Sustained Heterozygosity Across a Self-Incompatibility Locus in an Inbred Ascidian

Abstract

Because self-incompatibility loci are maintained heterozygous and recombination within self-incompatibility loci would be disadvantageous, self-incompatibility loci are thought to contribute to structural and functional differentiation of chromosomes. Although the hermaphrodite chordate, Ciona intestinalis, has two self-incompatibility genes, this incompatibility system is incomplete and self-fertilization occurs under laboratory conditions. Here, we established an inbred strain of C. intestinalis by repeated self-fertilization. Decoding genome sequences of sibling animals of this strain identified a 2.4-Mbheterozygous region on chromosome 7. A self-incompatibility gene, Themis-B, was encoded within this region. This observation implied that this self-incompatibility locus and the linkage disequilibrium of its flanking region contribute to the formation of the 2.4-Mb heterozygous region, probably through recombination suppression. We showed that different individuals in natural populations had different numbers and different combinations of Themis-B variants, and that the rate of self-fertilization varied among these animals. Our result explains why self-fertilization occurs under laboratory conditions. It also supports the concept that the Themis-B locus is preferentially retained heterozygous in the inbred line and contributes to the formation of the 2.4-Mb heterozygous region. High structural variations might suppress recombination, and this long heterozygous region might represent a preliminary stage of structural differentiation of chromosomes.

A Nearly Complete Genome of Ciona intestinalis Type A (C. robusta) Reveals the Contribution of Inversion to Chromosomal Evolution in the Genus Ciona

“…For PacBio RSII sequencing, we used sperm obtained from an animal in the eighth generation of self-fertilization, as described previously (Satou et al. 2015).…”

“…2014). Illumina sequencing reads (paired 101 base reads, 16.6 Gb in total; SRA accession number DRR018354) for a 11th generation animal (Satou et al. 2015) were mapped with bowtie2 (Langmead et al.…”

Three multi-allelic gene pairs are responsible for self-sterility in the ascidian Ciona intestinalis

“…We compared these 17 alleles with 12 alleles (designated A -L) identified by Satou et al 17 and examined whether each allele matched with the s/v-Themis-B allele or the s/v-Themis-B2 allele by amplifying the DNA of the respective HVR. As a result, 7 alleles reported by Satou et al 17 matched our s/v-Themis-B and s/v-Themis-B2 alleles (see Table S1). Importantly, 22 alleles belonged to either s/v-Themis-B or s/v-Themis-B2 but not to both.…”

“…We thank the National BioResource Project (NBRP) of AMED and all members of the Maizuru Fisheries Research Station and Yutaka Satou lab of Kyoto University and the Misaki Marine Biological Station of the University of Tokyo for providing C. intestinalis type A adults. We are indebted to Kazuhiro W. Makabe of Tokushima University, who donated the BAC library of genomic DNA of C. intestinalis type A, and Yutaka Satou of Kyoto University, who donated the genomic DNA of 12 identified alleles of s/v-Themis-B 17 . We also thank Yoshito Harada of Nagoya University for his valuable comments.…”

“…We previously reported that one additional B-type s/v-Themis gene pair may exist near the s/v-Themis-B gene in locus B, since three alleles of B-type v-Themis proteins were detected in the VC by mass spectrometry 13,14 ; further, one additional s/v-Themis-B gene pair has been proposed to exist in locus B on the basis of the Ghost database (C. intestinalis type A genome database) 16 . In addition, it was recently reported that only the s/v-Themis-B gene region showed heterogeneity in an inbred strain and that the copy number of s/v-Themis-B gene pairs is variable among individuals 17 . These unexpected results led us to further investigate the gene structures and their roles in the self-sterility of B-type s/v-Themis.…”