From: Charles Date: Fri, 22 Mar 2019 02:18:32 +0000 (+0900) Subject: Lost genes and pathways. X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=25454ce30f415192b0283c66dafe610aee0b888a;p=source%2F.git Lost genes and pathways. --- diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn index b639ee0c..04e24f6c 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]]).