From: Charles Date: Tue, 17 Mar 2020 03:14:59 +0000 (+0900) Subject: Reorganise X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=4b8cd79d7a072af8a09ba809339f8655d149df26;p=source.git Reorganise --- diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn index 4cc9f38c..bd9ccec8 100644 --- a/tags/Oikopleura.mdwn +++ b/tags/Oikopleura.mdwn @@ -110,9 +110,6 @@ Genome 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]]). - - The main groups of retrotransposons present in _O. dioica_ are Odin (Oikopleura dioicanon-LTR), - Tor (Ty3/gypsy Oikopleura retrotransposon), DIRS1-like and Penelope-like - [[Volff and coll., 2004|biblio/15254255]]. - The mitochondrial COI sequence AY116609 and the 18S rRNA sequence AB013014 in Genbank are probably a contamination and a misidentification, respectively ([[Sakaguchi and coll., 2017|biblio/10.1007_s12562-017-1106-0]]). @@ -131,18 +128,6 @@ Genome ([[Frey and Pucker, 2020|biblio/32085510]]). - Operons are enriched for houskeeping genes and depleted for developmental genes ([[Denoeud et al., 2010|biblio/21097902]]). - - “LTR retrotransposons account for a significant part of the indel polymorphism - in the _Oikopleura_ genome.” - “Tor-3G elements are frequently inserted into exons and can be transcribed - together with their host gene, although transcripts initiated in the LTR - are also detected (Figure S11).” - “The low allelic frequency of Tor-3G insertions is correlated with the - almost exclusive occurrence of heterozygous genotypes in the populations. - Moreover, experimental crosses between selected heterozygous parents for - the same insertion have thus far not resulted in homozygous offsprings.” - ([[Denoeud et al., 2010|biblio/21097902]]). - - SINE and MITE account for a large part of genome expansion in larger oikopleurid - species ([[Naville and coll., 2019|biblio/30880010]]). - “Highly conserved elements (HCEs) lie around these developmental genes.” “Spots of sequence ultraconservation are almost systematically located in non coding regions, including introns that are larger than average @@ -159,6 +144,26 @@ Genome from other chrodates ([[Berná and Alvarez-Valin, 2015|biblio/26228312]]). +Repeat elements +--------------- + + - The main groups of retrotransposons present in _O. dioica_ are Odin (Oikopleura dioicanon-LTR), + Tor (Ty3/gypsy Oikopleura retrotransposon), DIRS1-like and Penelope-like + [[Volff and coll., 2004|biblio/15254255]]. + - “LTR retrotransposons account for a significant part of the indel polymorphism + in the _Oikopleura_ genome.” + “Tor-3G elements are frequently inserted into exons and can be transcribed + together with their host gene, although transcripts initiated in the LTR + are also detected (Figure S11).” + “The low allelic frequency of Tor-3G insertions is correlated with the + almost exclusive occurrence of heterozygous genotypes in the populations. + Moreover, experimental crosses between selected heterozygous parents for + the same insertion have thus far not resulted in homozygous offsprings.” + ([[Denoeud et al., 2010|biblio/21097902]]). + - SINE and MITE account for a large part of genome expansion in larger oikopleurid + species ([[Naville and coll., 2019|biblio/30880010]]). + + Genes and pathways ------------------