From: Charles Date: Tue, 17 Mar 2020 02:44:51 +0000 (+0900) Subject: Café X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=4ba15e59277e00ec36966fc72fed5725a5224f14;p=source%2F.git Café --- diff --git a/biblio/15254255.mdwn b/biblio/15254255.mdwn new file mode 100644 index 00000000..4970d59e --- /dev/null +++ b/biblio/15254255.mdwn @@ -0,0 +1,18 @@ +[[!meta title="Retroelement dynamics and a novel type of chordate retrovirus-like element in the miniature genome of the tunicate Oikopleura dioica."]] +[[!tag repeat transposon Oikopleura]] + +Mol Biol Evol. 2004 Nov;21(11):2022-33 doi:10.1093/molbev/msh207 + +Volff JN, Lehrach H, Reinhardt R, Chourrout D. + +Retroelement dynamics and a novel type of chordate retrovirus-like element in the miniature genome of the tunicate Oikopleura dioica. + +[[!pmid 15254255 desc="Primary paper for Odin (Oikopleura dioicanon-LTR) and Tor (Ty3/gypsy Oikopleura retrotransposon) elements. + +TBlastN search for reverse-transcriptases suggests “extinction, or at least strong copy number reduction, of major clades of non-LTR retrotransposons”. “About 80 Odin reverse transcriptase sequences were detected by TBlastN analysis in the 41 Mb genome assembly of O. dioica using a 335 amino acid reverse transcriptase sequence as a query (we can not exclude that some nonoverlapping short hits might belong to a same partially sequenced element). About 30% of Odin endonuclease and reverse transcriptase-encoding sequences were corrupted by stop or frameshift mutations, suggesting that an important proportion of Odin elements is not functional. The degree of nucleotide sequence identity between Odin elements ranged from less than 60% up to 90%.” + +“About 180 Tor reverse transcriptase sequences were detected in the 41 Mb genome assembly (about 50 sequences for Tor2, Tor3, and Tor4, but only two for Tor1; the remaining sequences were too short to be classified unambiguously). The degree of nucleotide identity inside of the Tor2, Tor3, and Tor4 families ranged from less than 60% up to 98–99% (the two Tor1 elements showed 70% nucleotide identity). On average, open reading frame–corrupting mutations were observed each 7.5 kb, 2.8 kb, and 16 kb for Tor2, Tor3, and Tor4, respectively.” “The Tor4b family might have acquired its env-like gene from a paramyxovirus.” + +“Among other groups of LTR retrotransposons, only DIRS1-like elements were found in Oikopleura.” “About 70 reverse transcriptase sequences from DIRS1-related elements were detected in the 41 Mb genome assembly, with degrees of nucleotide identity ranging from less than 60% up to 90%. DIRS1-related elements were apparently absent from the sea squirt genome and would therefore represent the only type of autonomous retroelement lost in C. intestinalis but present in O. dioica.” + +“Penelope-like retroelements were detected in the genome of both O. dioica and C. intestinalis. [...] Complete elements with an apparently intact unique open reading frame encoding a reverse transcriptase and a C-terminal YIG endonuclease were identified, suggesting recent activity. This was confirmed by the presence of very similar elements presenting 98–99% nucleotide identity. However, the high divergence between some copies (less than 60% nucleotide identity) showed the diversity and ancient origin of the group [...]. About 60 reverse transcriptase sequences were detected in the 41 Mb genome assembly.”"]] diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn index ed44af89..4cc9f38c 100644 --- a/tags/Oikopleura.mdwn +++ b/tags/Oikopleura.mdwn @@ -110,6 +110,9 @@ 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]]).