Mightychondrion

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+[[!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
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+[[!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
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--- 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
 ---------------