From: Charles Plessy Date: Mon, 26 Aug 2024 01:30:27 +0000 (+0900) Subject: Mightychondrion X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=585a64a1983b3d3f8050a7fd841d26a5c3d84ae8;p=source%2B%2B%2F.git Mightychondrion --- diff --git a/biblio/39162185.mdwn b/biblio/39162185.mdwn new file mode 100644 index 00000000..b185d547 --- /dev/null +++ b/biblio/39162185.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Tracing Homopolymers in Oikopleura dioica's mitogenome."]] +[[!tag Oikopleura mitochondrion OIST]] + +Tracing Homopolymers in Oikopleura dioica's mitogenome. + +Dierckxsens N, Watanabe K, Tan Y, Masunaga A, Mansfield MJ, Miao J, Luscombe NM, Plessy C. + +Genome Biol Evol. 2024 Aug 20:evae182. doi: 10.1093/gbe/evae182 + +[[!pmid 39162185 desc="Our PacBio I25 assembly"]] diff --git a/biblio/39162337.mdwn b/biblio/39162337.mdwn new file mode 100644 index 00000000..3af777bd --- /dev/null +++ b/biblio/39162337.mdwn @@ -0,0 +1,10 @@ +[[!meta title="Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss"]] +[[!tag Oikopleura mitochondrion]] + +Klirs Y, Novosolov M, Gissi C, Garic R, Pupko T, Stach T, Huchon D. + +Genome Biol Evol. 2024 Aug 20:evae181. doi:10.1093/gbe/evae181 + +Evolutionary Insights from the Mitochondrial Genome of Oikopleura dioica: Sequencing Challenges, RNA Editing, Gene Transfers to the Nucleus, and tRNA Loss. + +[[!pmid 39162337 desc="“the nad3 gene has been transferred to the nucleus and acquired a mitochondria-targeting signal“ Cs are occasionally found in edited poly-T regions."]] diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn index 2722d14c..c09c7449 100644 --- a/tags/Oikopleura.mdwn +++ b/tags/Oikopleura.mdwn @@ -121,19 +121,6 @@ Genome [[Schulmeister, Schmid and Thompson, 2007|biblio/17333540]]. - Genome compaction in _Oikopleura_ and _Ciona_ have been reviewed in parallel by [[Berná and Alvarez-Valin (2014)|biblio/25008364]]. - - 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. 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 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]]). - - [[Pichon, Luscombe and Plessy, 2019|biblio/32148763]] confirms that _O. dioica_'s - mitochondrial sequences can be translated with the ascidian genetic code, and - suggests that _O. lon_, _B. sty_ and perhaps _M. ery_ (all in the _Coecaria_ genus) - use different code(s). - Analysis of sex-linked markers supports genetic sex determination with male heterogamety – that is: X chromosomes for females and Y for males. ([[Denoeud et al., 2010|biblio/21097902]]) - The major spliceosome is hypothethised to have evolved @@ -163,6 +150,28 @@ Genome pairwise non-coding conservation that “may have utility in the analysis of” conserved non-coding elements in _Oikopleura_. +Mitogenome +---------- + + - A partial mitochondrial genome was reconstituted in [[Denoeud et al., + 2010|biblio/21097902]], where edited oligo-dT stretches were discovered. + A/T-rich codons are more frequent than in human. + - Long-read mitochondrial assemblies confirmed the gene content (atp6, cob, + cox1, cox2, cox3, nad1, nad4, nad5 and a putative nad2 ORF), and showed + that the poly-T regions could contain Cs that do not interrupt editing + ([[Dierckxsens and coll, 2024|biblio/39162185]], [[Klirs et and coll., 2024|biblio/39162337]]). + - The _nad3_ gene was transferred to the nuclear genome ([[Klirs et and coll., 2024|biblio/39162337]]). + - 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 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]]). + - [[Pichon, Luscombe and Plessy, 2019|biblio/32148763]] confirms that _O. dioica_'s + mitochondrial sequences can be translated with the ascidian genetic code, and + suggests that _O. lon_, _B. sty_ and perhaps _M. ery_ (all in the _Coecaria_ genus) + use different code(s). + Repeat elements ---------------