From: Charles Plessy <plessy@riken.jp>
Date: Wed, 30 May 2018 04:28:47 +0000 (+0900)
Subject: Genome paper.
X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=3aca3f69eda0d7926889bc4414e74be1ae70a32f;p=source%2F.git

Genome paper.
---

diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 0a7822ed..f8b73630 100644
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -36,9 +36,18 @@ Genome
 
  - Size estimated to 72 ± 13 Mb (min 32.6~65 Mb) by [[Seo et al, 2001|biblio/11752568]].
  - Each cell only contains 70 fg of DNA ([Animal Genome Size Database](http://www.genomesize.com/result_species.php?id=1308)).
+ - “No signal of synteny conservation is detected between _Oikopleura_ and _Ciona
+   intestinalis_. (...) _Oikopleura_ showed a local gene order that is
+   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]])
  - CYP1 family genes and their regulator AhR are not detectable ([[Yadetie et al, 2012|biblio/22300585]]).
  - ~80 "house proteins" have been identified and more than half lack similarity
    to known proteins ([[Hosp et al., 2012|biblio/22792236]]). 
+ - 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.
 
 
 Transcriptome
@@ -53,8 +62,11 @@ Transcriptome
    SL and that 42% of SL transcripts are monocistronic ([[Danks et al., 2015|biblio/25525214]]).
  - 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 subjected to a large turnover: many ancestral introns are lost, and many
-   new species-specific introns found ([[Edvarsen et al., 2004|biblio/15638456]]).
+ - Introns are very small (peak at 47 base pairs, 2.4% > 1 kb) [[Denoeud et
+   al., 2010|biblio/21097902]] and subjected to a large turnover: many ancestral
+   introns are lost, and many new species-specific introns found ([[Edvarsen et
+   al., 2004|biblio/15638456]]).  Introns are gained by insertion of transposon-like elements and
+   by reverse splicing, ([[Denoeud et al., 2010|biblio/21097902]]).  
 
 
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