inopinata

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+[[!meta title="Biology and genome of a newly discovered sibling species of Caenorhabditis elegans"]]
+[[!tag nematode genome]]
+
+Nat Commun. 2018 Aug 10;9(1):3216. doi:10.1038/s41467-018-05712-5
+
+Kanzaki N, Tsai IJ, Tanaka R, Hunt VL, Liu D, Tsuyama K, Maeda Y, Namai S,
+Kumagai R, Tracey A, Holroyd N, Doyle SR, Woodruff GC, Murase K, Kitazume H, Chai
+C, Akagi A, Panda O, Ke HM, Schroeder FC, Wang J, Berriman M, Sternberg PW,
+Sugimoto A, Kikuchi T.
+
+Biology and genome of a newly discovered sibling species of Caenorhabditis elegans
+
+[[!pmid 30097582 desc="123-Mb genome assembled into six chromosomes.  Divergence time between C. elegans and C. inopinata estimated to about 10.5 Mya (142.73 million generations ago, assuming a generation time of 30 days).  Proliferation of transposons and other repetitive elements (LTR, LINE, and Tc1/mariner).  “The C. inopinata genome contains 641 LTR retrotransposon elements, 104 of which contain full protein domains (intact LTRs) In comparison, C. elegans and C. briggsae have 62 and 128 LTR retrotransposon elements, respectively, with 10 intact LTRs found in each.”  “The most common type of repetitive sequence in the C. inopinata genome is the TcMar transposase Tc1 family [...] comprising 8.85% of the genome, compared with 1.31% and 3.04% of the C. elegans and C. briggsae genomes, respectively”.  “Gene collinearity is largely conserved despite frequent intra chromosomal rearrangements.”  “Higher synonymous substitution rates (dS) in autosomal arm regions than in the centre regions for C. elegans and C. inopinata one-to-one orthologues.”  “Notably, C. inopinata has highly conserved gene synteny and orthology of essential genes with C. elegans and C. briggsae, but differs substantially in morphology and ecology. We hypothesise that activation of transposable elements possibly due to de-silencing through an altered small RNA pathway could be a driving force of rapid diversification of C. inopinata from other Caenorhabditis species.”"]]

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- - _C. inopinata_ travels from fig to fig on Ceratosolen pollinating wasps and
-   is specialised on both its prefered fig and wasp [[(Woodruff and Phillips,
-   2018)|biblio/30129423]].
+... in progress ...
+
+### _C. inopinata_
+
+ - _C. inopinata_ was discovered in 2018 to be the closest species to _C.
+   elegans_ despite stronger differences (compared with more distant species)
+   in morphology and ecological niche ([[Kanzaki and coll.,
+   2018|biblio/30097582]]).
+
+ - _C. inopinata_ travels from fig to fig on _Ceratosolen_ pollinating wasps
+   and is specialised on both its prefered fig and wasp [[(Woodruff and
+   Phillips, 2018)|biblio/30129423]].
+
+ - The _C. inopinata_ genome is ~123 Mb and contains active transposons that
+   may explain the increased genome size compared with _C. elegans_.
+   Structural changes between both species are mainly intra-chromosomal ([[Kanzaki
+   and coll., 2018|biblio/30097582]]).
+
+### Other nematodes
 
  - _Diploscapter pachys_ has a single chromosome, that is still organised in
    ancestral domains homologous to the ones of other nematodes ([[Fradin and