Lost genes and pathways.

diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index b639ee0c2893090bf9bbf3d35b8d3466a8baddff..04e24f6cdf6927396a40f4efcd12ce2e1d3b3cfc 100644 (file)
--- 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]]).