Dernières modifications :

Lost genes.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 04e24f6..420e327 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -73,10 +73,6 @@ Genome
    by [[Berná and Alvarez-Valin (2014)|biblio/25008364]].
  - Chromatin domains are rarely longer than 7 nucleosomes ([[Navratilova et al., 2017|biblio/28115992]]).
  - Some 5-methylcytosine was detected by MeDIP-chip by ([[Navratilova et al., 2017|biblio/28115992]]).
- - The entire machinery required for performing classical NHEJ repair of DSB (which is
-   conserved from yeast to mammals) is undetectable ([[Denoeud et al., 2010|biblio/21097902]]).
- - An alternative or microhomology (MH)-driven end joining pathway is active
-   and triggers microdeletions at the joining site ([[Deng, Henriet and Chourrout, 2018|biblio/30293719]]).
  - Only a partial mitochondrial genome was reconstituted in [[Denoeud et al.,
    2010|biblio/21097902]], due to cloning and sequencing difficulties that may
    have been caused by oligo-dT stretches.  A/T-rich codons are more frequent than
@@ -85,10 +81,7 @@ Genome
    2008|biblio/18612321]]).
  - Analysis of sex-linked markers supports genetic sex determination with male heterogamety –
    that is: X chromosomes for females and Y for males.  ([[Denoeud et al., 2010|biblio/21097902]])
- - The minor spliceosome could not be found in _Oikopleura_'s genome ([[Martz
-   et al., 2008|biblio/19030770]], [[Denoeud et al., 2010|biblio/21097902]]).
-   It is found in _Ciona_ but not in _C. elegans_ ()[[Martz et al.,
-   2008|biblio/19030770]]. The major spliceosome is hypothethised to have evolved
+ - The major spliceosome is hypothethised to have evolved
    to become more permissive in order to splice G*-AG sites.  ”A large fraction
    (more than 10%) of the (...) introns displayed non-canonical (non GT-AG)
    splice sites, whereas the usual proportion is around 1%-1.5% in other genomes”
@@ -161,6 +154,15 @@ Genes and pathways
    ([[Niimura, 2009|biblio/20333175]]).
  - Most members of retinoic acid pathway gene network (biosynthesis, signalling
    and degradation) are lost in _O. dioica_ ([[Martí-Solans et al., 2016|biblio/27406791]]).
+ - The entire machinery required for performing classical NHEJ repair of DSB (which is
+   conserved from yeast to mammals) is undetectable ([[Denoeud et al., 2010|biblio/21097902]]).
+   An alternative or microhomology (MH)-driven end joining pathway is active
+   and triggers microdeletions at the joining site ([[Deng, Henriet and Chourrout, 2018|biblio/30293719]]).
+ - The minor spliceosome could not be found in _Oikopleura_'s genome ([[Martz
+   et al., 2008|biblio/19030770]], [[Denoeud et al., 2010|biblio/21097902]]).
+   It is found in _Ciona_ but not in _C. elegans_ ()[[Martz et al.,
+   2008|biblio/19030770]].
+
 
 
 Transcriptome

Lost genes and pathways.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index b639ee0..04e24f6 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -124,6 +124,8 @@ Genome
 Genes and pathways
 ------------------
 
+### Present or gained
+
 (See also other sections)
 
  - ~80 "house proteins" have been identified and more than half lack similarity
@@ -137,17 +139,11 @@ Genes and pathways
    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_ lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]]).
-   It has Dnmt2, but this is a tRNA methyltransferase and it was later renamed Trdmt1 accordingly.
- - CYP1 family genes and their regulator AhR are not detectable
-   ([[Yadetie et al, 2012|biblio/22300585]]).
  - _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
    ([[Inoue & Satoh|biblio/29319812]]), prehaps reflecting the importance of
    tail movements at larval and adult stages.
- - No olfactory receptors have been found in _Oikopleura_ nor in _Ciona_
-   ([[Niimura, 2009|biblio/20333175]]).
  - Defensome genes such as dehydrogenases and  (Glutamate-cysteine ligase modifier subunit; Gclm)
    are activated by polyunsaturated aldehydes produced by diatoms
    ([[Torres-Águila and coll., 2018|biblio/30272001]]).
@@ -155,6 +151,18 @@ Genes and pathways
  - Southern blot analysis suggest the presence of a SCO-spondin gene in _O.
    dioica_ ([[Gobron and coll., 1999|biblio/10197783]]).
 
+### Lost
+
+ - _O. dioica_ lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]]).
+   It has Dnmt2, but this is a tRNA methyltransferase and it was later renamed Trdmt1 accordingly.
+ - CYP1 family genes and their regulator AhR are not detectable
+   ([[Yadetie et al, 2012|biblio/22300585]]).
+ - No olfactory receptors have been found in _Oikopleura_ nor in _Ciona_
+   ([[Niimura, 2009|biblio/20333175]]).
+ - Most members of retinoic acid pathway gene network (biosynthesis, signalling
+   and degradation) are lost in _O. dioica_ ([[Martí-Solans et al., 2016|biblio/27406791]]).
+
+
 Transcriptome
 -------------
 
@@ -254,8 +262,7 @@ Physiology
  - Adh3 is the only medium-chain alcohol dehydrogenase (MDR-Adh) in _Oikopleura_
    (like in other non-vertebrates).  Conservation of critical residues and similarity
    in expression pattern suggest that its metabolic targets are the same as in other species.
- - Most members of retinoic acid pathway gene network (biosynthesis, signalling
-   and degradation) are lost in _O. dioica_.  Some of the remaining ones show
+ - Some members of retinoic acid pathway gene network that were not lost in _O. dioica_ show
    signs of neofunctionalisation or specialisation in their ancestral activity in
    digestion or chemical defence ([[Martí-Solans et al., 2016|biblio/27406791]]).
 

Dnmt2 renamed Trdmt1.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 885d8d7..b639ee0 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -137,7 +137,8 @@ Genes and pathways
    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_ only has the Dnmt2 methyltransferase, and lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]]).
+ - _O. dioica_ lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]]).
+   It has Dnmt2, but this is a tRNA methyltransferase and it was later renamed Trdmt1 accordingly.
  - CYP1 family genes and their regulator AhR are not detectable
    ([[Yadetie et al, 2012|biblio/22300585]]).
  - _O. dioica_, like other deuterostomes, has acid-sensing ion channels (ASICs).

Add reference
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 8a07b6a..885d8d7 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -137,7 +137,7 @@ Genes and pathways
    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_ only has the Dnmt2 methyltransferase, and lacks Dnmt1 and Dnmt3.
+ - _O. dioica_ only has the Dnmt2 methyltransferase, and lacks Dnmt1 and Dnmt3 ([[Cañestro, Yokoi and Postlethwait, 2007|biblio/18007650]]).
  - CYP1 family genes and their regulator AhR are not detectable
    ([[Yadetie et al, 2012|biblio/22300585]]).
  - _O. dioica_, like other deuterostomes, has acid-sensing ion channels (ASICs).

CAPsmart
diff --git a/biblio/25003736.mdwn b/biblio/25003736.mdwn
index 878bb0f..6f72640 100644
--- a/biblio/25003736.mdwn
+++ b/biblio/25003736.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Four methods of preparing mRNA 5' end libraries using the illumina sequencing platform."]]
-[[!tag template_switching method oligo-capping benchmark]]
+[[!tag cap template_switching method oligo-capping benchmark]]
 
 Machida RJ, Lin YY.
 
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 34d054e..8e2ae7f 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -56,6 +56,13 @@ in the [[template_switching]] tag page.
  - [[Kwak et al., 2013|biblio/23430654]] modified oligo-capping to create Pro-cap, a method for nuclear
    run-on analysis at single-nucleotide resulution.
 
+ - CapSMART ([[Machida and Lin, 2014|biblio/25003736]]): non-capped RNAs are
+   dephosphorylated, rephoshporylated and a blocking linker containing
+   isoguanosines and isocytidines (so that it can not be reverse-transcribed) is
+   ligated to them.  A classical SMART protocol follows.  cDNAs are amplified with
+   biotinylated forward primers, so that the 5′ end can be recovered after
+   mechanical fragmentation.
+
 Atypical caps (work in progress)
 --------------------------------
 

crosslink
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 351bb60..34d054e 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -21,6 +21,9 @@ Methods for enriching capped RNAs
    uncover functional phosphate with decapping enzyme, and ligate RNA adaptor
    with T4 RNA ligase.
 
+(wip: template-switching: find original publication. Described in deeper details
+in the [[template_switching]] tag page.
+
 (wip: Fromont-racine et al.)
 
  - CAPture ([[Edery, Chu, Sonenberg and Pelletier, 1995|biblio/7760832]]):
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index 5226ece..ece2741 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -1,6 +1,6 @@
 [[!meta title="pages tagged template_switching"]]
 
-(work in progress)
+(work in progress.  For alternative cap enrichement methods see the [[cap]] tag page)
 
  - In the "_CapSelect_" method, [[Schmidt and Mueller, 1999|biblio/10518626]]
    stimulate template switching with manganese (see below), tail the first-strand

Café
diff --git a/biblio/3028775.mdwn b/biblio/3028775.mdwn
new file mode 100644
index 0000000..2962fcd
--- /dev/null
+++ b/biblio/3028775.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Cloning of the human cDNA for the U1 RNA-associated 70K protein."]]
+[[!tag cap method library]]
+
+Theissen H, Etzerodt M, Reuter R, Schneider C, Lottspeich F, Argos P, Lührmann R, Philipson L.
+
+EMBO J. 1986 Dec 1;5(12):3209-17.
+
+Cloning of the human cDNA for the U1 RNA-associated 70K protein.
+
+[[!pmid 3028775 desc="Clones the full-length cDNA by affinity purification with m7G antibodies, and RNAse A digestion of the incomplete cDNA/RNA duplexes.  Cites Schneider 1986 for the method, but could not find this reference."]]
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index afc78ea..351bb60 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -10,6 +10,11 @@ Methods for enriching capped RNAs
 
  - See the Wikipedia for [[CAGE methods|https://en.wikipedia.org/wiki/Cap_analysis_gene_expression]] (Cap Analysis Gene Expression).
 
+ - [[Thiessen and coll., 1986|biblio/3028775]] cloned the full-length cDNA by
+   affinity purification with m7G antibodies, and RNAse A digestion of the
+   incomplete cDNA/RNA duplexes.  They cite Schneider 1986 for the method, but
+   I could not find this reference.
+
  - A method similar to oligo-capping was reported by [[Sekine and Kato|biblio/8247743]] in 1993.
 
  - Oligo-capping ([[Maruyama et al., 1994|biblio/8125298]]): dephosphorylate,

Café
diff --git a/biblio/12777618.mdwn b/biblio/12777618.mdwn
new file mode 100644
index 0000000..24066c3
--- /dev/null
+++ b/biblio/12777618.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Purifying mRNAs with a high-affinity eIF4E mutant identifies the short 3' poly(A) end phenotype."]]
+[[!tag method cap library]]
+
+Proc Natl Acad Sci U S A. 2003 Jun 10;100(12):7033-8 doi:10.1073/pnas.1232347100
+
+Choi YH, Hagedorn CH.
+
+Purifying mRNAs with a high-affinity eIF4E mutant identifies the short 3' poly(A) end phenotype.
+
+[[!pmid 12777618 desc="Increases cap specificity with a K119A mutation.  This mutant is fused to GST instead of protein A."]]
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index e3333e7..afc78ea 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -33,6 +33,9 @@ Methods for enriching capped RNAs
    reads through the cap structure and chemical bond, and integrates the reverse
    complement of the oligonucleotide to the first-strand cDNA.
 
+ - [[Choi and Hagedorn (2003)|biblio/12777618]] improved the CAPture method by using
+   a K119A mutant of eIF4E.  It is fused to GST instead of protein A.
+
  - [[Clepet et al., 2004|biblio/14704363]] modified oligo-capping, to use T4
    DNA ligase and a double-stranded adapter with NNNNNN overhang instead of T4
    RNA ligase and a single-stranded linker.

RNA captor
diff --git a/biblio/21533245.mdwn b/biblio/21533245.mdwn
new file mode 100644
index 0000000..dd6a5b5
--- /dev/null
+++ b/biblio/21533245.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="RNA captor: a tool for RNA characterization."]]
+[[!tag cap library method]]
+
+Clepet C.
+
+PLoS One. 2011 Apr 13;6(4):e18445. doi:10.1371/journal.pone.0018445
+
+RNA captor: a tool for RNA characterization.
+
+[[!pmid 21533245 desc="Modified oligo-capping reaction using T4 RNA ligase 2 and a double-stranded adaptor with a 5′-protrusive NNN end and a  3′-amine blocking group on the other end of the same oligonucleotide."]]
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index 6e01b64..e3333e7 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -37,6 +37,11 @@ Methods for enriching capped RNAs
    DNA ligase and a double-stranded adapter with NNNNNN overhang instead of T4
    RNA ligase and a single-stranded linker.
 
+ - RNA captor ([[Clepet, 2011|biblio/21533245]]): a modified oligo-capping using
+   T4 RNA ligase 2 and a double-stranded adaptor.  The shorter oligonucleotide in
+   the adaptor is blocked by an amine group on its 3′ end, and protrudes with 3
+   random bases (NNN) on its 5′ end.
+
  - [[Kwak et al., 2013|biblio/23430654]] modified oligo-capping to create Pro-cap, a method for nuclear
    run-on analysis at single-nucleotide resulution.
 

Correction.
diff --git a/biblio/28369459.mdwn b/biblio/28369459.mdwn
index 3592b9c..b399a99 100644
--- a/biblio/28369459.mdwn
+++ b/biblio/28369459.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer."]]
-[[!tag assenbly Nanopore yeast mitochondrion]]
+[[!tag assembly Nanopore yeast mitochondrion]]
 
 Istace B, Friedrich A, d'Agata L, Faye S, Payen E, Beluche O, Caradec C,
 Davidas S, Cruaud C, Liti G, Lemainque A, Engelen S, Wincker P, Schacherer J,
diff --git a/tags/assenbly.mdwn b/tags/assenbly.mdwn
deleted file mode 100644
index 10481ce..0000000
--- a/tags/assenbly.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged assenbly"]]
-
-[[!inline pages="tagged(assenbly)" actions="no" archive="yes"
-feedshow=10]]

Document CAPture.
diff --git a/tags/cap.mdwn b/tags/cap.mdwn
index b5bfe73..6e01b64 100644
--- a/tags/cap.mdwn
+++ b/tags/cap.mdwn
@@ -1,6 +1,10 @@
 [[!meta title="pages tagged cap"]]
 
-Methods for enriching capped RNAs.
+RNA caps
+========
+
+Methods for enriching capped RNAs
+---------------------------------
 
 (work in progress)
 
@@ -14,6 +18,12 @@ Methods for enriching capped RNAs.
 
 (wip: Fromont-racine et al.)
 
+ - CAPture ([[Edery, Chu, Sonenberg and Pelletier, 1995|biblio/7760832]]):
+   a protein fusion of mouse eIF4E (for cap binding) and protein A
+   (for IgG binding) is used to capture capped RNA/cDNA duplexes on a
+   sepharose IgG column.  Completion of first-strand synthesis is ascertained
+   by RNAse A digestion.
+
  - CapSelect ([[Schmidt et al., 1999|biblio/10518626]]): Add a poly-A tail to
    the first-strand cDNA, ligate a double-stranded adapter ending with a
    single-strand (T)TTTGGG overhang, and prime second-strand synthesis.
@@ -30,7 +40,8 @@ Methods for enriching capped RNAs.
  - [[Kwak et al., 2013|biblio/23430654]] modified oligo-capping to create Pro-cap, a method for nuclear
    run-on analysis at single-nucleotide resulution.
 
-Atypical caps (work in progress).
+Atypical caps (work in progress)
+--------------------------------
 
  - 5′-phospho-ADP-ribosylated RNA/DNA cap, synthethysed by RNA
    2′-phosphotransferase Tpt1 ([[Munir, Banerjee and Shuman, 2018|biblio/30202863]]).

creating tag page tags/assenbly
diff --git a/tags/assenbly.mdwn b/tags/assenbly.mdwn
new file mode 100644
index 0000000..10481ce
--- /dev/null
+++ b/tags/assenbly.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged assenbly"]]
+
+[[!inline pages="tagged(assenbly)" actions="no" archive="yes"
+feedshow=10]]

Add tag
diff --git a/biblio/28369459.mdwn b/biblio/28369459.mdwn
index 9946480..3592b9c 100644
--- a/biblio/28369459.mdwn
+++ b/biblio/28369459.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer."]]
-[[!tag Nanopore yeast mitochondrion]]
+[[!tag assenbly Nanopore yeast mitochondrion]]
 
 Istace B, Friedrich A, d'Agata L, Faye S, Payen E, Beluche O, Caradec C,
 Davidas S, Cruaud C, Liti G, Lemainque A, Engelen S, Wincker P, Schacherer J,

Mitochondrion
diff --git a/biblio/28369459.mdwn b/biblio/28369459.mdwn
new file mode 100644
index 0000000..9946480
--- /dev/null
+++ b/biblio/28369459.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer."]]
+[[!tag Nanopore yeast mitochondrion]]
+
+Istace B, Friedrich A, d'Agata L, Faye S, Payen E, Beluche O, Caradec C,
+Davidas S, Cruaud C, Liti G, Lemainque A, Engelen S, Wincker P, Schacherer J,
+Aury JM.
+
+Gigascience. 2017 Feb 1;6(2):1-13. doi:10.1093/gigascience/giw018
+
+de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer.
+
+[[!pmid 28369459 desc="Assembled mitochondrial genomes with ABruijn."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 1777372..b36d5f8 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -13,6 +13,10 @@ The Flye assembler ([[Kolmogorov and coll, bioRxiv
 contigs using long error-prone reads, untangles the graph by resolving repeats,
 and then uses it to refine the contings and increase their accuracy.
 
+The predecessor of Flye, ABruijn, was reported by [[Istace and coll.
+(2017)|biblio/28369459]] to be able to assemble mitochondrial genomes (unlike
+Canu and other assemblers).
+
 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]])

SALSA2
diff --git a/biblio/10.1101_261149.mdwn b/biblio/10.1101_261149.mdwn
new file mode 100644
index 0000000..cf7b5e5
--- /dev/null
+++ b/biblio/10.1101_261149.mdwn
@@ -0,0 +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
+
+bioRxiv, first February 07, 2018.
+
+Integrating Hi-C links with assembly graphs for chromosome-scale assembly
+
+[[!doi 10.1101/261149 desc="Uses unitigs and the assembly graph as input."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 9dc13ef..1777372 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -35,7 +35,9 @@ assembly_”.
 
 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.
+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]]).
 
 BUSCO ([[Simão and coll., 2015|biblio/26059717]], [[Waterhouse and coll.,
 2017|biblio/29220515]]) assesses the presence of evolutionary conserved single-copy

SALSA
diff --git a/biblio/28701198.mdwn b/biblio/28701198.mdwn
new file mode 100644
index 0000000..a853897
--- /dev/null
+++ b/biblio/28701198.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Scaffolding of long read assemblies using long range contact information."]]
+[[!tag genome assembly software]]
+
+Ghurye J, Pop M, Koren S, Bickhart D, Chin CS.
+
+BMC Genomics. 2017 Jul 12;18(1):527. doi:10.1186/s12864-017-3879-z
+
+Scaffolding of long read assemblies using long range contact information.
+
+[[!pmid 28701198 desc="Does not require a priori knowledge on the number of chromosomes.  Outperforms LACHESIS on noisy data."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index f1f20f0..9dc13ef 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -33,6 +33,10 @@ 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_”.
 
+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.
+
 BUSCO ([[Simão and coll., 2015|biblio/26059717]], [[Waterhouse and coll.,
 2017|biblio/29220515]]) assesses the presence of evolutionary conserved single-copy
 genes in the assemblies.

Café
diff --git a/biblio/10.1101_247148.mdwn b/biblio/10.1101_247148.mdwn
new file mode 100644
index 0000000..3b80d26
--- /dev/null
+++ b/biblio/10.1101_247148.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Assembly of Long Error-Prone Reads Using Repeat Graphs"]]
+[[!tag genome assembly method]]
+
+Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin, Pavel Pevzner
+
+bioRxiv, Posted January 12, 2018.
+
+Assembly of Long Error-Prone Reads Using Repeat Graphs
+
+[[!doi 10.1101/247148 desc="“Flye constructs (overlapping) contigs with possible assembly errors at the initial stage, combines them into an accurate assembly graph, resolves repeats in the assembly graph using small variations between various repeat instances that were left unresolved during the initial assembly stage, constructs a new, less tangled assembly graph based on resolved repeats, and finally outputs accurate contigs as paths in this graph.”"]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index c0b2a60..f1f20f0 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -8,6 +8,11 @@ Prior assembly, MinIONQC ([[Lanfear and coll., 2018|biblio/30052755]]) allows
 for the comparison of multiple Nanopore runs on the same plot, to assess if
 read length is satisfactory.
 
+The Flye assembler ([[Kolmogorov and coll, bioRxiv
+2018|biblio/10.1101_247148]]) creates an A-Bruijn (assembly) graph from draft
+contigs using long error-prone reads, untangles the graph by resolving repeats,
+and then uses it to refine the contings and increase their accuracy.
+
 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]])

savignyi
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index 75b30b3..77551c2 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -1,9 +1,11 @@
 [[!meta title="pages tagged Ciona"]]
 
 
-      - Ciona robusta Hoshino & Tokioka, 1967 [WoRMS ID 252565](http://www.marinespecies.org/aphia.php?p=taxdetails&id=252565)
+        -- Ciona robusta Hoshino & Tokioka, 1967 [WoRMS ID 252565](http://www.marinespecies.org/aphia.php?p=taxdetails&id=252565)
+      -|
+     |  -- Ciona intestinalis Linnaeus, 1767 [WoRMS ID 103732](http://www.marinespecies.org/aphia.php?p=taxdetails&id=103732)
     -|
-      - Ciona intestinalis Linnaeus, 1767 [WoRMS ID 103732](http://www.marinespecies.org/aphia.php?p=taxdetails&id=103732)
+      ---- Ciona savignyi Herdman, 1882 [WoRMS ID 250292](http://www.marinespecies.org/aphia.php?p=taxdetails&id=250292)
 
 _C. intestinalis_ and _C. savignyi_ can cross-fertilise after removal of the
 vitelline enveloppe ([[Byrd and Lambert, 2000|biblio/10602281]]).  They are

trans-splicing
diff --git a/biblio/27791007.mdwn b/biblio/27791007.mdwn
new file mode 100644
index 0000000..e482b5d
--- /dev/null
+++ b/biblio/27791007.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora."]]
+[[!tag trans-splicing endosymbiosis]]
+
+Proc Natl Acad Sci U S A. 2016 Oct 25;113(43):12214-12219 doi:10.1073/pnas.1608016113
+
+Nowack EC, Price DC, Bhattacharya D, Singer A, Melkonian M, Grossman AR.
+
+Gene transfers from diverse bacteria compensate for reductive genome evolution in the chromatophore of Paulinella chromatophora.
+
+[[!pmid 27791007 desc="Found splice leaders in P. chromatophora.  Horizontal gene transfer as a possible mechanism facilitating gene loss in endosymbionts."]]
diff --git a/biblio/30024971.mdwn b/biblio/30024971.mdwn
index afe04a3..766b54b 100644
--- a/biblio/30024971.mdwn
+++ b/biblio/30024971.mdwn
@@ -7,4 +7,4 @@ Matsuo M, Katahata A, Satoh S, Matsuzaki M, Nomura M, Ishida KI, Inagaki Y, Obok
 
 Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer.
 
-[[!pmid 30024971 desc="Found trans-splicing in P. micropora, and discussed a possible link with endosymbiosis and horizontal gene transfer."]]
+[[!pmid 30024971 desc="Characterised two splice leaders in P. micropora, and discussed a possible link with endosymbiosis and horizontal gene transfer."]]
diff --git a/tags/trans-splicing.mdwn b/tags/trans-splicing.mdwn
index 6acdd07..7ded5bd 100644
--- a/tags/trans-splicing.mdwn
+++ b/tags/trans-splicing.mdwn
@@ -4,4 +4,8 @@ Trans-splicing was discovered in tunicates by [[Vandenberghe, Meedel and Hasting
 
 The splice leader is 16-nt in C. intestinalis ([[Satou et al, 2006|biblio/16822859]]) and 40-nt in O. dioica ([[Ganot et al., 2004|biblio/15314184]]).
 
+A splice leader was found in the endosymbiotic amoeba _Paulinella
+chromatophora_ by [[Nowack and coll, 2016|biblio/27791007]], and characterised
+by [[Matsuo and coll., 2018|biblio/30024971]].
+
 [[!inline pages="tagged(trans-splicing)" actions="no" limit=0]]

creating tag page tags/endosymbiosis
diff --git a/tags/endosymbiosis.mdwn b/tags/endosymbiosis.mdwn
new file mode 100644
index 0000000..4eab08d
--- /dev/null
+++ b/tags/endosymbiosis.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged endosymbiosis"]]
+
+[[!inline pages="tagged(endosymbiosis)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/30024971.mdwn b/biblio/30024971.mdwn
new file mode 100644
index 0000000..afe04a3
--- /dev/null
+++ b/biblio/30024971.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer."]]
+[[!tag trans-splicing endosymbiosis]]
+
+PLoS One. 2018 Jul 19;13(7):e0200961. doi:10.1371/journal.pone.0200961
+
+Matsuo M, Katahata A, Satoh S, Matsuzaki M, Nomura M, Ishida KI, Inagaki Y, Obokata J.
+
+Characterization of spliced leader trans-splicing in a photosynthetic rhizarian amoeba, Paulinella micropora, and its possible role in functional gene transfer.
+
+[[!pmid 30024971 desc="Found trans-splicing in P. micropora, and discussed a possible link with endosymbiosis and horizontal gene transfer."]]

Café
diff --git a/biblio/reissner_oik.mdwn b/biblio/reissner_oik.mdwn
new file mode 100644
index 0000000..f7197dc
--- /dev/null
+++ b/biblio/reissner_oik.mdwn
@@ -0,0 +1,12 @@
+[[!meta title="The origin of Reissner's fibre in an appendicularian, Oikopleura dioica"]]
+[[!tag Oikopleura]]
+
+Kaj Holmberg and Ragnar Olsson
+
+Vidensk. Meddr. dansk naturh. Foren. (1984) 145:43—52  (no DOI found)
+
+The origin of Reissner's fibre in an appendicularian, Oikopleura dioica
+
+The Reissner's fiber in _O. dioica_ is produced by a single ”fibrogen” cell.
+Electron microsocopy of this cell show a large perikaryon, cisternas, and a
+single cilium, which is inserted in the central canal.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index ea5726c..8a07b6a 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -240,8 +240,10 @@ Anatomy
  - Two subchordal cells are found in the haemocel of the tail.  Utrastructure analysis
    suggests the alternance of highly exocytic and highly endocytic states
    ([[Fredriksson and Olsson, 1991|biblio/10.1111_j.1463-6395.1991.tb01203.x]]).
- - The tail's neural tube as a "fibrogen cell" at its anterior ends, which is
+ - The tail's neural tube has a ”fibrogen cell” at its anterior ends, which is
    secreting the Reissner's fiber (reviewed in [[Olsson, 1993|biblio/10.1007_978-3-642-78013-4_5]]).
+   Electron microscopy shows a large perikaryon, cisternas and a cilium which is inserted
+   in the central canal ([[Holmberg and Olsson, 1984|biblio/reissner_oik]]).
 
 Physiology
 ----------

Café
diff --git a/biblio/26228312.mdwn b/biblio/26228312.mdwn
new file mode 100644
index 0000000..3f45917
--- /dev/null
+++ b/biblio/26228312.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evolutionary volatile Cysteines and protein disorder in the fast evolving tunicate Oikopleura dioica."]]
+[[!tag Oikopleura]]
+
+Berná L and Alvarez-Valin F.
+
+Mar Genomics. 2015 Dec;24 Pt 1:47-54. doi:10.1016/j.margen.2015.07.007
+
+Evolutionary volatile Cysteines and protein disorder in the fast evolving tunicate Oikopleura dioica.
+
+[[!pmid 26228312 desc="O. dioica proteins are shorter and proportionally less disordered than in other chordates. Correlation between presence of cysteines (thought to be stabilising) and disorder is lower in O. dioica. Cysteines in ordered domains are also less conserved in O dioica compared to other chordates."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 60bf09a..ea5726c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -115,6 +115,10 @@ Genome
  - Regulatory genes evolve faster.  All aminoacids, including cystein, show reduced
    conservation, suggesting relaxation of functional constraints.  Compared with
    Ciona, 10% of the cysteins are lost ([[Berná and coll., 2012|biblio/22120064]]).
+   Cystein loss happened in both the disordered and ordered protein domains
+   ([[Berná and Alvarez-Valin, 2015|biblio/26228312]]).
+ - Proteins of O. dioica are shorter and contain less disordored domains than proteins
+   from other chrodates ([[Berná and Alvarez-Valin, 2015|biblio/26228312]]).
 
 
 Genes and pathways

Café
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index 921821d..75b30b3 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -1,5 +1,10 @@
 [[!meta title="pages tagged Ciona"]]
 
+
+      - Ciona robusta Hoshino & Tokioka, 1967 [WoRMS ID 252565](http://www.marinespecies.org/aphia.php?p=taxdetails&id=252565)
+    -|
+      - Ciona intestinalis Linnaeus, 1767 [WoRMS ID 103732](http://www.marinespecies.org/aphia.php?p=taxdetails&id=103732)
+
 _C. intestinalis_ and _C. savignyi_ can cross-fertilise after removal of the
 vitelline enveloppe ([[Byrd and Lambert, 2000|biblio/10602281]]).  They are
 estimated to have diverged 122 ± 33 million years ago ([[Delsuc and coll.,

Café
diff --git a/biblio/17640763.mdwn b/biblio/17640763.mdwn
new file mode 100644
index 0000000..717b501
--- /dev/null
+++ b/biblio/17640763.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Mitogenomics reveals two cryptic species in Ciona intestinalis."]]
+[[!tag Ciona speciation]]
+
+Mitogenomics reveals two cryptic species in Ciona intestinalis.
+
+Trends Genet. 2007 Sep;23(9):419-22 doi:10.1016/j.tig.2007.07.001
+
+Iannelli F, Pesole G, Sordino P, Gissi C.
+
+[[!pmid 17640763 desc="Mitochondrial gene order differs between C. robusta and C. intestinalis."]]
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index 701f976..921821d 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -18,12 +18,13 @@ were F1 and of _C. int_ maternal origin.
 Comparison of mitochnodrial CO1 sequences show that _C. intestinalis_ types A
 and B (now renamed _robusta_ and _intestinalis sensu_) are as distant as
 distinct species ([[Nydam and Harrison,
-2007|biblio/10.1007_s00227-007-0617-0]]).  Sequencing of nuclear genes showed
-intragenic recombination in _C. robusta_ and _C. intestinalis_, buy supported
-monophyly of these two species.  Both data also supported paraphyly of
-_C. intestinalis_ with respcet to _C. roulei_ ([[Nydam and Harrison,
-2010|biblio/20403444]]).  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]]).
+2007|biblio/10.1007_s00227-007-0617-0]]).  Mitochondrial gene order differ
+between the two species ([[Ianelli and coll., 2007|biblio/17640763]]).
+Sequencing of nuclear genes showed intragenic recombination in _C. robusta_ and
+_C. intestinalis_, buy supported monophyly of these two species.  Both data
+also supported paraphyly of _C. intestinalis_ with respcet to _C. roulei_
+([[Nydam and Harrison, 2010|biblio/20403444]]).  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]]).
 
 [[!inline pages="tagged(Ciona)" actions="no" limit=0]]

Café
diff --git a/biblio/23564941.mdwn b/biblio/23564941.mdwn
new file mode 100644
index 0000000..cb3a790
--- /dev/null
+++ b/biblio/23564941.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Crossing the species barrier: genomic hotspots of introgression between two highly divergent Ciona intestinalis species."]]
+[[!tag Ciona speciation]]
+
+Mol Biol Evol. 2013 Jul;30(7):1574-87. doi:10.1093/molbev/mst066
+
+Roux C, Tsagkogeorga G, Bierne N, Galtier N.
+
+Crossing the species barrier: genomic hotspots of introgression between two highly divergent Ciona intestinalis species.
+
+[[!pmid 23564941 desc="Speciation during the Pliocene (≈ 3.8 Ma) and then recent introgression 15,000 years ago."]]
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index b2b5d74..701f976 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -22,6 +22,8 @@ distinct species ([[Nydam and Harrison,
 intragenic recombination in _C. robusta_ and _C. intestinalis_, buy supported
 monophyly of these two species.  Both data also supported paraphyly of
 _C. intestinalis_ with respcet to _C. roulei_ ([[Nydam and Harrison,
-2010|biblio/20403444]]).
+2010|biblio/20403444]]).  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]]).
 
 [[!inline pages="tagged(Ciona)" actions="no" limit=0]]

Markupdown
diff --git a/biblio/10.1007_978-3-642-78013-4_5.mdwn b/biblio/10.1007_978-3-642-78013-4_5.mdwn
index de6bf23..0cde9d0 100644
--- a/biblio/10.1007_978-3-642-78013-4_5.mdwn
+++ b/biblio/10.1007_978-3-642-78013-4_5.mdwn
@@ -3,7 +3,7 @@
 
 Olsson R.
 
-1993. Book chapter in Oksche A., Rodríguez E.M., Fernández-Llebrez P. (eds) The Subcommissural Organ. Springer, Berlin, Heidelberg. pp 33—39
+(1993). Book chapter in Oksche A., Rodríguez E.M., Fernández-Llebrez P. (eds) The Subcommissural Organ. Springer, Berlin, Heidelberg. pp 33—39
 
 Reissner’s Fiber Mechanisms: Some Common Denominators.
 

Café
diff --git a/biblio/10.1007_978-3-642-78013-4_5.mdwn b/biblio/10.1007_978-3-642-78013-4_5.mdwn
new file mode 100644
index 0000000..de6bf23
--- /dev/null
+++ b/biblio/10.1007_978-3-642-78013-4_5.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Reissner’s Fiber Mechanisms: Some Common Denominators."]]
+[[!tag Oikopleura review]]
+
+Olsson R.
+
+1993. Book chapter in Oksche A., Rodríguez E.M., Fernández-Llebrez P. (eds) The Subcommissural Organ. Springer, Berlin, Heidelberg. pp 33—39
+
+Reissner’s Fiber Mechanisms: Some Common Denominators.
+
+[[!doi 10.1007/978-3-642-78013-4_5 desc="Figure 2 panel 6 schematises Oikopleura's fibrogen cell."]]
diff --git a/biblio/10197783.mdwn b/biblio/10197783.mdwn
new file mode 100644
index 0000000..d756417
--- /dev/null
+++ b/biblio/10197783.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="SCO-spondin is evolutionarily conserved in the central nervous system of the chordate phylum."]]
+[[!tag Oikopleura]]
+
+Neuroscience. 1999 Jan;88(2):655-64 doi:10.1016/S0306-4522(98)00252-8
+
+Gobron S, Creveaux I, Meiniel R, Didier R, Dastugue B, Meiniel A.
+
+SCO-spondin is evolutionarily conserved in the central nervous system of the chordate phylum.
+
+[[!pmid 10197783 desc="A Southern blot suggests the presence of a gene encoding a SCO-spondin in Oikopleura."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 91ad3f9..60bf09a 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -147,7 +147,8 @@ 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]].
-
+ - Southern blot analysis suggest the presence of a SCO-spondin gene in _O.
+   dioica_ ([[Gobron and coll., 1999|biblio/10197783]]).
 
 Transcriptome
 -------------
@@ -235,6 +236,8 @@ Anatomy
  - Two subchordal cells are found in the haemocel of the tail.  Utrastructure analysis
    suggests the alternance of highly exocytic and highly endocytic states
    ([[Fredriksson and Olsson, 1991|biblio/10.1111_j.1463-6395.1991.tb01203.x]]).
+ - The tail's neural tube as a "fibrogen cell" at its anterior ends, which is
+   secreting the Reissner's fiber (reviewed in [[Olsson, 1993|biblio/10.1007_978-3-642-78013-4_5]]).
 
 Physiology
 ----------

Café
diff --git a/biblio/27662427.mdwn b/biblio/27662427.mdwn
new file mode 100644
index 0000000..c018ed9
--- /dev/null
+++ b/biblio/27662427.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Distinguishing contemporary hybridization from past introgression with postgenomic ancestry-informative SNPs in strongly differentiated Ciona species."]]
+[[!tag Ciona speciation]]
+
+Bouchemousse S, Liautard-Haag C, Bierne N, Viard F.
+
+Mol Ecol. 2016 Nov;25(21):5527-5542. doi:10.1111/mec.13854
+
+Distinguishing contemporary hybridization from past introgression with postgenomic ancestry-informative SNPs in strongly differentiated Ciona species.
+
+[[!pmid 27662427 desc="The only hybrids detected are F1 and have a C. int mitochondrial haplotype."]]
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index 3cf11b9..b2b5d74 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -11,7 +11,9 @@ Nishikawa and Bird, 2005|biblio/16205978]], [[Caputi and coll.,
 2007|biblio/17517633]], [[Malfant, Darras and Viart, 2018|biblio/29367599]]).
 Hybrids were infertile and a _C. rob_ - _C. int_ cross from two sympatric
 strains from Plymouth did not develop beyond cleavage ([[Caputi and coll.,
-2007|biblio/17517633]]).
+2007|biblio/17517633]]).  In line with this, the only hybdids found by the SNP
+analysis of wild animals of ([[Bouchemousse and coll., 2016|biblio/27662427]])
+were F1 and of _C. int_ maternal origin.
 
 Comparison of mitochnodrial CO1 sequences show that _C. intestinalis_ types A
 and B (now renamed _robusta_ and _intestinalis sensu_) are as distant as

Café
diff --git a/biblio/17517633.mdwn b/biblio/17517633.mdwn
new file mode 100644
index 0000000..afd511a
--- /dev/null
+++ b/biblio/17517633.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Cryptic speciation in a model invertebrate chordate."]]
+[[!tag Ciona speciation]]
+
+Caputi L, Andreakis N, Mastrototaro F, Cirino P, Vassillo M, Sordino P.
+
+Proc Natl Acad Sci U S A. 2007 May 29;104(22):9364-9 doi:10.1073/pnas.0610158104
+
+Cryptic speciation in a model invertebrate chordate.
+
+[[!pmid 17517633 desc="Only C. robusta female gametes could be fertilised by sperm from either C. rob or C. int.  Hybrids were infertile.  Allospecific crosses between two sympatric strains from Plymouth could not develop beyond a few cell cleavages."]]
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index 4485321..3cf11b9 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -7,8 +7,11 @@ estimated to have diverged 122 ± 33 million years ago ([[Delsuc and coll.,
 
 _Ciona robusta_'s sperm can efficiently fertilise _C. intestinalis_ eggs, but
 the fertilisation rates are much lower in the reciprocal crosses ([[Suzuki,
-Nishikawa and Bird, 2005|biblio/16205978]], [[Malfant, Darras and Viart,
-2018|biblio/29367599]]).
+Nishikawa and Bird, 2005|biblio/16205978]], [[Caputi and coll.,
+2007|biblio/17517633]], [[Malfant, Darras and Viart, 2018|biblio/29367599]]).
+Hybrids were infertile and a _C. rob_ - _C. int_ cross from two sympatric
+strains from Plymouth did not develop beyond cleavage ([[Caputi and coll.,
+2007|biblio/17517633]]).
 
 Comparison of mitochnodrial CO1 sequences show that _C. intestinalis_ types A
 and B (now renamed _robusta_ and _intestinalis sensu_) are as distant as

Café
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index fac3c3d..4485321 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -1,7 +1,9 @@
 [[!meta title="pages tagged Ciona"]]
 
 _C. intestinalis_ and _C. savignyi_ can cross-fertilise after removal of the
-vitelline enveloppe ([[Byrd and Lambert, 2000|biblio/10602281]]).
+vitelline enveloppe ([[Byrd and Lambert, 2000|biblio/10602281]]).  They are
+estimated to have diverged 122 ± 33 million years ago ([[Delsuc and coll.,
+2018|biblio/29653534]]).
 
 _Ciona robusta_'s sperm can efficiently fertilise _C. intestinalis_ eggs, but
 the fertilisation rates are much lower in the reciprocal crosses ([[Suzuki,

Too much café.
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index 20d50d4..fac3c3d 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -14,7 +14,7 @@ distinct species ([[Nydam and Harrison,
 2007|biblio/10.1007_s00227-007-0617-0]]).  Sequencing of nuclear genes showed
 intragenic recombination in _C. robusta_ and _C. intestinalis_, buy supported
 monophyly of these two species.  Both data also supported paraphyly of
-_C. intestinalis_ with respcet to _C. roulei" ([[Nydam and Harrison,
+_C. intestinalis_ with respcet to _C. roulei_ ([[Nydam and Harrison,
 2010|biblio/20403444]]).
 
 [[!inline pages="tagged(Ciona)" actions="no" limit=0]]

Café
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index 6d46602..20d50d4 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -13,8 +13,8 @@ and B (now renamed _robusta_ and _intestinalis sensu_) are as distant as
 distinct species ([[Nydam and Harrison,
 2007|biblio/10.1007_s00227-007-0617-0]]).  Sequencing of nuclear genes showed
 intragenic recombination in _C. robusta_ and _C. intestinalis_, buy supported
-monophyly of these two species.  Both data also supported paraphyly of C.
-intestinalis with respcet to Ciona roulei ([[Nydam and Harrison,
+monophyly of these two species.  Both data also supported paraphyly of
+_C. intestinalis_ with respcet to _C. roulei" ([[Nydam and Harrison,
 2010|biblio/20403444]]).
 
 [[!inline pages="tagged(Ciona)" actions="no" limit=0]]

Café
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index 1d4c265..6d46602 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -9,11 +9,12 @@ Nishikawa and Bird, 2005|biblio/16205978]], [[Malfant, Darras and Viart,
 2018|biblio/29367599]]).
 
 Comparison of mitochnodrial CO1 sequences show that _C. intestinalis_ types A
-and B (now renamed _robusta_ and _intestinalis sensu_ ) are as distant as
-distinc species [[Nydam and Harrison, 2007|biblio/10.1007_s00227-007-0617-0]].
-Sequencing of nuclear genes showed intragenic recombination in C. robusta and
-C. intestinalis, buy supported monophyly of these two species.  Both data also
-supported paraphyly of C. intestinalis with respcet to Ciona roulei ([[Nydam
-and Harrison, 2010|biblio/20403444]]).
+and B (now renamed _robusta_ and _intestinalis sensu_) are as distant as
+distinct species ([[Nydam and Harrison,
+2007|biblio/10.1007_s00227-007-0617-0]]).  Sequencing of nuclear genes showed
+intragenic recombination in _C. robusta_ and _C. intestinalis_, buy supported
+monophyly of these two species.  Both data also supported paraphyly of C.
+intestinalis with respcet to Ciona roulei ([[Nydam and Harrison,
+2010|biblio/20403444]]).
 
 [[!inline pages="tagged(Ciona)" actions="no" limit=0]]

Café
diff --git a/biblio/20403444.mdwn b/biblio/20403444.mdwn
new file mode 100644
index 0000000..0a029d8
--- /dev/null
+++ b/biblio/20403444.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Polymorphism and divergence within the ascidian genus Ciona."]]
+[[!tag Ciona speciation]]
+
+Mol Phylogenet Evol. 2010 Aug;56(2):718-26. doi:10.1016/j.ympev.2010.03.042
+
+Nydam ML and Harrison RG
+
+Polymorphism and divergence within the ascidian genus Ciona.
+
+[[!pmid 20403444 desc="Sequencing of nuclear genes show intragenic recombination in C. robusta and C. intestinalis, buy supports monophyly of these two species.  The data also supports paraphyly of C. intestinalis with respcet to Ciona roulei."]]
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index f186e49..1d4c265 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -11,5 +11,9 @@ Nishikawa and Bird, 2005|biblio/16205978]], [[Malfant, Darras and Viart,
 Comparison of mitochnodrial CO1 sequences show that _C. intestinalis_ types A
 and B (now renamed _robusta_ and _intestinalis sensu_ ) are as distant as
 distinc species [[Nydam and Harrison, 2007|biblio/10.1007_s00227-007-0617-0]].
+Sequencing of nuclear genes showed intragenic recombination in C. robusta and
+C. intestinalis, buy supported monophyly of these two species.  Both data also
+supported paraphyly of C. intestinalis with respcet to Ciona roulei ([[Nydam
+and Harrison, 2010|biblio/20403444]]).
 
 [[!inline pages="tagged(Ciona)" actions="no" limit=0]]

Café
diff --git a/biblio/10.1007_s00227-007-0617-0.mdwn b/biblio/10.1007_s00227-007-0617-0.mdwn
new file mode 100644
index 0000000..8783f14
--- /dev/null
+++ b/biblio/10.1007_s00227-007-0617-0.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genealogical relationships within and among shallow-water Ciona species (Ascidiacea)"]]
+[[!tag Ciona speciation]]
+
+Nydam ML and Harrison RG.
+
+Mar Biol (2007) 151: 1839. doi:10.1007/s00227-007-0617-0
+
+Genealogical relationships within and among shallow-water Ciona species (Ascidiacea)
+
+[[!doi 10.1007/s00227-007-0617-0 desc="Mitochondrial CO1 sequencing shows that Type A and B Ciona intestinalis are as distant as separate species."]]
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index 9c0d5b8..f186e49 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -1,11 +1,15 @@
 [[!meta title="pages tagged Ciona"]]
 
+_C. intestinalis_ and _C. savignyi_ can cross-fertilise after removal of the
+vitelline enveloppe ([[Byrd and Lambert, 2000|biblio/10602281]]).
+
 _Ciona robusta_'s sperm can efficiently fertilise _C. intestinalis_ eggs, but
-the fertilisation crosses are much lower in the reciprocal crosses ([[Suzuki,
+the fertilisation rates are much lower in the reciprocal crosses ([[Suzuki,
 Nishikawa and Bird, 2005|biblio/16205978]], [[Malfant, Darras and Viart,
 2018|biblio/29367599]]).
 
-_C. intestinalis_ and _C. savignyi_ can cross-fertilise after removal of the
-vitelline enveloppe ([[Byrd and Lambert, 2000|biblio/10602281]]).
+Comparison of mitochnodrial CO1 sequences show that _C. intestinalis_ types A
+and B (now renamed _robusta_ and _intestinalis sensu_ ) are as distant as
+distinc species [[Nydam and Harrison, 2007|biblio/10.1007_s00227-007-0617-0]].
 
 [[!inline pages="tagged(Ciona)" actions="no" limit=0]]

Café
diff --git a/biblio/10602281.mdwn b/biblio/10602281.mdwn
index 72badfd..1fb4eab 100644
--- a/biblio/10602281.mdwn
+++ b/biblio/10602281.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Mechanism of the block to hybridization and selfing between the sympatric ascidians Ciona intestinalis and Ciona savignyi."]]
-[[!tag tunicate speciation]]
+[[!tag Ciona speciation]]
 
 Mol Reprod Dev. 2000 Jan;55(1):109-16 doi:10.1002/(SICI)1098-2795(200001)55:1%3C109::AID-MRD15%3E3.0.CO;2-B
 
diff --git a/biblio/16205978.mdwn b/biblio/16205978.mdwn
new file mode 100644
index 0000000..3e72651
--- /dev/null
+++ b/biblio/16205978.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Genomic approaches reveal unexpected genetic divergence within Ciona intestinalis."]]
+[[!tag Ciona speciation]]
+
+Suzuki MM, Nishikawa T and Bird A.
+
+J Mol Evol. 2005 Nov;61(5):627-35. Epub 2005 Oct 4.
+
+Genomic approaches reveal unexpected genetic divergence within Ciona intestinalis.
+
+[[!pmid 16205978 desc="C. robusta sperm can fertilise C. intestinalis eggs.  In 3 reciprocal crosses, C. int sperm was less efficient (40~70%) and in 2 crosses, it was ver inefficient (~5 %).  Hybrids developed to young adults in laboratory.  Reproductive isolation estimated to have started 30 MY ago.  Ideal temperature for breeding differs of 5 °C."]]
diff --git a/biblio/29367599.mdwn b/biblio/29367599.mdwn
index 3359e4d..e1868b7 100644
--- a/biblio/29367599.mdwn
+++ b/biblio/29367599.mdwn
@@ -7,4 +7,7 @@ Malfant M, Darras S and Viard F.
 
 Coupling molecular data and experimental crosses sheds light about species delineation: a case study with the genus Ciona.
 
-[[!pmid 29367599 desc="C. robusta sperm can fertilise C. intestinalis eggs, but not the converse.  Phylogenetic analysis of mitochondrial CO1 sequences suggests that there are no hybrids in wild populations."]]
+[[!pmid 29367599 desc="C. robusta sperm can fertilise C. intestinalis eggs, but
+fertilisation rates in the converse crosses are much lower.  Phylogenetic
+analysis of mitochondrial CO1 sequences suggests that there are no hybrids in
+wild populations."]]
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
index d903408..9c0d5b8 100644
--- a/tags/Ciona.mdwn
+++ b/tags/Ciona.mdwn
@@ -1,4 +1,11 @@
 [[!meta title="pages tagged Ciona"]]
 
-[[!inline pages="tagged(Ciona)" actions="no" archive="yes"
-feedshow=10]]
+_Ciona robusta_'s sperm can efficiently fertilise _C. intestinalis_ eggs, but
+the fertilisation crosses are much lower in the reciprocal crosses ([[Suzuki,
+Nishikawa and Bird, 2005|biblio/16205978]], [[Malfant, Darras and Viart,
+2018|biblio/29367599]]).
+
+_C. intestinalis_ and _C. savignyi_ can cross-fertilise after removal of the
+vitelline enveloppe ([[Byrd and Lambert, 2000|biblio/10602281]]).
+
+[[!inline pages="tagged(Ciona)" actions="no" limit=0]]

Normalise tags.
diff --git a/biblio/14722352.mdwn b/biblio/14722352.mdwn
index f8f60e5..652f911 100644
--- a/biblio/14722352.mdwn
+++ b/biblio/14722352.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="A functional cellulose synthase from ascidian epidermis."]]
-[[!tag Ciona_intestinalis trans-splicing cellulose]]
+[[!tag Ciona trans-splicing cellulose]]
 
 Matthysse AG, Deschet K, Williams M, Marry M, White AR, Smith WC.
 
diff --git a/biblio/16822859.mdwn b/biblio/16822859.mdwn
index 651deb5..757b533 100644
--- a/biblio/16822859.mdwn
+++ b/biblio/16822859.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Genomic overview of mRNA 5'-leader trans-splicing in the ascidian Ciona intestinalis."]]
-[[!tag trans-splicing Ciona_intestinalis]]
+[[!tag trans-splicing Ciona]]
 
 Nucleic Acids Res. 2006 Jul 5;34(11):3378-88 doi:10.1093/nar/gkl418
 
diff --git a/biblio/26668163.mdwn b/biblio/26668163.mdwn
index 873c1b0..9917e4f 100644
--- a/biblio/26668163.mdwn
+++ b/biblio/26668163.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Genome-wide identification and characterization of transcription start sites and promoters in the tunicate Ciona intestinalis."]]
-[[!tag Ciona_intestinalis oligo-capping trans-splicing]]
+[[!tag Ciona oligo-capping trans-splicing]]
 
 Yokomori R, Shimai K, Nishitsuji K, Suzuki Y, Kusakabe TG, Nakai K.
 
diff --git a/biblio/30228204.mdwn b/biblio/30228204.mdwn
index 079e2f1..e590f34 100644
--- a/biblio/30228204.mdwn
+++ b/biblio/30228204.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Regulatory cocktail for dopaminergic neurons in a protovertebrate identified by whole-embryo single-cell transcriptomics."]]
-[[!tag single_cell Ciona_intestinalis]]
+[[!tag single_cell Ciona]]
 
 Genes Dev. 2018 Sep 18. doi:10.1101/gad.317669.118
 
diff --git a/tags/Ciona_intestinalis.mdwn b/tags/Ciona_intestinalis.mdwn
deleted file mode 100644
index 84c7dee..0000000
--- a/tags/Ciona_intestinalis.mdwn
+++ /dev/null
@@ -1,4 +0,0 @@
-[[!meta title="pages tagged Ciona intestinalis"]]
-
-[[!inline pages="tagged(Ciona_intestinalis)" actions="no" archive="yes"
-feedshow=10]]

Café
diff --git a/biblio/29367599.mdwn b/biblio/29367599.mdwn
new file mode 100644
index 0000000..3359e4d
--- /dev/null
+++ b/biblio/29367599.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Coupling molecular data and experimental crosses sheds light about species delineation: a case study with the genus Ciona."]]
+[[!tag speciation Ciona]]
+
+Sci Rep. 2018 Jan 24;8(1):1480. doi:10.1038/s41598-018-19811-2
+
+Malfant M, Darras S and Viard F.
+
+Coupling molecular data and experimental crosses sheds light about species delineation: a case study with the genus Ciona.
+
+[[!pmid 29367599 desc="C. robusta sperm can fertilise C. intestinalis eggs, but not the converse.  Phylogenetic analysis of mitochondrial CO1 sequences suggests that there are no hybrids in wild populations."]]

creating tag page tags/speciation
diff --git a/tags/speciation.mdwn b/tags/speciation.mdwn
new file mode 100644
index 0000000..240b8e8
--- /dev/null
+++ b/tags/speciation.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged speciation"]]
+
+[[!inline pages="tagged(speciation)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/10602281.mdwn b/biblio/10602281.mdwn
new file mode 100644
index 0000000..72badfd
--- /dev/null
+++ b/biblio/10602281.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Mechanism of the block to hybridization and selfing between the sympatric ascidians Ciona intestinalis and Ciona savignyi."]]
+[[!tag tunicate speciation]]
+
+Mol Reprod Dev. 2000 Jan;55(1):109-16 doi:10.1002/(SICI)1098-2795(200001)55:1%3C109::AID-MRD15%3E3.0.CO;2-B
+
+Byrd J and Lambert CC.
+
+Mechanism of the block to hybridization and selfing between the sympatric ascidians Ciona intestinalis and Ciona savignyi.
+
+[[!pmid 10602281 desc="C. intestinalis and C. savignyi can cross-fertilise after removal of the vitelline enveloppe."]]

RT specificity
diff --git a/biblio/30573814.mdwn b/biblio/30573814.mdwn
new file mode 100644
index 0000000..c7bbe4b
--- /dev/null
+++ b/biblio/30573814.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Detection of splice isoforms and rare intermediates using multiplexed primer extension sequencing."]]
+[[!tag reverse_transcription method]]
+
+Nat Methods. 2019 Jan;16(1):55-58. doi:10.1038/s41592-018-0258-x
+
+Xu H, Fair BJ, Dwyer ZW, Gildea M, Pleiss JA.
+
+Detection of splice isoforms and rare intermediates using multiplexed primer extension sequencing.
+
+[[!pmid 30573814 desc="Specificity of RT priming can be increased by increasing temperature from 47 °C to 55 °C."]]

Specificity of RT priming at higher temperatures.
diff --git a/tags/reverse_transcription.mdwn b/tags/reverse_transcription.mdwn
index 9e31aa1..c73e930 100644
--- a/tags/reverse_transcription.mdwn
+++ b/tags/reverse_transcription.mdwn
@@ -89,6 +89,9 @@ nucleotide as a template.
  - Reported by [[Mizuno et al., 1999|biblio/9973624]].
  - Utilised in [[Arnaud et al., 2016|biblio/27071605]] to reduce priming or
    ribosomal or hemoglobin RNA.
+ - Specificity of RT nevertheless increases with reaction temperature.  For
+   instance, [[Xu and coll., 2019|biblio/30573814]] increased it from
+   ~30 % at 47 °C to ~75 % at 55 °C.
 
 ### Reverse-transcription primers
 

Bathochordaeus charon isolate D449ss10 18S ribosomal RNA gene, partial sequence
diff --git a/biblio/10.1186_s41200-016-0075-9.mdwn b/biblio/10.1186_s41200-016-0075-9.mdwn
index b1f373e..665b07f 100644
--- a/biblio/10.1186_s41200-016-0075-9.mdwn
+++ b/biblio/10.1186_s41200-016-0075-9.mdwn
@@ -7,4 +7,4 @@ Marine Biodiversity Records 2016 9:79 doi:10.1186/s41200-016-0075-9
 
 The first definitive record of the giant larvacean, _Bathochordaeus charon_, since its original description in 1900 and a range extension to the northeast Pacific Ocean
 
-[[!doi 10.1186/s41200-016-0075-9 desc="“In over two decades of exploring the mesopelagic waters of Monterey Bay, CA, remarkably few Bathochordaeus charon (n = 15) were observed, while thousands of B. stygius have been encountered.”"]]
+[[!doi 10.1186/s41200-016-0075-9 desc="“In over two decades of exploring the mesopelagic waters of Monterey Bay, CA, remarkably few Bathochordaeus charon (n = 15) were observed, while thousands of B. stygius have been encountered.” Accession number for 18S rRNA: KT881545"]]

Café
diff --git a/biblio/18612321.mdwn b/biblio/18612321.mdwn
new file mode 100644
index 0000000..27a5974
--- /dev/null
+++ b/biblio/18612321.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species."]]
+[[!tag review tunicate mitochondrion]]
+
+Heredity (Edinb). 2008 Oct;101(4):301-20. doi:10.1038/hdy.2008.62
+
+Gissi C, Iannelli F, Pesole G.
+
+Evolution of the mitochondrial genome of Metazoa as exemplified by comparison of congeneric species.
+
+[[!pmid 18612321 desc="Mitochondrial genomes of tunicates have all genes colinear on the same strand, and usually encode 24 tRNAs (instead of 22 in vertebrates).  Their rRNA genes are separated."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index d1feecc..91ad3f9 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -80,7 +80,9 @@ Genome
  - Only a partial mitochondrial genome was reconstituted in [[Denoeud et al.,
    2010|biblio/21097902]], due to cloning and sequencing difficulties that may
    have been caused by oligo-dT stretches.  A/T-rich codons are more frequent than
-   in human.
+   in human.  In other tunicates, all mitochondrial genes are on the same DNA strand
+   and 24 tRNAs are present, instead of 22 in other chordates (reviewed by [[Gissi and coll.,
+   2008|biblio/18612321]]).
  - Analysis of sex-linked markers supports genetic sex determination with male heterogamety –
    that is: X chromosomes for females and Y for males.  ([[Denoeud et al., 2010|biblio/21097902]])
  - The minor spliceosome could not be found in _Oikopleura_'s genome ([[Martz

Cystein
diff --git a/biblio/22120064.mdwn b/biblio/22120064.mdwn
new file mode 100644
index 0000000..0c8ed12
--- /dev/null
+++ b/biblio/22120064.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Peculiar patterns of amino acid substitution and conservation in the fast evolving tunicate Oikopleura dioica."]]
+[[!tag Oikopleura]]
+
+Berná L, D'Onofrio G, Alvarez-Valin F.
+
+Mol Phylogenet Evol. 2012 Feb;62(2):708-17. doi:10.1016/j.ympev.2011.11.013
+
+Peculiar patterns of amino acid substitution and conservation in the fast evolving tunicate Oikopleura dioica.
+
+[[!pmid 22120064 desc="Faster evolution for regulatory genes.  High and even mutation rates for every aminoacid suggest a relaxation of functional constraints.  This is particularly surpising for cystein, which is highly conserved in other fast-evolving species such as Ciona.  The frequency of C is reduced of 10% compared with Ciona."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 3087f6a..d1feecc 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -110,6 +110,9 @@ Genome
  - Transcriptome comparisons between Atlantic and Pacific strains showed
    nucleotide and amino acid sequence similarities of 91.0 and 94.8 %,
    respectively ([[Wang and coll., 2015|biblio/26032664]]).
+ - Regulatory genes evolve faster.  All aminoacids, including cystein, show reduced
+   conservation, suggesting relaxation of functional constraints.  Compared with
+   Ciona, 10% of the cysteins are lost ([[Berná and coll., 2012|biblio/22120064]]).
 
 
 Genes and pathways

creating tag page tags/Ciona
diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn
new file mode 100644
index 0000000..d903408
--- /dev/null
+++ b/tags/Ciona.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged Ciona"]]
+
+[[!inline pages="tagged(Ciona)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/25008364.mdwn b/biblio/25008364.mdwn
new file mode 100644
index 0000000..7532b59
--- /dev/null
+++ b/biblio/25008364.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Evolutionary genomics of fast evolving tunicates."]]
+[[!tag Oikopleura Ciona genome]]
+
+Berná L and Alvarez-Valin F.
+
+Genome Biol Evol. 2014 Jul 8;6(7):1724-38. doi:10.1093/gbe/evu122
+
+Evolutionary genomics of fast evolving tunicates.
+
+[[!pmid 25008364 desc="Parallel review about genome compaction in Ciona and Oikopleura."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 055f33b..3087f6a 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -69,6 +69,8 @@ Genome
    indistinguishable from random for distances smaller than 30 genes and a modest
    level of conserved synteny at larger distances.” ([[Denoeud et al.,
    2010|biblio/21097902]])
+ - Genome compaction in _Oikopleura_ and _Ciona_ have been reviewed in parallel
+   by [[Berná and Alvarez-Valin (2014)|biblio/25008364]].
  - Chromatin domains are rarely longer than 7 nucleosomes ([[Navratilova et al., 2017|biblio/28115992]]).
  - Some 5-methylcytosine was detected by MeDIP-chip by ([[Navratilova et al., 2017|biblio/28115992]]).
  - The entire machinery required for performing classical NHEJ repair of DSB (which is

creating tag page tags/tunicate
diff --git a/tags/tunicate.mdwn b/tags/tunicate.mdwn
new file mode 100644
index 0000000..428204c
--- /dev/null
+++ b/tags/tunicate.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged tunicate"]]
+
+[[!inline pages="tagged(tunicate)" actions="no" archive="yes"
+feedshow=10]]

Mot-clé
diff --git a/biblio/29615780.mdwn b/biblio/29615780.mdwn
index c0092c7..4c79ae1 100644
--- a/biblio/29615780.mdwn
+++ b/biblio/29615780.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution."]]
-[[!tag evolution genome]]
+[[!tag tunicate evolution genome]]
 
 Blanchoud S, Rutherford K, Zondag L, Gemmell NJ, Wilson MJ.
 

Café
diff --git a/biblio/10.1002_lno.10395.mdwn b/biblio/10.1002_lno.10395.mdwn
new file mode 100644
index 0000000..39f291b
--- /dev/null
+++ b/biblio/10.1002_lno.10395.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Comparative metatranscriptomics reveals decline of a neustonic planktonic population"]]
+[[!tag Oikopleura]]
+
+N. Mojib, M. Thimma, M. Kumaran, R. Sougrat and X. Irigoien
+
+Limnology and Oceanography. Volume 62, Issue 1, January 2017, Pages 299-310
+
+Comparative metatranscriptomics reveals decline of a neustonic planktonic population
+
+[[!doi 10.1002/lno.10395  desc="Decrease of appendicularians and copeopds during a Trichodesmium in the Red sea in 2012."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index fcea99a..055f33b 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -294,6 +294,8 @@ Ecology
    more abundant in slope waters, compared with Kuroshio and subtropical
    waters, on the Pacific side of the Japan coast ([[Hidaka,
    2008|biblio/10.3800_pbr.3.152]]).
+ - Meta-transcriptomic analysis in the Red sea showed a decrease of appendicularians during
+   a Trichodesmium bloom in 2012 ([[Mojib and coll., 2017|biblio/10.1002_lno.10395]]).
  - As of August 2018, _O. dioica_ is not yet found in the [BOLD](http://www.boldsystems.org/)
    database of DNA barcodes.
  - Carbon output of _O. dioica_ is either their house or fecal pellets, the

Ragout 1.
diff --git a/biblio/24931998.mdwn b/biblio/24931998.mdwn
new file mode 100644
index 0000000..360c2cd
--- /dev/null
+++ b/biblio/24931998.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Ragout-a reference-assisted assembly tool for bacterial genomes."]]
+[[!tag genome assembly chromosome software method]]
+
+Bioinformatics. 2014 Jun 15;30(12):i302-9. doi:10.1093/bioinformatics/btu280
+
+Kolmogorov M, Raney B, Paten B, Pham S.
+
+Ragout-a reference-assisted assembly tool for bacterial genomes.
+
+[[!pmid 24931998 desc="Can accept multiple reference genomes.  Decomposes refernces and target in synteny blocks and assemble them in a graph."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 9020cbe..c0b2a60 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -9,11 +9,12 @@ for the comparison of multiple Nanopore runs on the same plot, to assess if
 read length is satisfactory.
 
 When coverage is too low for efficient reference-free assembly, related
-references can be used as a guide.  The Ragout 2 software ([[Kolmogorov and
-coll., 2018|biblio/30341161]]) can take multiple reference genomes as input and
-automatically infers phylogenetic relationship between them.  Polymorphisms
-unique to the target genome can be recovered, but chromosome fusions are
-typically hard to detect.
+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.
 
 The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a
 diploid assembly and outputs a reference and an alternative sub-assembly for

Ragout 2.
diff --git a/biblio/30341161.mdwn b/biblio/30341161.mdwn
new file mode 100644
index 0000000..6ea6945
--- /dev/null
+++ b/biblio/30341161.mdwn
@@ -0,0 +1,11 @@
+[[!meta title="Chromosome assembly of large and complex genomes using multiple references."]]
+[[!tag genome chromosome assembly software method]]
+
+Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D,
+Flicek P, Keane TM, Thybert D, Paten B, Pham S.
+
+Genome Res. 2018 Nov;28(11):1720-1732. doi:10.1101/gr.236273.118
+
+Chromosome assembly of large and complex genomes using multiple references.
+
+[[!pmid 30341161 desc="Ragout 2 can take multiple reference genomes as input and automatically infers phylogenetic relationship between them.  Polymorphisms unique to the target genome can be recovered, but chromosome fusions are typically hard to detect."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 5e269c6..9020cbe 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -8,6 +8,13 @@ Prior assembly, MinIONQC ([[Lanfear and coll., 2018|biblio/30052755]]) allows
 for the comparison of multiple Nanopore runs on the same plot, to assess if
 read length is satisfactory.
 
+When coverage is too low for efficient reference-free assembly, related
+references can be used as a guide.  The Ragout 2 software ([[Kolmogorov and
+coll., 2018|biblio/30341161]]) can take multiple reference genomes as input and
+automatically infers phylogenetic relationship between them.  Polymorphisms
+unique to the target genome can be recovered, but chromosome fusions are
+typically hard to detect.
+
 The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a
 diploid assembly and outputs a reference and an alternative sub-assembly for
 each haplotype.  However, they are not phased: “_If only one allele is

Café
diff --git a/biblio/10.3800_pbr.3.152.mdwn b/biblio/10.3800_pbr.3.152.mdwn
new file mode 100644
index 0000000..4038201
--- /dev/null
+++ b/biblio/10.3800_pbr.3.152.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Species composition and horizontal distribution of the appendicularian community in waters adjacent to the Kuroshio in winter–early spring"]]
+[[!tag Oikopleura]]
+
+Kiyotaka Hidaka
+
+Plankton and Benthos Research 2008 Volume 3 Issue 3 Pages 152-164
+
+Species composition and horizontal distribution of the appendicularian community in waters adjacent to the Kuroshio in winter–early spring
+
+[[!pmid 10.3800/pbr.3.152 desc="In 1972, 1976, 1977, 1978, 1982 or 1986, O. dioica was rare but relatively more abuntant in slope waters, which are colder (~15—17°C) as opposed to oceanic area Kuroshio (18.5–20.0°C) or subtropical waters (similar temperatures as Kuroshio)."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index dc1b33b..fcea99a 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -290,6 +290,10 @@ Ecology
  - _O. dioica_ was found all year in the Fukuyama harbour, Japan in 1986—7
    [[Uye and Ichino, 1995|biblio/10.1016_0022-0981_95_00004-B]]).  Mature stages were also
    found all year, and trunk length was shorter in summer.
+ - In 1972, 1976, 1977, 1978, 1982 or 1986, _O. dioica_ was rare but relatively
+   more abundant in slope waters, compared with Kuroshio and subtropical
+   waters, on the Pacific side of the Japan coast ([[Hidaka,
+   2008|biblio/10.3800_pbr.3.152]]).
  - As of August 2018, _O. dioica_ is not yet found in the [BOLD](http://www.boldsystems.org/)
    database of DNA barcodes.
  - Carbon output of _O. dioica_ is either their house or fecal pellets, the

Café
diff --git a/biblio/10.1016_0022-0981_95_00004-B.mdwn b/biblio/10.1016_0022-0981_95_00004-B.mdwn
new file mode 100644
index 0000000..a3598a3
--- /dev/null
+++ b/biblio/10.1016_0022-0981_95_00004-B.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Seasonal variations in abundance, size composition, biomass and production rate of Oikopleura dioica (Fol) (Tunicata: Appendicularia) in a temperate eutrophic inlet"]]
+[[!tag Oikopleura]]
+
+Journal of Experimental Marine Biology and Ecology Volume 189, Issues 1–2, 28 June 1995, Pages 1-11
+
+Shin-ichi Uye and Seiko Ichino
+
+Seasonal variations in abundance, size composition, biomass and production rate of Oikopleura dioica (Fol) (Tunicata: Appendicularia) in a temperate eutrophic inlet
+
+[[!doi 10.1016/0022-0981(95)00004-B desc="Reproduction all year (mature stages detected in winter).  Trunk length higher in winter than in summer."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index ba045e7..dc1b33b 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -287,6 +287,9 @@ Ecology
    population size” ([[Denoeud et al., 2010|biblio/21097902]], according to a study
    of silent and non-silent substitution rates in coding sequences).
  - It was already reported to be frequent in Japanese waters [[in 1907 by T. Aida|biblio/AA0069577]].
+ - _O. dioica_ was found all year in the Fukuyama harbour, Japan in 1986—7
+   [[Uye and Ichino, 1995|biblio/10.1016_0022-0981_95_00004-B]]).  Mature stages were also
+   found all year, and trunk length was shorter in summer.
  - As of August 2018, _O. dioica_ is not yet found in the [BOLD](http://www.boldsystems.org/)
    database of DNA barcodes.
  - Carbon output of _O. dioica_ is either their house or fecal pellets, the

Cellulose café
diff --git a/biblio/14722352.mdwn b/biblio/14722352.mdwn
new file mode 100644
index 0000000..f8f60e5
--- /dev/null
+++ b/biblio/14722352.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A functional cellulose synthase from ascidian epidermis."]]
+[[!tag Ciona_intestinalis trans-splicing cellulose]]
+
+Matthysse AG, Deschet K, Williams M, Marry M, White AR, Smith WC.
+
+A functional cellulose synthase from ascidian epidermis.
+
+Proc Natl Acad Sci U S A. 2004 Jan 27;101(4):986-91.
+
+[[!pmid 14722352 desc="The CesA mRNA is trans-spliced in Ciona intestinalis."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 1f04403..ba045e7 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -118,10 +118,12 @@ Genes and pathways
  - ~80 "house proteins" have been identified and more than half lack similarity
    to known proteins ([[Hosp et al., 2012|biblio/22792236]]).
  - 2 cellulose synthase genes, possibly acquired by horizontal gene transfer
-   from an actinobacteria([[Nakashima and coll., 2004|biblio/14740209]]), were
+   from an actinobacteria ([[Nakashima and coll., 2004|biblio/14740209]]), were
    found by [[Sagane et al. (2010)|biblio/20335363]] and [[Nakashima et al.
    (2011)|biblio/20972815]].  They are used to produce different crystalline forms
-   of cellulose ([[Nakashima et al., 2011|biblio/20972815]]).
+   of cellulose ([[Nakashima et al., 2011|biblio/20972815]]).  The CesA gene
+   is trans-spliced in the ascidian _Ciona 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_ only has the Dnmt2 methyltransferase, and lacks Dnmt1 and Dnmt3.

trans-splicing and café
diff --git a/biblio/11159910.mdwn b/biblio/11159910.mdwn
new file mode 100644
index 0000000..a3cec3a
--- /dev/null
+++ b/biblio/11159910.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="mRNA 5'-leader trans-splicing in the chordates."]]
+[[!tag trans-splicing]]
+
+Vandenberghe AE, Meedel TH, Hastings KE.
+
+mRNA 5'-leader trans-splicing in the chordates.
+
+Genes Dev. 2001 Feb 1;15(3):294-303.
+
+[[!pmid 11159910 desc="Discovery of trans-splicing in Tunicates."]]
diff --git a/tags/trans-splicing.mdwn b/tags/trans-splicing.mdwn
index 31411ab..6acdd07 100644
--- a/tags/trans-splicing.mdwn
+++ b/tags/trans-splicing.mdwn
@@ -1,5 +1,7 @@
 [[!meta title="pages tagged trans-splicing"]]
 
+Trans-splicing was discovered in tunicates by [[Vandenberghe, Meedel and Hastings, 2001|biblio/11159910]].
+
 The splice leader is 16-nt in C. intestinalis ([[Satou et al, 2006|biblio/16822859]]) and 40-nt in O. dioica ([[Ganot et al., 2004|biblio/15314184]]).
 
 [[!inline pages="tagged(trans-splicing)" actions="no" limit=0]]

creating tag page tags/cellulose
diff --git a/tags/cellulose.mdwn b/tags/cellulose.mdwn
new file mode 100644
index 0000000..b6209c3
--- /dev/null
+++ b/tags/cellulose.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged cellulose"]]
+
+[[!inline pages="tagged(cellulose)" actions="no" archive="yes"
+feedshow=10]]

Cellulose café
diff --git a/biblio/14740209.mdwn b/biblio/14740209.mdwn
new file mode 100644
index 0000000..f9b97a1
--- /dev/null
+++ b/biblio/14740209.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The evolutionary origin of animal cellulose synthase."]]
+[[!tag Oikopleura cellulose]]
+
+Nakashima K, Yamada L, Satou Y, Azuma J, Satoh N.
+
+Dev Genes Evol. 2004 Feb;214(2):81-8.
+
+The evolutionary origin of animal cellulose synthase.
+
+[[!pmid 14740209 desc="The cellulose synthase genes in Tunicates are thought to be of actinobacterial origin, because the tunicate CesA gene contains two domains with similarity with a cellulose synthase and a cellulase of the glycoside hydrolase (GH)-6 family, and these genes are often found in proximity in actinobacteria."]]
diff --git a/biblio/20335363.mdwn b/biblio/20335363.mdwn
index afde758..3ea8aa2 100644
--- a/biblio/20335363.mdwn
+++ b/biblio/20335363.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="Functional specialization of cellulose synthase genes of prokaryotic origin in chordate larvaceans."]]
-[[!tag Oikopleura]]
+[[!tag Oikopleura cellulose]]
 
 Development. 2010 May;137(9):1483-92. doi:10.1242/dev.044503
 
diff --git a/biblio/20972815.mdwn b/biblio/20972815.mdwn
index 9f2f695..791f61e 100644
--- a/biblio/20972815.mdwn
+++ b/biblio/20972815.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="The crystalline phase of cellulose changes under developmental control in a marine chordate."]]
-[[!tag Oikopleura]]
+[[!tag Oikopleura cellulose]]
 
 Cell Mol Life Sci. 2011 May;68(9):1623-31. doi:10.1007/s00018-010-0556-7
 
diff --git a/biblio/22792236.mdwn b/biblio/22792236.mdwn
index a9e7c5f..8f579b7 100644
--- a/biblio/22792236.mdwn
+++ b/biblio/22792236.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="The evolving proteome of a complex extracellular matrix, the Oikopleura house."]]
-[[!tag Oikopleura]]
+[[!tag Oikopleura cellulose]]
 
 PLoS One. 2012;7(7):e40172. doi:10.1371/journal.pone.0040172
 
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 9702849..1f04403 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -117,9 +117,11 @@ Genes and pathways
 
  - ~80 "house proteins" have been identified and more than half lack similarity
    to known proteins ([[Hosp et al., 2012|biblio/22792236]]).
- - 2 cellulose synthase genes were found by [[Sagane et al. (2010)|biblio/20335363]]
-   and [[Nakashima et al. (2011)|biblio/20972815]].  They are used to produce different
-   crystalline forms of cellulose ([[Nakashima et al., 2011|biblio/20972815]]).
+ - 2 cellulose synthase genes, possibly acquired by horizontal gene transfer
+   from an actinobacteria([[Nakashima and coll., 2004|biblio/14740209]]), were
+   found by [[Sagane et al. (2010)|biblio/20335363]] and [[Nakashima et al.
+   (2011)|biblio/20972815]].  They are used to produce different crystalline forms
+   of cellulose ([[Nakashima et al., 2011|biblio/20972815]]).
  - _O. dioica_ has multiple CDK1 and Cyclin B paraplogs, some of which are
    implicated in oogenesis ([[Feng & Thompson, 2018|biblio/29969934]]).
  - _O. dioica_ only has the Dnmt2 methyltransferase, and lacks Dnmt1 and Dnmt3.

Café
diff --git a/biblio/26032664.mdwn b/biblio/26032664.mdwn
new file mode 100644
index 0000000..3f38d16
--- /dev/null
+++ b/biblio/26032664.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: novel protein-encoding genes, intra-species sequence variations, and trans-spliced RNA leader."]]
+[[!tag Oikopleura trans-splicing]]
+
+Wang K, Omotezako T, Kishi K, Nishida H, Onuma TA.
+
+Dev Genes Evol. 2015 Jun;225(3):149-59. doi:10.1007/s00427-015-0502-7
+
+Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: novel protein-encoding genes, intra-species sequence variations, and trans-spliced RNA leader.
+
+[[!pmid 26032664 desc="Only one splice leader was found and it was identical to the one reported by Ganot. “Samples were prepared from cohorts of a single pair.” “The transcript sequences showed a high degree of variability between the Japanese and Norwegian O. dioica populations. The average degrees of nucleotide and amino acid sequence conservation were 91.0 and 94.8 %, respectively.” “In the present analysis, the SL was observed in 40.8 % of mRNA species. It showed preferential linkage to adenine at the 5′ ends of the downstream exons. Intriguingly, the trans-splicing occurs more frequently in eggs than in larvae.” “Among the 12,311 assembled transcripts, 63 and 99 % were detected in eggs and larvae, respectively. Thus, the mRNAs of most of genes are present at the developing larval stage. In this quick developer, it is most probable that residual maternal mRNAs are still preserved in 8 hpf larvae.” “The raw data were deposited in the National Center for Biotechnology Information (NCBI) Short Read Archive (SRP accession number: SRP050571, run accession numbers are SRR1693762, SRR1693765, SRR1693766, and SRR1693767) and Gene Expression Omnibus (GEO accession: GSE64421).”"]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 9eca5a9..9702849 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -105,6 +105,9 @@ Genome
    “Spots of sequence ultraconservation are almost systematically located
    in non coding regions, including introns that are larger than average
    in such genes than in others.” ([[Denoeud et al., 2010|biblio/21097902]]).
+ - Transcriptome comparisons between Atlantic and Pacific strains showed
+   nucleotide and amino acid sequence similarities of 91.0 and 94.8 %,
+   respectively ([[Wang and coll., 2015|biblio/26032664]]).
 
 
 Genes and pathways
@@ -134,6 +137,7 @@ Genes and pathways
    ([[Torres-Águila and coll., 2018|biblio/30272001]]).
  - _O. dioica_ has 83 homeobox genes, according to [[Edvardsen and coll., 2005|biblio/15649342]].
 
+
 Transcriptome
 -------------
 
@@ -142,8 +146,12 @@ Transcriptome
    The SL gene is found downstream of the 5S RNA gene, which is repeated multiple
    times in the genome.  The 3′ acceptor site has a strong UUU(C/U/A)AG consensus
    ([[Ganot et al., 2004|biblio/15314184]]).
+ - The splice leader found in the Norwegian strain by ([[Ganot et al., 2004|biblio/15314184]])
+   was found indentical in a Japanese strain by ([[Wang and coll., 2015|biblio/26032664]]).
  - A study using CAGE found that 39% of annotated gene models are trans-spliced with the
    SL and that 42% of SL transcripts are monocistronic ([[Danks et al., 2015|biblio/25525214]]).
+ - Embryonic RNAs are more trans-spliced than larval RNAs ([[Danks et al., 2015|biblio/25525214]],
+   [[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]]).
  - Introns are very small (peak at 47 base pairs, 2.4% > 1 kb, [[Denoeud et

Merge branch 'master' of ssh://charles-plessy-org.branchable.com
Café
diff --git a/biblio/10.1007_978-1-4020-8278-8_41.mdwn b/biblio/10.1007_978-1-4020-8278-8_41.mdwn
new file mode 100644
index 0000000..5aa5d51
--- /dev/null
+++ b/biblio/10.1007_978-1-4020-8278-8_41.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Appendicularians (Urochordata)"]]
+[[!tag Oikopleura]]
+
+Castellanos I.A., Morales-Ramírez Á., Suárez-Morales E.
+
+In: Wehrtmann I.S., Cortés J. (eds) Marine Biodiversity of Costa Rica, Central America. Monographiae Biologicae, vol 86. Springer, Dordrecht
+
+Appendicularians (Urochordata)
+
+[[!doi 10.1007/978-1-4020-8278-8_41 desc="O. dioica not reported in Costa Rica, but presence considered plausible."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 172e1aa..cc4587c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -286,5 +286,8 @@ Ecology
  - _O. dioica_ can filter, ingest and defecate the _Emiliania huxleyi_ virus
    ([[Lawrence and coll., 2017|biblio/10.1002_lno.10734]]).  This study does not assess
    whether the viruses are digested.
+ - While _O. dioica_ was not reported on the atlantic and pacific coasts of Costa Rica, its
+   presence is considered plausible ([[Castellanos, Morales-Ramírez and Suárez-Morales,
+   2009|biblio/10.1007_978-1-4020-8278-8_41]]).
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

Chromosome number.
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 172e1aa..630a454 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -53,6 +53,8 @@ Genome
 ------
 
  - Germ cells contain 3 haploid chromosomes ([[Körner, 1952|biblio/43261846]]).
+   This is a low number in the animal reign, although at least one mammal has
+   a similar number ([[Wurster and Benirschke 1970|biblio/5444269]]), and some insects have even less.
    There are also intriguing observations of somatic mitotic cells with 7
    chromosomes ([[Körner, 1952|biblio/43261846]]) and meiotic cells with
    8 haploid chromosomes ([[Colombera & Fenaux, 1973|biblio/10.1080_11250007309429248]]).

Wikipedia
diff --git a/biblio/5444269.mdwn b/biblio/5444269.mdwn
new file mode 100644
index 0000000..a5a15f8
--- /dev/null
+++ b/biblio/5444269.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Indian muntjac, Muntiacus muntjak: a deer with a low diploid chromosome number."]]
+[[!tag chromosome]]
+
+Science. 1970 Jun 12;168(3937):1364-6 doi:10.1126/science.168.3937.1364
+
+Wurster DH, Benirschke K
+
+Indian muntjac, Muntiacus muntjak: a deer with a low diploid chromosome number.
+
+[[!pmid 5444269 desc="Males have 7 chromosomes and females have 6.  The X chromosome is linked to an autosome by a thin neck, while the Y chromosome is free."]]

Café
diff --git a/biblio/24803335.mdwn b/biblio/24803335.mdwn
new file mode 100644
index 0000000..8b1b771
--- /dev/null
+++ b/biblio/24803335.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Carotenoid metabolic profiling and transcriptome-genome mining reveal functional equivalence among blue-pigmented copepods and appendicularia."]]
+[[!tag Oikopleura]]
+
+Mol Ecol. 2014 Jun;23(11):2740-56. doi:10.1111/mec.12781
+
+Mojib N, Amad M, Thimma M, Aldanondo N, Kumaran M, Irigoien X.
+
+Carotenoid metabolic profiling and transcriptome-genome mining reveal functional equivalence among blue-pigmented copepods and appendicularia.
+
+[[!pmid 24803335 desc="Mass spectrometry shows that astaxanthin is the main carotenoid pigment in O. dioica.  β‐carotene is probably taken from the food chain.  Two cytochrome P450 β‐carotene hydroxylase genes were identified (CBY21750 and CBY13480) and may be involved in the conversion to astaxanthin.  Three carotenoid‐binding proteins from the lipocalin family were found in the genome, and may be implicated in providing blue color by binding to astaxanthin."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index b58bbfa..172e1aa 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -254,7 +254,10 @@ Phenotypes
    ([[Denoeud et al., 2010|biblio/21097902]], Fig. S20).  It deviates from
    mendelian inheritance (Table S10), but is is recovered after sperm
    cryopreservation of male carriers.
-
+ - Blue pigmentation may arise from the conversion of β‐carotene from the
+   dietary algae into astaxanthin with cytochrome‐P450 hydroxylases, and
+   binding to protein from the lipocalin family, to change the color from
+   red to blue ([[Mojib and coll., 2014|biblio/24803335]]).
 
 Ecology
 -------

HM2 sub-assemblies are not haplotype-phased.
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 1057204..5e269c6 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -8,8 +8,17 @@ Prior assembly, MinIONQC ([[Lanfear and coll., 2018|biblio/30052755]]) allows
 for the comparison of multiple Nanopore runs on the same plot, to assess if
 read length is satisfactory.
 
-The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a diploid
-assembly and outputs a reference and an alternative assembly for each haplotype.
+The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a
+diploid assembly and outputs a reference and an alternative sub-assembly for
+each haplotype.  However, they are not phased: “_If only one allele is
+available for a locus (often due to haplotype collapsing or the allele is
+simply discarded by the de novo assembler), HM2 puts this allele into both
+sub-assemblies. In the sub-assemblies, the allelic scaffolds are given the same
+scaffold name. Finally, because there are switches between haplotypes in the
+rebuilt haploid sub-assemblies, the sub-assemblies are not haplotype phased._”
+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_”.
 
 BUSCO ([[Simão and coll., 2015|biblio/26059717]], [[Waterhouse and coll.,
 2017|biblio/29220515]]) assesses the presence of evolutionary conserved single-copy

Café
diff --git a/biblio/30052755.mdwn b/biblio/30052755.mdwn
new file mode 100644
index 0000000..d8df28a
--- /dev/null
+++ b/biblio/30052755.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="MinIONQC: fast and simple quality control for MinION sequencing data."]]
+[[!tag Nanopore assembly]]
+
+Lanfear R, Schalamun M, Kainer D, Wang W, Schwessinger B.
+
+Bioinformatics. 2018 Jul 23. doi:10.1093/bioinformatics/bty654
+
+MinIONQC: fast and simple quality control for MinION sequencing data.
+
+[[!pmid 30052755 desc="Allows for comparison of multiple runs on the same plot."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 28eed85..1057204 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -4,6 +4,10 @@
 
 _In progress..._
 
+Prior assembly, MinIONQC ([[Lanfear and coll., 2018|biblio/30052755]]) allows
+for the comparison of multiple Nanopore runs on the same plot, to assess if
+read length is satisfactory.
+
 The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a diploid
 assembly and outputs a reference and an alternative assembly for each haplotype.
 

Café
diff --git a/biblio/30609939.mdwn b/biblio/30609939.mdwn
new file mode 100644
index 0000000..947852b
--- /dev/null
+++ b/biblio/30609939.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="plyranges: a grammar of genomic data transformation."]]
+[[!tag software]]
+
+Lee S, Cook D, Lawrence M.
+
+Genome Biol. 2019 Jan 4;20(1):4. doi:10.1186/s13059-018-1597-8
+
+plyranges: a grammar of genomic data transformation.
+
+[[!pmid 30609939 desc="Bioconductor API for the pipe operator %>%."]]

Typography
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index ee4450e..28eed85 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -7,7 +7,7 @@ _In progress..._
 The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a diploid
 assembly and outputs a reference and an alternative assembly for each haplotype.
 
-BUSCO ([[Simão and coll., 2015|biblio/26059717]]), ([[Waterhouse and coll.,
+BUSCO ([[Simão and coll., 2015|biblio/26059717]], [[Waterhouse and coll.,
 2017|biblio/29220515]]) assesses the presence of evolutionary conserved single-copy
 genes in the assemblies.
 

Café
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index b1daa02..ee4450e 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -8,7 +8,7 @@ The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a di
 assembly and outputs a reference and an alternative assembly for each haplotype.
 
 BUSCO ([[Simão and coll., 2015|biblio/26059717]]), ([[Waterhouse and coll.,
-2017|29220515]]) assesses the presence of evolutionary conserved single-copy
+2017|biblio/29220515]]) assesses the presence of evolutionary conserved single-copy
 genes in the assemblies.
 
 [[!inline pages="tagged(assembly)" actions="no" limit=0]]

Café
diff --git a/biblio/26059717.mdwn b/biblio/26059717.mdwn
index 7e725d2..5ad2a2b 100644
--- a/biblio/26059717.mdwn
+++ b/biblio/26059717.mdwn
@@ -1,6 +1,8 @@
 [[!meta title="BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs."]]
 [[!tag assembly]]
 
+Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM.
+
 Bioinformatics. 2015 Oct 1;31(19):3210-2. doi:10.1093/bioinformatics/btv351
 
 BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 4a703d7..b1daa02 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -7,4 +7,8 @@ _In progress..._
 The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a diploid
 assembly and outputs a reference and an alternative assembly for each haplotype.
 
+BUSCO ([[Simão and coll., 2015|biblio/26059717]]), ([[Waterhouse and coll.,
+2017|29220515]]) assesses the presence of evolutionary conserved single-copy
+genes in the assemblies.
+
 [[!inline pages="tagged(assembly)" actions="no" limit=0]]

Café
diff --git a/biblio/28407147.mdwn b/biblio/28407147.mdwn
new file mode 100644
index 0000000..0b2c53e
--- /dev/null
+++ b/biblio/28407147.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly."]]
+[[!tag assembly]]
+
+Huang S, Kang M, Xu A.
+
+Bioinformatics. 2017 Aug 15;33(16):2577-2579. doi:10.1093/bioinformatics/btx220
+
+HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome assembly.
+
+[[!pmid 28407147 desc="Produces a reference and an alternate assembly.  Scaffolding is improved by cross-comparison of the assemblies."]]
diff --git a/tags/assembly.mdwn b/tags/assembly.mdwn
index 5715125..4a703d7 100644
--- a/tags/assembly.mdwn
+++ b/tags/assembly.mdwn
@@ -1,4 +1,10 @@
 [[!meta title="pages tagged assembly"]]
 
-[[!inline pages="tagged(assembly)" actions="no" archive="yes"
-feedshow=10]]
+# Genome assembly software
+
+_In progress..._
+
+The HaploMerger2 pipeline ([[Huang and coll., 2017|biblio/28407147]]) takes a diploid
+assembly and outputs a reference and an alternative assembly for each haplotype.
+
+[[!inline pages="tagged(assembly)" actions="no" limit=0]]

creating tag page tags/mosquito
diff --git a/tags/mosquito.mdwn b/tags/mosquito.mdwn
new file mode 100644
index 0000000..54da32e
--- /dev/null
+++ b/tags/mosquito.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged mosquito"]]
+
+[[!inline pages="tagged(mosquito)" actions="no" archive="yes"
+feedshow=10]]

Café
diff --git a/biblio/10.1101_499954.mdwn b/biblio/10.1101_499954.mdwn
new file mode 100644
index 0000000..438c86f
--- /dev/null
+++ b/biblio/10.1101_499954.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="A High-Quality De Novo Genome Assembly from a Single Mosquito using PacBio Sequencing"]]
+[[!tag genome assembly mosquito method extraction]]
+
+Sarah Kingan, Haynes Heaton, Juliana Cudini, Christine Lambert, Primo Baybayan, Brendan Galvin, Richard Durbin, Jonas Korlach, Mara Lawniczak
+
+bioRxiv preprint
+
+A High-Quality De Novo Genome Assembly from a Single Mosquito using PacBio Sequencing
+
+[[!doi 10.1101/499954 desc="Single individual ground with no twisting (only up-down movements).  DNA extracted with Qiagen MagAttract HMW kit, gentle flipping and wide-bore tips.  One contig was a bacterial genome, probably from gut flora.  Two contigs contained multiple copies of the mitochondrial chromosome.  Comparison with Sanger assembly corrected repeat compression."]]

Café
diff --git a/biblio/2541059.mdwn b/biblio/2541059.mdwn
new file mode 100644
index 0000000..bee2f66
--- /dev/null
+++ b/biblio/2541059.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes."]]
+[[!tag genome alignment]]
+
+Treangen TJ, Ondov BD, Koren S, Phillippy AM.
+
+Genome Biol. 2014;15(11):524.
+
+The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes.
+
+[[!pmid 25410596 desc="Requires > 97% similarity between genomes.  Species with a too low Maximal Unit Match (MUM) index distance are not incorporated in the core genome alignment."]]

updated PO files
diff --git "a/Debian/debi\303\242neries/r-packages.en.po" "b/Debian/debi\303\242neries/r-packages.en.po"
index e7aeaf8..e294f4c 100644
--- "a/Debian/debi\303\242neries/r-packages.en.po"
+++ "b/Debian/debi\303\242neries/r-packages.en.po"
@@ -6,14 +6,14 @@
 msgid ""
 msgstr ""
 "Project-Id-Version: \n"
-"POT-Creation-Date: 2018-12-22 00:04+0000\n"
+"POT-Creation-Date: 2018-12-22 00:13+0000\n"
 "PO-Revision-Date: 2018-12-22 01:12+0100\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 1.8.11\n"
 
 #. type: Plain text

English
diff --git "a/Debian/debi\303\242neries/r-packages.en.po" "b/Debian/debi\303\242neries/r-packages.en.po"
index f7bd36c..e7aeaf8 100644
--- "a/Debian/debi\303\242neries/r-packages.en.po"
+++ "b/Debian/debi\303\242neries/r-packages.en.po"
@@ -3,38 +3,40 @@
 # 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: 2018-12-22 00:04+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: 2018-12-22 01:12+0100\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 1.8.11\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta date=\"Sat, 22 Dec 2018 01:02:02 +0100\"]]\n"
-msgstr ""
+msgstr "[[!meta date=\"Sat, 22 Dec 2018 01:02:02 +0100\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta updated=\"Sat, 22 Dec 2018 01:02:02 +0100\"]]\n"
-msgstr ""
+msgstr "[[!meta updated=\"Sat, 22 Dec 2018 01:02:02 +0100\"]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!tag Debian]]\n"
-msgstr ""
+msgstr "[[!tag Debian]]\n"
 
 #. type: Plain text
 #, no-wrap
 msgid "[[!meta title=\"De l'utilité des paquets R dans Debian\"]]\n"
 msgstr ""
+"[[!meta title=\"On how useful are R packages in Debian\n"
+"\"]]\n"
 
 #. type: Plain text
 msgid ""
@@ -50,6 +52,16 @@ msgid ""
 "parfois pourquoi utiliser les paquets Debian au lieu d'utiliser le "
 "directement le gestionnaire de paquet amont."
 msgstr ""
+"Debian distributes the R language for statistical analysis, data mining or "
+"bioinformatics (among others).  Satellite to R are hundreds of packages "
+"(kind of function libraries), mostly distributed by CRAN and Bioconductor, "
+"which contribute a lot to the richness and versatility of the R ecosystem.  "
+"Debian redistributes some of these packages in the Debian format.  Like in "
+"all similar cases of \"redistribution of a distribution\", there is a "
+"tension between Debian's goals for its stable version, and the expectations "
+"of novelty for the users (in part because the development cycle of R is 6 "
+"months), and one sometimes wonder if there is a point for using the packages "
+"through Debian and not through the upstream repositories."
 
 #. type: Plain text
 msgid ""
@@ -62,3 +74,11 @@ msgid ""
 "j'aurais pu remplacer par quelques minutes avec quelques « apt install » "
 "bien placés.  Merci à tout ceux qui maintiennent ces paquets R dans Debian !"
 msgstr ""
+"Today, after installing a minimal system in a \"schroot\" container, I "
+"installed a R package and all its dependencies natively, that is by "
+"downloading their sources through the R command line, which made me wait for "
+"90 minutes until everything compiles, while the R packages redistributed in "
+"Debian are already compiled.  90 minutes of compilation for 10 minutes of "
+"work; 90 minutes of waiting that I could have avoided with a couple of well-"
+"chosen \"apt install\" commands.  Thus, many thanks to all who maintain R "
+"packages in Debian! "

updated PO files
diff --git "a/Debian/debi\303\242neries/r-packages.en.po" "b/Debian/debi\303\242neries/r-packages.en.po"
new file mode 100644
index 0000000..f7bd36c
--- /dev/null
+++ "b/Debian/debi\303\242neries/r-packages.en.po"
@@ -0,0 +1,64 @@
+# 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: 2018-12-22 00:04+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=\"Sat, 22 Dec 2018 01:02:02 +0100\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta updated=\"Sat, 22 Dec 2018 01:02:02 +0100\"]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!tag Debian]]\n"
+msgstr ""
+
+#. type: Plain text
+#, no-wrap
+msgid "[[!meta title=\"De l'utilité des paquets R dans Debian\"]]\n"
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Debian distribue le logiciel R pour faire des analyses statistiques, de la "
+"fouille de données, de la bioinformatique et d'autres tâches.  Gravitant "
+"autour de R, existent des centaines de paquets de fonctions, principalement "
+"distribués par CRAN et Bioconductor, qui font toute la richesse de "
+"l'écosystème R.  Debian redistribue certains de ces paquets au format "
+"Debian.  Comme dans tous les cas similaires de « redistribution de "
+"distribution », il existe une tension entre les objectifs de Debian pour sa "
+"version stable et les attentes de nouveauté pour les utilisateurs (pour "
+"partie liés au cycle de développement de 6 mois de R), et l'on se demande "
+"parfois pourquoi utiliser les paquets Debian au lieu d'utiliser le "
+"directement le gestionnaire de paquet amont."
+msgstr ""
+
+#. type: Plain text
+msgid ""
+"Aujourd'hui, après avoir installé un système minimal dans un conteneur "
+"« schroot », j'ai installé un paquet R et toutes ses dépendances nativement, "
+"c'est à dire en téléchargeant les sources via la ligne de commande de R, ce "
+"qui m'a fait poireauter 90 minutes le temps que tout compile, alors que les "
+"paquets R redistribués par Debian sont déjà pré-compilés.  90 minutes de "
+"compilation pour 10 minutes de travail; 90 minutes de compilation que "
+"j'aurais pu remplacer par quelques minutes avec quelques « apt install » "
+"bien placés.  Merci à tout ceux qui maintiennent ces paquets R dans Debian !"
+msgstr ""

R
diff --git "a/Debian/debi\303\242neries/r-packages.mdwn" "b/Debian/debi\303\242neries/r-packages.mdwn"
new file mode 100644
index 0000000..698bc9f
--- /dev/null
+++ "b/Debian/debi\303\242neries/r-packages.mdwn"
@@ -0,0 +1,25 @@
+[[!meta date="Sat, 22 Dec 2018 01:02:02 +0100"]]
+[[!meta updated="Sat, 22 Dec 2018 01:02:02 +0100"]]
+[[!tag Debian]]
+
+[[!meta title="De l'utilité des paquets R dans Debian"]]
+
+Debian distribue le logiciel R pour faire des analyses statistiques, de la
+fouille de données, de la bioinformatique et d'autres tâches.  Gravitant autour
+de R, existent des centaines de paquets de fonctions, principalement distribués
+par CRAN et Bioconductor, qui font toute la richesse de l'écosystème R.  Debian
+redistribue certains de ces paquets au format Debian.  Comme dans tous les cas
+similaires de « redistribution de distribution », il existe une tension entre
+les objectifs de Debian pour sa version stable et les attentes de nouveauté
+pour les utilisateurs (pour partie liés au cycle de développement de 6 mois de
+R), et l'on se demande parfois pourquoi utiliser les paquets Debian au lieu
+d'utiliser le directement le gestionnaire de paquet amont.
+
+Aujourd'hui, après avoir installé un système minimal dans un conteneur
+« schroot », j'ai installé un paquet R et toutes ses dépendances nativement,
+c'est à dire en téléchargeant les sources via la ligne de commande de R, ce qui
+m'a fait poireauter 90 minutes le temps que tout compile, alors que les
+paquets R redistribués par Debian sont déjà pré-compilés.  90 minutes de
+compilation pour 10 minutes de travail; 90 minutes de compilation que j'aurais
+pu remplacer par quelques minutes avec quelques « apt install » bien placés.
+Merci à tout ceux qui maintiennent ces paquets R dans Debian !

Post-café
diff --git a/biblio/15649342.mdwn b/biblio/15649342.mdwn
new file mode 100644
index 0000000..d6b5ef3
--- /dev/null
+++ b/biblio/15649342.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Remodelling of the homeobox gene complement in the tunicate Oikopleura dioica."]]
+[[!tag Oikopleura]]
+
+Curr Biol. 2005 Jan 11;15(1):R12-3 doi:10.1016/j.cub.2004.12.010
+
+Edvardsen RB, Seo HC, Jensen MF, Mialon A, Mikhaleva J, Bjordal M, Cartry J, Reinhardt R, Weissenbach J, Wincker P, Chourrout D.
+
+Remodelling of the homeobox gene complement in the tunicate Oikopleura dioica.
+
+[[!pmid 15649342 desc="O. dioica has 83 homeobox genes.  Lost groups of genes do not fully overlap between O. dioica and C. intestinalis, suggesting a larger common core in the ancestral tunicate."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index d1f62e2..b58bbfa 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -130,6 +130,7 @@ Genes and pathways
  - Defensome genes such as dehydrogenases and  (Glutamate-cysteine ligase modifier subunit; Gclm)
    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]].
 
 Transcriptome
 -------------

Adapter sequences.
diff --git a/biblio/18987734.mdwn b/biblio/18987734.mdwn
index 0509d3d..243cf0a 100644
--- a/biblio/18987734.mdwn
+++ b/biblio/18987734.mdwn
@@ -1,3 +1,10 @@
 [[!meta title="Accurate whole human genome sequencing using reversible terminator chemistry."]]
 [[!tag method sequencing sequence_tags]]
+
+Nature. 2008 Nov 6;456(7218):53-9. doi: 10.1038/nature07517
+
+Bentley DR, many co-authors, and Smith AJ.
+
+Accurate whole human genome sequencing using reversible terminator chemistry.
+
 [[!pmid 18987734 desc="Primary paper for Illumina-Solexa technology. The supplemental information contains the sequence of the oligonucleotides used on the flow cells."]]
diff --git a/tags/sequencing.mdwn b/tags/sequencing.mdwn
index dcf670d..ac52df5 100644
--- a/tags/sequencing.mdwn
+++ b/tags/sequencing.mdwn
@@ -1,4 +1,19 @@
 [[!meta title="pages tagged sequencing"]]
 
-[[!inline pages="tagged(sequencing)" actions="no" archive="yes"
-feedshow=10]]
+Illumina flowcell adaptors
+--------------------------
+
+Information extracted from the supplemental information of [[Bentley et al., 2008|bilbio/18987734]] (Accurate whole human genome sequencing using reversible terminator chemistry, Nature *456*(7218):53–9)
+
+Single read flowcell
+
+    5´-PSTTTTTTTTTT-(diol)3-AATGATACGGCGACCACCGA-3´
+    5´-PSTTTTTTTTTTCAAGCAGAAGACGGCATACGA-3´
+
+Paired read flowcell
+
+    5´-PS-TTTTTTTTTTAATGATACGGCGACCACCGAGAUCTACAC-3´ (U = 2-deoxyuridine)
+    5´-PS-TTTTTTTTTTCAAGCAGAAGACGGCATACGAGoxoAT-3´  (Goxo = 8-oxoguanine)
+
+
+[[!inline pages="tagged(sequencing)" actions="no" limit=0]]

More on nanoPARE.
diff --git a/biblio/30355603.mdwn b/biblio/30355603.mdwn
index 6325877..fbb12b5 100644
--- a/biblio/30355603.mdwn
+++ b/biblio/30355603.mdwn
@@ -1,5 +1,5 @@
 [[!meta title="NanoPARE: parallel analysis of RNA 5' ends from low-input RNA."]]
-[[!tag RNA-seq sequence_tags method library template_switching software]]
+[[!tag RNA-seq miRNA sequence_tags method library template_switching software]]
 
 Genome Res. 2018 Dec;28(12):1931-1942. doi:10.1101/gr.239202.118
 
@@ -7,4 +7,4 @@ Schon MA, Kellner MJ, Plotnikova A, Hofmann F, Nodine MD.
 
 NanoPARE: parallel analysis of RNA 5' ends from low-input RNA.
 
-[[!pmid 30355603 desc="5′ ends tags and RNA-seq tags separately amplified in two libraries."]]
+[[!pmid 30355603 desc="5′ ends tags and RNA-seq tags separately amplified in two libraries. Non-TSS peaks (identify by low-extraG content) contain miRNA cleavage sites."]]

Café
diff --git a/biblio/30355603.mdwn b/biblio/30355603.mdwn
new file mode 100644
index 0000000..6325877
--- /dev/null
+++ b/biblio/30355603.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="NanoPARE: parallel analysis of RNA 5' ends from low-input RNA."]]
+[[!tag RNA-seq sequence_tags method library template_switching software]]
+
+Genome Res. 2018 Dec;28(12):1931-1942. doi:10.1101/gr.239202.118
+
+Schon MA, Kellner MJ, Plotnikova A, Hofmann F, Nodine MD.
+
+NanoPARE: parallel analysis of RNA 5' ends from low-input RNA.
+
+[[!pmid 30355603 desc="5′ ends tags and RNA-seq tags separately amplified in two libraries."]]
diff --git a/tags/template_switching.mdwn b/tags/template_switching.mdwn
index b78625d..5226ece 100644
--- a/tags/template_switching.mdwn
+++ b/tags/template_switching.mdwn
@@ -27,6 +27,12 @@
    circulating RNAs, to remove phosphates or cyclophosphates that would
    prevent the A-tailing.
 
+ - in _nanoPARE_ ([[Schon, Kellner and coll.|biblio/30355603]]), a template-switching
+   oligonucleotide (RNA-RNA-LNA, without UMIs) is used to add a linker on 5′ ends.
+   After tagmentation, two libraries are amplified: one for 5′ ends and one for RNA-seq.
+   ~15% of the 5′ end alignments have extra Gs, but the genomic distribution is
+   bimodal.  Peaks with significant amounts of "extra G" nucleotides are marked as TSS.
+
 ### Effect of chemical composition of the TS oligonucleotide
 
 Originally, the TSOs were all-RNA.  Since this is expensive to synthesise,

Correction.
diff --git a/biblio/28835922.mdwn b/biblio/28835922.mdwn
index 99f3258..e45f172 100644
--- a/biblio/28835922.mdwn
+++ b/biblio/28835922.mdwn
@@ -7,4 +7,4 @@ Katija K, Choy CA, Sherlock RE, Sherman AD, Robison BH.
 
 From the surface to the seafloor: How giant larvaceans transport microplastics into the deep sea.
 
-[[!pmid 28835922 desc="B. strygius fed with microplastic particles."]]
+[[!pmid 28835922 desc="B. stygius fed with microplastic particles."]]

italics
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 89fa6ef..d1f62e2 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -279,7 +279,7 @@ Ecology
    and _Bathochordaeus_ individuals in the Hatoma Knoll hydrothermal vent, Okinawa Trough.
  - Oikopleuridae have been reported to be able to ingest microplastics.  Example(s):
    _B. stygius_ ([[Katija and coll., 2017b|biblio/28835922]]).
- - O. dioica can filter, ingest and defecate the Emiliania huxleyi virus
+ - _O. dioica_ can filter, ingest and defecate the _Emiliania huxleyi_ virus
    ([[Lawrence and coll., 2017|biblio/10.1002_lno.10734]]).  This study does not assess
    whether the viruses are digested.
 

Cafés
diff --git a/biblio/10.1002_lno.10734.mdwn b/biblio/10.1002_lno.10734.mdwn
new file mode 100644
index 0000000..86789d5
--- /dev/null
+++ b/biblio/10.1002_lno.10734.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Viruses on the menu: The appendicularian Oikopleura dioica efficiently removes viruses from seawater"]]
+[[!tag Oikopleura]]
+
+Janice Lawrence, Joachim Töpper, Elżbieta Petelenz‐Kurdziel, Gunnar Bratbak, Aud Larsen, Eric Thompson, Christofer Troedsson and Jessica Louise Ray
+
+Limnol. Oceanogr. 63, 2018, S244–S253
+
+Viruses on the menu: The appendicularian Oikopleura dioica efficiently removes viruses from seawater
+
+[[!doi 10.1002/lno.10734 desc="O. dioica can filter, ingest and defecate the Emiliania huxleyi virus, but it is yet unclear if it is digested."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 7a81243..89fa6ef 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -279,5 +279,8 @@ Ecology
    and _Bathochordaeus_ individuals in the Hatoma Knoll hydrothermal vent, Okinawa Trough.
  - Oikopleuridae have been reported to be able to ingest microplastics.  Example(s):
    _B. stygius_ ([[Katija and coll., 2017b|biblio/28835922]]).
+ - O. dioica can filter, ingest and defecate the Emiliania huxleyi virus
+   ([[Lawrence and coll., 2017|biblio/10.1002_lno.10734]]).  This study does not assess
+   whether the viruses are digested.
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

Café
diff --git a/biblio/29720410.mdwn b/biblio/29720410.mdwn
new file mode 100644
index 0000000..0f94ada
--- /dev/null
+++ b/biblio/29720410.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Mammoth grazers on the ocean's minuteness: a review of selective feeding using mucous meshes."]]
+[[!tag Oikopleura review]]
+
+Proc Biol Sci. 2018 May 16;285(1878). pii: 20180056. doi:10.1098/rspb.2018.0056
+
+Conley KR, Lombard F, Sutherland KR.
+
+Mammoth grazers on the ocean's minuteness: a review of selective feeding using mucous meshes.
+
+[[!pmid 29720410 desc="Review on marine filter feeders."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 2cb054c..7a81243 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -242,7 +242,8 @@ House
    that 35 ml of water were filtered per hour.  In comparison, the giant
    species Bathochordaeus mcnutti was reported to filter as much as 76 L/h
    ([[Katija and coll., 2018|biblio/28508058]]).
-
+ - Filter-feeding in marine animals has been reviewed by [[Conley, Lombard and
+   Sutherland (2018)|biblio/29720410]].
 
 Phenotypes
 ----------

creating tag page tags/microplastic
diff --git a/tags/microplastic.mdwn b/tags/microplastic.mdwn
new file mode 100644
index 0000000..e43c169
--- /dev/null
+++ b/tags/microplastic.mdwn
@@ -0,0 +1,4 @@
+[[!meta title="pages tagged microplastic"]]
+
+[[!inline pages="tagged(microplastic)" actions="no" archive="yes"
+feedshow=10]]

Dans le train
diff --git a/biblio/28835922.mdwn b/biblio/28835922.mdwn
new file mode 100644
index 0000000..99f3258
--- /dev/null
+++ b/biblio/28835922.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="From the surface to the seafloor: How giant larvaceans transport microplastics into the deep sea."]]
+[[!tag Oikopleura microplastic]]
+
+Sci Adv. 2017 Aug 16;3(8):e1700715. doi:10.1126/sciadv.1700715
+
+Katija K, Choy CA, Sherlock RE, Sherman AD, Robison BH.
+
+From the surface to the seafloor: How giant larvaceans transport microplastics into the deep sea.
+
+[[!pmid 28835922 desc="B. strygius fed with microplastic particles."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index dc2e554..2cb054c 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -276,5 +276,7 @@ Ecology
  - Oikopleuridae can be found in the deep see.  For instance, [[Lindsay and
    coll., 2014|biblio/10.1007_978-4-431-54865-2_51]] reported _Oikopleura_, _Mesochordaeus_
    and _Bathochordaeus_ individuals in the Hatoma Knoll hydrothermal vent, Okinawa Trough.
+ - Oikopleuridae have been reported to be able to ingest microplastics.  Example(s):
+   _B. stygius_ ([[Katija and coll., 2017b|biblio/28835922]]).
 
 [[!inline pages="tagged(Oikopleura)" actions="no" limit=0]]

Dans le train
diff --git a/biblio/28508058.mdwn b/biblio/28508058.mdwn
new file mode 100644
index 0000000..d8c38c8
--- /dev/null
+++ b/biblio/28508058.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="New technology reveals the role of giant larvaceans in oceanic carbon cycling."]]
+[[!tag Oikopleura]]
+
+Sci Adv. 2017 May 3;3(5):e1602374. doi:10.1126/sciadv.1602374
+
+Katija K, Sherlock RE, Sherman AD, Robison BH.
+
+New technology reveals the role of giant larvaceans in oceanic carbon cycling.
+
+[[!pmid 28508058 desc="DeepPIV, particule image velocimetry in the deep see using laser sheet illumination.  B. stygius and mcnutti specimens with tail lenght ranging between 2.2 and 2.9 cm can filter between 22 and 76 liters per hour."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 0b0b6f7..dc2e554 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -239,7 +239,9 @@ House
    filter” by [[Conley and coll., 2017|biblio/10.1002_lno.10680]], who observed
    its expansion and contraction at high spatial and temporal resolution.
  - In _O. labradorensis_, [[Flood (1991)|biblio/10.1007_BF01986351]] estimated
-   that 35 ml of water were filtered per hour.
+   that 35 ml of water were filtered per hour.  In comparison, the giant
+   species Bathochordaeus mcnutti was reported to filter as much as 76 L/h
+   ([[Katija and coll., 2018|biblio/28508058]]).
 
 
 Phenotypes

Dans le train
diff --git a/biblio/25994148.mdwn b/biblio/25994148.mdwn
new file mode 100644
index 0000000..0f8185f
--- /dev/null
+++ b/biblio/25994148.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Split-alignment of genomes finds orthologies more accurately."]]
+[[!tag LAST alignment Drosophila]]
+
+Frith MC, Kawaguchi R.
+
+Genome Biol. 2015 May 21;16:106. doi:10.1186/s13059-015-0670-9
+
+Split-alignment of genomes finds orthologies more accurately.
+
+[[!pmid 25994148 desc="Optimal set of local alignments.  Striking example of intra-chromosomal loss of synteny between D. melanogaster and D. pseudoobscura."]]

Café
diff --git a/biblio/29904074.mdwn b/biblio/29904074.mdwn
new file mode 100644
index 0000000..acb14db
--- /dev/null
+++ b/biblio/29904074.mdwn
@@ -0,0 +1,10 @@
+[[!meta title="Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity."]]
+[[!tag Oikopleura]]
+
+Sci Rep. 2018 Jun 14;8(1):9106. doi:10.1038/s41598-018-27509-8
+
+López-Escardó D, Paps J, de Vargas C, Massana R, Ruiz-Trillo I, Del Campo J.
+
+Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity.
+
+[[!pmid 29904074 desc="28% of the RNA reads in the oxic micro/mesoplanktonic samples originate from tunicates, mostly appendicularian.  rRNA sequences with no known homologs suggest a new group of tunicates, “MAME 1”.  However, given very long branches in the phylogenetic tree, this finding needs to be confirmed."]]
diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index f074d6f..0b0b6f7 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -255,6 +255,8 @@ Phenotypes
 Ecology
 -------
 
+ - In a rRNA metabarcoding study [[López-Escardó and coll, 2018|biblio/29904074]] report that 28 %
+   of the RNA reads in oxic micro/mesoplanktonic samples originate from tunicates, mostly appendicularian.
  - _O. dioica_ populations may have a higher fitness in warmer and more acid oceans
    ([[Bouquet et al., 2018|biblio/29298334]]).
  - In California, _O. dioica_ was reported by C. Essenberg