--- /dev/null
+[[!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”.
[[!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,
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,
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]]
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