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.
“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”.