--- /dev/null
+++ b/biblio/31621849.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A nearly-complete genome of Ciona intestinalis type A (C. robusta) reveals the contribution of inversion to chromosomal evolution in the genus Ciona."]]
+[[!tag Ciona genome]]
+
+Genome Biology and Evolution, 2019 Oct 17, evz228, doi:10.1093/gbe/evz228
+
+Yutaka Satou, Ryohei Nakmura, Yu Deli, Reiko Yoshida, Mayuko Hamada, Manabu Fujie, Kanako Hisata, Hiroyuki Takeda, Noriyuki Satoh
+
+A nearly-complete genome of Ciona intestinalis type A (C. robusta) reveals the contribution of inversion to chromosomal evolution in the genus Ciona.
+
+[[!pmid 31621849 desc="More complete assembly (HT, standing for Hoya T-strain) where most protein-coding genes are included in chromosomal contigs. Finds and discusses inversions within Ciona robusta genomes and between Ciona robusta and savigniy."]]
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index eee06857..5b05baee 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -39,10 +39,12 @@ Speciation is estimated to have happened during the Pliocene (≈ 3.8 Ma); a
 recent introgression then happened 15,000 years ago ([[Roux and coll.,
 2013|biblio/23564941]]).
 
+Latest _Ciona robusta_ genome: version HT ([[Satou and coll.,
+2019|biblio/31621849]]) is a reassembly of the KS genome using Hi-C and PacBio
+additional data, in which over 95 % of the dequences is included in
+chromosomes.
+
 Mitochondrial gene order differs even within the _Ciona_ genus ([[Gissi,
 Iannelli and Pesole 2004|biblio/15114417]]).
 
-_Ciona savignyi_ uses the same mitochodrial genetic code as of other ascidians
-studied before ([[Yokobori, Watanabe and Oshima, 2003|biblio/14738316]]).
-
 [[!inline pages="tagged(Ciona)" actions="no" limit=0]]
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index a35fc849..20e369db 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -36,6 +36,9 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
    SR1 bacteria ([[Campbell and coll, 2013|biblio/23509275]]).
  - In the hemichordate _Balanoglossus carnosus_ ([[Castresana and coll.,
    1998|biblio/9799263]]): ATA → Ile, AGA → Ser, AGG → ø and AAA → ø.
+ - _Ciona savignyi_ uses the same mitochodrial genetic code as of other ascidians
+    studied before ([[Yokobori, Watanabe and Oshima, 2003|biblio/14738316]]).
+
 
 ```
                      AGA   AGG   ATA   AAA   TGA

Tag.
diff --git a/biblio/17333540.mdwn b/biblio/17333540.mdwn
index a4037046..56ea8e2e 100644
--- a/biblio/17333540.mdwn
+++ b/biblio/17333540.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Phosphorylation of the histone H3.3 variant in mitosis and meiosis of the urochordate Oikopleura dioica."]]
-[[!tag Oikopleura histone telomere]]
+[[!tag Oikopleura histone telomere H3S28p]]
 
 Chromosome Res. 2007;15(2):189-201. doi:10.1007/s10577-006-1112-z
 

To read
diff --git a/biblio/21734012.mdwn b/biblio/21734012.mdwn
new file mode 100644
index 00000000..02fec99d
--- /dev/null
+++ b/biblio/21734012.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Expansion of cyclin D and CDK1 paralogs in Oikopleura dioica, a chordate employing diverse cell cycle variants."]]
+[[!tag Oikopleura to_read H3S28p]]
+
+Mol Biol Evol. 2012 Feb;29(2):487-502. doi:10.1093/molbev/msr136
+
+Campsteijn C, Ovrebø JI, Karlsen BO, Thompson EM.
+
+Expansion of cyclin D and CDK1 paralogs in Oikopleura dioica, a chordate employing diverse cell cycle variants.
+
+[[!pmid 21734012 desc="to_read"]]

Café
diff --git a/biblio/25863176.mdwn b/biblio/25863176.mdwn
new file mode 100644
index 00000000..6914b681
--- /dev/null
+++ b/biblio/25863176.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Multiple horizontally acquired genes from fungal and prokaryotic donors encode cellulolytic enzymes in the bdelloid rotifer Adineta ricciae."]]
+[[!tag cellulose]]
+
+Gene. 2015 Jul 25;566(2):125-37. doi:10.1016/j.gene.2015.04.007
+
+Szydlowski L, Boschetti C, Crisp A, Barbosa EG, Tunnacliffe A.
+
+Multiple horizontally acquired genes from fungal and prokaryotic donors encode cellulolytic enzymes in the bdelloid rotifer _Adineta ricciae_.
+
+[[!pmid 25863176 desc="HGT from multiple donors."]]

À chacun son code !
diff --git a/tags/mitochondrion.mdwn b/tags/mitochondrion.mdwn
index bf68f92c..a35fc849 100644
--- a/tags/mitochondrion.mdwn
+++ b/tags/mitochondrion.mdwn
@@ -41,7 +41,9 @@ https://en.wikipedia.org/wiki/Ascidian_mitochondrial_code
                      AGA   AGG   ATA   AAA   TGA
 Vertebrates           *     *     M     K     W
 Tunicates             G     G     M     K     W   (O. di, salps, ascidians)
- O. lon and B. char?  G     G     I     K     W
+ O. lon ?             G     G     I     K     ø?
+ M. ery ?             G     G     ø?    K     ?
+ B. sty ?             G     G     I     K     R
 Cephalochordates      S    S,ø?   M     K     W   (standard invertebrate)
 Hemichordates         S     ø     I     ø     W
 Echinoderms           S     S     I     N     W

software
diff --git a/biblio/28655158.mdwn b/biblio/28655158.mdwn
new file mode 100644
index 00000000..db9be0df
--- /dev/null
+++ b/biblio/28655158.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes."]]
+[[!tag mitochondrion not_read]]
+
+Bioinformatics. 2017 Nov 1;33(21):3331-3339. doi: 10.1093/bioinformatics/btx421.
+
+Noutahi E, Calderon V, Blanchette M, Lang FB, El-Mabrouk N.
+
+CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes.
+
+[[!pmid desc="Not read.  For reference"]]

software
diff --git a/biblio/21653513.mdwn b/biblio/21653513.mdwn
new file mode 100644
index 00000000..6c237dc6
--- /dev/null
+++ b/biblio/21653513.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="FACIL: Fast and Accurate Genetic Code Inference and Logo."]]
+[[!tag mitochondrion software]]
+
+Bioinformatics. 2011 Jul 15;27(14):1929-33. doi:10.1093/bioinformatics/btr316
+
+Dutilh BE, Jurgelenaite R, Szklarczyk R, van Hijum SA, Harhangi HR, Schmid M, de Wild B, Françoijs KJ, Stunnenberg HG, Strous M, Jetten MS, Op den Camp HJ, Huynen MA.
+
+FACIL: Fast and Accurate Genetic Code Inference and Logo.
+
+[[!pmid 21653513 desc="Command-line still runs fine in 2019."]]

Tag
diff --git a/biblio/16495997.mdwn b/biblio/16495997.mdwn
index 2cd6d2d5..05d9de79 100644
--- a/biblio/16495997.mdwn
+++ b/biblio/16495997.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Tunicates and not cephalochordates are the closest living relatives of vertebrates."]]
-[[!tag evolution Oikopleura]]
+[[!tag evolution Oikopleura tunicate]]
 
 Delsuc F, Brinkmann H, Chourrout D, Philippe H.
 

Tag
diff --git a/biblio/17051155.mdwn b/biblio/17051155.mdwn
index 8a0ced07..94d7bed3 100644
--- a/biblio/17051155.mdwn
+++ b/biblio/17051155.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Deuterostome phylogeny reveals monophyletic chordates and the new phylum Xenoturbellida."]]
-[[!tag evolution]]
+[[!tag tunicate evolution]]
 
 Bourlat SJ1, Juliusdottir T, Lowe CJ, Freeman R, Aronowicz J, Kirschner M, Lander ES, Thorndyke M, Nakano H, Kohn AB, Heyland A, Moroz LL, Copley RR, Telford MJ.
 

Café
diff --git a/biblio/pubmedlater.mdwn b/biblio/pubmedlater.mdwn
new file mode 100644
index 00000000..f6c1e132
--- /dev/null
+++ b/biblio/pubmedlater.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Ultrasound imaging of gene expression in mammalian cells"]]
+[[!tag ultrasound]]
+
+Arash Farhadi, Gabrielle H. Ho, Daniel P. Sawyer, Raymond W. Bourdeau, Mikhail G. Shapiro
+
+Science  27 Sep 2019 Vol. 365, Issue 6460, pp. 1469-1475 doi:10.1126/science.aax4804 
+
+Ultrasound imaging of gene expression in mammalian cells
+
+[[!pmid later desc="Bacillus megaterium gas vesicle genes were codon-optimised and transfected into mammalian cells.  What is detected is the collapse of the gas vesicles under ultrasound exposure."]]

OSA2016 genome on Aniseed
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index abf940d5..2e2b9b02 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -21,6 +21,7 @@ Some links:
  - Études sur les Appendiculaires du Détroit de Messine, Hermann Fol, 1872
    ([[ark:/13960/t7fr0vj77|https://archive.org/details/cbarchive_100233_etudessurlesappendiculairesdud1821]]).
  - [A day in the life of an Oikopleura lab](http://thenode.biologists.com/day-life-oikopleura-lab/).
+ - OSA2016 genome on aniseed: <https://www.aniseed.cnrs.fr/aniseed/species/show_species?unique_name=Oikopleura_dioica>
 
 Food tested in laboratory (totally incomplete list): _Isochrysis galbana_ (5.5
 µm in size), _Tetraselmis suecica_ (9.5 µm), and the chlorophyte _Chlorella

Café
diff --git a/biblio/10.1017_S0954102003001585.mdwn b/biblio/10.1017_S0954102003001585.mdwn
new file mode 100644
index 00000000..c22eeb7c
--- /dev/null
+++ b/biblio/10.1017_S0954102003001585.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The classification of Antarctic appendicularians: the Oikopleura gaussica group"]]
+[[!tag Oikopleura]]
+
+Capitanio FL, Daponte MC and Esnal GB.
+
+Antarctic Science 15 (4): 476–482 (2003) doi:10.1017/S0954102003001585
+
+The classification of Antarctic appendicularians: the Oikopleura gaussica group
+
+[[!doi 10.1017/S0954102003001585 desc="Proposes that O. gaussica, O. valdiviae, O. drygalskii, and O. weddelli actually form a single species.  It has oral gland cells, and a variable (8~14) number of subchordal cells, on the right (ventral) side of the tail."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 1780e5e2..abf940d5 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -511,6 +511,9 @@ Ecology
  - Mesopelagic oikopleura were described by [[R. Fenaux
    (1993)|biblio/10.1017_S0025315400033178]] in Bahamian and Bermudian
    and in mediterranean waters.
-
+ - Oikopleuridae can be found in polar waters.  [[Capitanio, Daponte and Esnal
+   (2003)|biblio/10.1017_S0954102003001585]] proposed that _O. gaussica_, _O.
+   valdiviae_, _O. drygalskii_, and _O. weddelli_ are actually a single species
+   (with oral gland cells and ~8 to 14 subchordal cells).
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

Café
diff --git a/biblio/10.1017_S0025315400033178.mdwn b/biblio/10.1017_S0025315400033178.mdwn
new file mode 100644
index 00000000..b7970490
--- /dev/null
+++ b/biblio/10.1017_S0025315400033178.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A new genus of midwater appendicularian: Mesoikopleura with four species"]]
+[[!tag Oikopleura]]
+
+Robert Fenaux
+
+Journal of the Marine Biological Association of the United Kingdom. Volume 73, Issue 3, August 1993, pp. 635-646
+
+A new genus of midwater appendicularian: Mesoikopleura with four species
+
+[[!doi 10.1017/S0025315400033178 desc="Sampled at 700-900 m depth.  No buccal glands.  Trunk sizes 740~1400 µm.  Tail sizes of 7200~8750 µm.  Either numerous small amphicordal cells on both sides of the tail (M. enterospira, M. youngbluthi) or seven (4+3) fusiform amphicordal celss (gyroceanis).  Splits Oikopleurinae into two groups according to the presence or absence of buccal lips: Alabiata and Labiata."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 42a1a74c..1780e5e2 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -508,5 +508,9 @@ Ecology
  - Southen sea of Cortez (Mexico), near Isla El Paradito (water temperature =
    30 °C; night dives), _O. dioica_ was found but not as abundant as other
    larvaceans ([[Galt, Grober and Sykes, 1985|biblio/10.2307_1541178]]).
+ - Mesopelagic oikopleura were described by [[R. Fenaux
+   (1993)|biblio/10.1017_S0025315400033178]] in Bahamian and Bermudian
+   and in mediterranean waters.
+
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

To read
diff --git a/biblio/15632085.mdwn b/biblio/15632085.mdwn
new file mode 100644
index 00000000..01812256
--- /dev/null
+++ b/biblio/15632085.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution."]]
+[[!tag to_read]]
+
+Genome Res. 2005 Jan;15(1):1-18 doi:10.1101/gr.3059305
+
+Richards S, Liu Y, Bettencourt BR, Hradecky P, Letovsky S, Nielsen R, Thornton K, Hubisz MJ, Chen R, Meisel RP, Couronne O, Hua S, Smith MA, Zhang P, Liu J, Bussemaker HJ, van Batenburg MF, Howells SL, Scherer SE, Sodergren E, Matthews BB, Crosby MA, Schroeder AJ, Ortiz-Barrientos D, Rives CM, Metzker ML, Muzny DM, Scott G, Steffen D, Wheeler DA, Worley KC, Havlak P, Durbin KJ, Egan A, Gill R, Hume J, Morgan MB, Miner G, Hamilton C, Huang Y, Waldron L, Verduzco D, Clerc-Blankenburg KP, Dubchak I, Noor MA, Anderson W, White KP, Clark AG, Schaeffer SW, Gelbart W, Weinstock GM, Gibbs RA.
+
+Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution.
+
+[[!pmid 15632085 desc="To read"]]

creating tag page tags/frog
diff --git a/tags/frog.mdwn b/tags/frog.mdwn
new file mode 100644
index 00000000..4fda82ce
--- /dev/null
+++ b/tags/frog.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged frog"]]
+
+[[!inline pages="tagged(frog)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/31578486.mdwn b/biblio/31578486.mdwn
new file mode 100644
index 00000000..947e0388
--- /dev/null
+++ b/biblio/31578486.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Imprinting sets the stage for speciation."]]
+[[!tag frog speciation population model]]
+
+Yang Y, Servedio MR, Richards-Zawacki CL.
+
+Nature. 2019 Oct;574(7776):99-102. doi:10.1038/s41586-019-1599-z
+
+Imprinting sets the stage for speciation.
+
+[[!pmid desc="Oophaga pumilio tadpoles learn congeneric coat color from their mother."]]

To read
diff --git a/biblio/20075246.mdwn b/biblio/20075246.mdwn
new file mode 100644
index 00000000..ce617726
--- /dev/null
+++ b/biblio/20075246.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Hungry codons promote frameshifting in human mitochondrial ribosomes."]]
+[[!tag to_read]]
+
+Temperley R, Richter R, Dennerlein S, Lightowlers RN, Chrzanowska-Lightowlers ZM.
+
+Science. 2010 Jan 15;327(5963):301. doi:10.1126/science.1180674
+
+Hungry codons promote frameshifting in human mitochondrial ribosomes.
+
+[[!pmid 20075246 desc="To read"]]

To read
diff --git a/biblio/10.1016_0198-0149_92_90070-A.mdwn b/biblio/10.1016_0198-0149_92_90070-A.mdwn
new file mode 100644
index 00000000..373c1d7c
--- /dev/null
+++ b/biblio/10.1016_0198-0149_92_90070-A.mdwn
@@ -0,0 +1,9 @@
+[[!meta title="In situ observations of giant appendicularians in Monterey Bay"]]
+[[!tag to_read]]
+
+Author links open overlay panelWilliam MHamner∗†Bruce HRobison∗
+
+Volume 39, Issues 7–8, July–August 1992, Pages 1299-1313 doi:10.1016/0198-0149(92)90070-A
+
+In situ observations of giant appendicularians in Monterey Bay
+[[!doi 10.1016/0198-0149(92)90070-A desc="To read"]]

Café
diff --git a/biblio/12481130.mdwn b/biblio/12481130.mdwn
new file mode 100644
index 00000000..4d5683a7
--- /dev/null
+++ b/biblio/12481130.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins."]]
+[[!tag Ciona genome cellulose]]
+
+Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, Gelpke M, Goodstein DM, Harafuji N, Hastings KE, Ho I, Hotta K, Huang W, Kawashima T, Lemaire P, Martinez D, Meinertzhagen IA, Necula S, Nonaka M, Putnam N, Rash S, Saiga H, Satake M, Terry A, Yamada L, Wang HG, Awazu S, Azumi K, Boore J, Branno M, Chin-Bow S, DeSantis R, Doyle S, Francino P, Keys DN, Haga S, Hayashi H, Hino K, Imai KS, Inaba K, Kano S, Kobayashi K, Kobayashi M, Lee BI, Makabe KW, Manohar C, Matassi G, Medina M, Mochizuki Y, Mount S, Morishita T, Miura S, Nakayama A, Nishizaka S, Nomoto H, Ohta F, Oishi K, Rigoutsos I, Sano M, Sasaki A, Sasakura Y, Shoguchi E, Shin-i T, Spagnuolo A, Stainier D, Suzuki MM, Tassy O, Takatori N, Tokuoka M, Yagi K, Yoshizaki F, Wada S, Zhang C, Hyatt PD, Larimer F, Detter C, Doggett N, Glavina T, Hawkins T, Richardson P, Lucas S, Kohara Y, Levine M, Satoh N, Rokhsar DS.
+
+Science. 2002 Dec 13;298(5601):2157-67 doi: 10.1126/science.1080049
+
+The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.
+
+[[!pmid 12481130 desc="The genome of _C. intestinalis_ contains at least one cellulose synthans and multiple endoglycanases."]]
diff --git a/tags/cellulose.mdwn b/tags/cellulose.mdwn
index ee088b09..5bf15a48 100644
--- a/tags/cellulose.mdwn
+++ b/tags/cellulose.mdwn
@@ -11,4 +11,7 @@ Sasakura and coll. ([[2016|biblio/28003446]] have proposed that the GC-rich
 genome of actinobacteria might have provided an AP-2 binding site promoting
 expression in the epidermis.
 
+A cellulose synthase and several endoglycanase genes were observed in the _C.
+intestinalis_ genome by [[Dehal and coll., 2002|biblio/12481130]].
+
 [[!inline pages="tagged(cellulose)" limit=0]]

Café
diff --git a/biblio/7579513.mdwn b/biblio/7579513.mdwn
new file mode 100644
index 00000000..0af7dd3a
--- /dev/null
+++ b/biblio/7579513.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Gene duplications and the origins of vertebrate development."]]
+[[!tag Oikopleura]]
+
+Holland PW, Garcia-Fernàndez J, Williams NA, Sidow A.
+
+Dev Suppl. 1994:125-33.
+
+Gene duplications and the origins of vertebrate development.
+
+[[!pmid 7579513 desc="Attempt to clone Hox genes with degenerate primers only yielded one clone."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 591388f3..42a1a74c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -174,6 +174,8 @@ Genes and pathways
    are activated by polyunsaturated aldehydes produced by diatoms
    ([[Torres-Águila and coll., 2018|biblio/30272001]]).
  - _O. dioica_ has 83 homeobox genes, according to [[Edvardsen and coll., 2005|biblio/15649342]].
+   Illustrating how diverged are the sequences, earlier attempts to clone Hox genes yielded
+   only a single clone ([[Holland and coll. 1994|biblio/7579513]]).
  - Southern blot analysis suggest the presence of a SCO-spondin gene in _O.
    dioica_ ([[Gobron and coll., 1999|biblio/10197783]]).
  - A single ortholog of _Brachyury_ (_TBXT_, or _T_) was cloned by [[Bassham

Café
diff --git a/biblio/24817302.mdwn b/biblio/24817302.mdwn
new file mode 100644
index 00000000..654f8132
--- /dev/null
+++ b/biblio/24817302.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Yellow-stained oikopleurid appendicularians are caused by bacterial parasitism"]]
+[[!tag Oikopleura]]
+
+Flood, P. R.
+
+MEPS 71:291-295 
+
+Yellow-stained oikopleurid appendicularians are caused by bacterial parasitism
+
+[Rod-shaped (0.6 or 0.4 µm-wide) bacteria observed by transmission and electron microscopy in O. dioica and O. vanhoeffeni](https://www.jstor.org/stable/24817302)
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 711c336f..591388f3 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -363,7 +363,8 @@ Physiology
    the rectum.  Lipid uptake might happen in the right lobe of the stomach
    ([[Burighel, Brena, Martinucci and Cima
    (2005)|biblio/10.1111_j.1744-7410.2001.tb00038.x]]).
-
+ - Yellow color can be caused by bacterial infection.  [[Flood (1991)|biblio/24817302]]
+   observed rod-shaped bacteria (0.6 or 0.4 µm-wide) in _O. doica_ or _O. vanhoeffeni_.
 
 House
 -----