From: Charles Date: Thu, 17 Jun 2021 12:32:17 +0000 (+0900) Subject: Café X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=b2b8977ebc528af4621035c9e5ed0197e9c512f5;p=source.git Café --- diff --git a/biblio/33822040.mdwn b/biblio/33822040.mdwn new file mode 100644 index 00000000..55bdd55a --- /dev/null +++ b/biblio/33822040.mdwn @@ -0,0 +1,20 @@ +[[!meta title="Chromosomal Inversion Polymorphisms in Two Sympatric Ascidian Lineages."]] +[[!tag Ciona genome variants]] + +Satou Y, Sato A, Yasuo H, Mihirogi Y, Bishop J, Fujie M, Kawamitsu M, Hisata K, Satoh N. + +Genome Biol Evol. 2021 Jun 8;13(6):evab068. doi:10.1093/gbe/evab068 + +Chromosomal Inversion Polymorphisms in Two Sympatric Ascidian Lineages. + +[[!pmid 33822040 desc="Chromosoma assembly of _Ciona intestinalis_ finds ~20 inversions compared to _C. robusta_. Some inversions are heterozygous."]] + +“Chromosomal-level assemblies for the two type-B individuals, sampled at Roscoff (France; specimen R) and Plymouth (England; specimen P)” “For each specimen, we built contigs from long Nanopore reads with the NECAT assembler and polished obtained contigs with Illumina reads using the Nextpolish software [and removed overlaping contigs] using the purge_dups software [...]. Both of these contig sets were 140 Mb in length (table 1).” “Although the heterozygosity rate of type-A animals has been estimated to be 1.1–1.2% (Dehal et al. 2002; Satou et al. 2012), those of specimens R and P were 3.0% and 3.6%, respectively.” + +“Exons are highly conserved between type-A and type-B animals, whereas intergenic regions are highly varied between the two types.” [Supplemental material shows 97% similarity in aligned regions between R and P and 94% similarity between R/P and A] + +“To identify translocations, we searched the genomic sequences for blocks containing three or more genes that were not found in the positions expected from the type-A genome. We found two small interchromosomal translocations between the genomes of specimen P and type A, [but] we did not find such translocations between the genomes of specimen R and type A.” + +“Similarly, to identify inversions, we searched the genomic sequences for blocks containing three or more genes that were mapped in the reverse direction to the order in the type-A genome. We found 21 and 20 inversions in the genomes of specimens R and P, respectively (supplementary fig. S7, Supplementary Material online). Among them, 15 sites were common, and the remaining 11 sites were specific to specimen R or P (supplementary fig. S10 and tables S3 and S4, Supplementary Material online). Thus, our data indicate that there are structural variations not only between type-A and type-B animals but also between specimens R and P.” + +“We found R-derived haplotype contigs that were structurally different from the chromosome of specimen R, but the same as both the specimen-P and the type-A chromosomes. [In “an inversion in chromosome 7 [that] contained the largest number of genes over an ∼900-kb region”] genomic PCR using four primers flanking the junctional sites demonstrated that specimen R was indeed heterozygous” “We also confirmed experimentally an inversion on chromosome 3 [...]. A PCR analysis demonstrated that specimen P was indeed heterozygous in this region.” “we manually inspected genomic alignments of the two type-B specimens against the type-A genome, and found nine additional inversions.” “To understand how prevalent the inversions we found were in type-B populations, we collected eight wild specimens at Roscoff and Plymouth, RO1–RO4 and PL1–PL4, respectively, and performed genomic PCR [that demonstrated that] type-B animals indeed have inversion polymorphisms.” “The inversions we found in the present study are relatively small (3 kb ∼ 873 kb)” “our data highlight the likely importance of inversions in speciation of _Ciona_, an invertebrate with mating governed by interactions of aquatic gametes”. diff --git a/tags/Ciona.mdwn b/tags/Ciona.mdwn index 55873314..c127a741 100644 --- a/tags/Ciona.mdwn +++ b/tags/Ciona.mdwn @@ -1,19 +1,25 @@ [[!meta title="pages tagged Ciona"]] +## Phylogeny + -- Ciona robusta Hoshino & Tokioka, 1967 [WoRMS ID 252565](http://www.marinespecies.org/aphia.php?p=taxdetails&id=252565) -| | -- Ciona intestinalis Linnaeus, 1767 [WoRMS ID 103732](http://www.marinespecies.org/aphia.php?p=taxdetails&id=103732) -| ---- Ciona savignyi Herdman, 1882 [WoRMS ID 250292](http://www.marinespecies.org/aphia.php?p=taxdetails&id=250292) -_C. intestinalis_ and _C. savignyi_ can cross-fertilise after removal of the -vitelline enveloppe ([[Byrd and Lambert, 2000|biblio/10602281]]). They are -estimated to have diverged ~184 (±15) My ago based on protein sequence -comparisons and estimation of the acceleration of the molecular clock in -tunicates [[Berná, Alvarez-Valin and D'Onofrio, 2009|biblio/20052388]] or -122 ± 33 million years ago based on sequence analysis of 258 proteins from 63 -species ([[Delsuc and coll., 2018|biblio/29653534]]). +_C. savignyi is estimated to have diverged from the two others ~184 (±15) My +ago based on protein sequence comparisons and estimation of the acceleration of +the molecular clock in tunicates [[Berná, Alvarez-Valin and D'Onofrio, +2009|biblio/20052388]] or 122 ± 33 million years ago based on sequence analysis +of 258 proteins from 63 species ([[Delsuc and coll., 2018|biblio/29653534]]). + +The _intestinalis_ and _robusta_ speciation is estimated to have happened +during the Pliocene (≈ 3.8 Ma); a recent introgression then happened 15,000 +years ago ([[Roux and coll., 2013|biblio/23564941]]). + +## Hybridisation between species _Ciona robusta_'s sperm can efficiently fertilise _C. intestinalis_ eggs, but the fertilisation rates are much lower in the reciprocal crosses ([[Suzuki, @@ -25,6 +31,11 @@ strains from Plymouth did not develop beyond cleavage ([[Caputi and coll., analysis of wild animals of ([[Bouchemousse and coll., 2016|biblio/27662427]]) were F1 and of _C. int_ maternal origin. +_C. intestinalis_ and _C. savignyi_ can cross-fertilise after removal of the +vitelline enveloppe ([[Byrd and Lambert, 2000|biblio/10602281]]). + +## Detailed evidence for speciation + Comparison of mitochnodrial CO1 sequences show that _C. intestinalis_ types A and B (now renamed _robusta_ and _intestinalis sensu_) are as distant as distinct species ([[Nydam and Harrison, @@ -35,22 +46,29 @@ coll|biblio/10.1111_jzs.12101]] proposed the presence of “tubercular prominences” in the tunic as a more accurate morphological marker. Mitochondrial gene order differ between the two species ([[Ianelli and coll., 2007|biblio/17640763]]). Sequencing of nuclear genes showed intragenic -recombination in _C. robusta_ and _C. intestinalis_, buy supported monophyly of +recombination in _C. robusta_ and _C. intestinalis_, but supported monophyly of these two species. Both data also supported paraphyly of _C. intestinalis_ with respcet to _C. roulei_ ([[Nydam and Harrison, 2010|biblio/20403444]]). -Speciation is estimated to have happened during the Pliocene (≈ 3.8 Ma); a -recent introgression then happened 15,000 years ago ([[Roux and coll., -2013|biblio/23564941]]). - -Latest _Ciona robusta_ genome: version HT ([[Satou and coll., -2019|biblio/31621849]]) is a reassembly of the KS genome using Hi-C and PacBio -additional data, in which over 95 % of the dequences is included in -chromosomes. Out of 14 pairs of chromosomes, 10 are metacentric ([[Shoguchi -and coll., 2005|biblio/15930823]]); the Hi-C contact map suggests that their -arms interact with each other almost as much as with themselves. -Inter-chromosomal contacts are much more rare in comparison. - -Mitochondrial gene order differs even within the _Ciona_ genus ([[Gissi, -Iannelli and Pesole 2004|biblio/15114417]]). + + +## Genomes + + - _Ciona robusta_ latest genome: version HT ([[Satou and coll., + 2019|biblio/31621849]]) is a reassembly of the KS genome using Hi-C and + PacBio additional data, in which over 95 % of the dequences is included in + chromosomes. Out of 14 pairs of chromosomes, 10 are metacentric ([[Shoguchi + and coll., 2005|biblio/15930823]]); the Hi-C contact map suggests that their + arms interact with each other almost as much as with themselves. + Inter-chromosomal contacts are much more rare in comparison. + + - _Ciona intestinalis_: chromosome-level assemblies of two individuals + ([[Satou and coll., 2021|biblio/]]) suggests that there are ~20 inversions + (containing at least 3 genes) between the two species. Some of them are + not fixed. + + - _Ciona savignyi_: [paper to read] + + - Mitochondrial gene order differs even within the _Ciona_ genus ([[Gissi, + Iannelli and Pesole 2004|biblio/15114417]]). [[!inline pages="tagged(Ciona)" actions="no" limit=0]]