Biology subjects

Hirase, S.

Publications and source records attributed to Hirase, S..

4 recordsLinked to original sources

bioRxiv2025

Ancestral origin and structural characteristics of non-syntenic homologous chromosomes in abalones

Structural variation is increasingly recognized as a pivotal contributor to genomic diversity in marine invertebrates, yet its extent and evolutionary significance remain poorly characterized in many species. Haplotype-phased genome assembly is an excellent method for studying such variations by comparing homologous chromosomes. In this study, we constructed a haplotype-phased genome assembly for the western Pacific abalone, Haliotis gigantea, using high-fidelity (HiFi) long-read sequencing and high-resolution chromosome conformation capture (Hi-C) data. The primary and alternative assemblies each comprised 18 long scaffolds (>50 Mb), consistent with the species diploid chromosome number (2n = 36), and contained 96.5% and 96.2% complete single-copy Metazoa Benchmarking Universal Single-Copy Orthologs genes, respectively, indicating high assembly quality. Comparative analysis of the two haplotypes revealed three homologous chromosomes with large-scale non-syntenic regions caused by extensive segmental duplications, with each enriched in distinct gene domains. These non-syntenic chromosomes likely originated in abalone evolution, as they were conserved across both closely and distantly related species. Our findings highlight the evolutionary importance of non-syntenic structural variation in shaping genome architecture and suggest that such variation may play a broader role in functional diversification across abalones.

genomics↗

bioRxiv2024

Identification of the sex determination region and the development of a marker to distinguish males and females in megai abalone (Haliotis gigantea)

Sex identification markers are of considerable value to aquaculture and fisheries as they enable pre-maturity prediction of the genotypic sex of individuals as well as of the sex ratio in offspring. For these reasons, extensive investigations of the mechanisms of sex determination have been conducted in commercially important finfish species, resulting in the development of sex identification markers for many of these. However, research on shellfish is still in its infancy stage. In this study, we investigated the genomic basis of sex determination in megai abalone (Haliotis gigantea), a gastropod species of economic importance in fisheries and aquaculture in East Asia, with the aim of developing a sex identification marker. Initially, we examined the applicability of sex identification markers reported for two other Haliotis species, but found they were not transferable to H. gigantea. We then analyzed the sex chromosomes in H. gigantea using a whole-genome resequencing approach. By calculating the fixation index value between 10 females and 10 males, we identified a genomic region spanning approximately 2 Mb that exhibited nucleotide sequence divergence between the sexes (from the position 260,372 bp to 1,930,278 bp in chromosome 18). This region was located next to the pseudoautosomal region which is characterized by an absence of sequence differentiation between the sexes. In the divergent region, male-specific SNPs were identified but no female-specific SNPs were detected, indicating that this species has an XX-XY sex determination system. By exploring Indel polymorphisms in the divergent region, we successfully developed a codominant PCR marker for sex identification that could be applied to wild individuals from geographically distant locations. A cross-species analysis suggested that the sex determination region in H. gigantea was unlikely to be shared with the closely related species H. discus hannai. This raises the possibility of a widespread, rapid turnover of sex chromosomes or sex determination regions in abalones, similar to certain vertebrate lineages such as finfish.

genomics↗

bioRxiv2024

Silver chimaera genome assembly and identification of the holocephalan sex chromosome sequence

Cartilaginous fishes are divided into holocephalans and elasmobranchs, and comparative studies involving them are expected to elucidate how variable phenotypes and distinctive genomic properties were established in those ancient vertebrate lineages. To date, molecular-level studies on holocephalans have concentrated on the family Callorhinchidae, with a chromosome-scale genome assembly of Callorhinchus milii available. In this study, we focused on the most species-rich holocephalan family Chimaeridae and sequenced the genome of its member, silver chimaera (Chimaera phantasma). We report the first chromosome-scale genome assembly of the Chimaeridae, with high continuity and completeness, which exhibited a large intragenomic variation of chromosome lengths, which is correlated with intron size. This pattern is observed more widely in vertebrates and at least partly accounts for cross-species genome size variation. A male-female comparison identified a silver chimaera genomic scaffold with a double sequence depth for females, which we identify as an X chromosome fragment. This is the first DNA sequence-based evidence of a holocephalan sex chromosome, suggesting a male heterogametic sex determination system. This study, allowing the first chromosome-level comparison among holocephalan genomes, will trigger in-depth understanding of the genomic diversity among vertebrates as well as species population genetic structures based on the genome assembly of high completeness.

genomics↗

bioRxiv2021

Repeated translocation of a supergene underlying rapid sex chromosome turnover in Takifugu fish

Recent studies have revealed a surprising diversity of sex chromosomes in vertebrates. However, the detailed mechanism of their turnover is still elusive. To understand this process, it is necessary to compare closely related species in terms of sex-determining genes and the chromosomes harboring them. Here, we explored the genus Takifugu, in which one strong candidate sex-determining gene, Amhr2, has been identified. To trace the processes involved in transitions in the sex determination system in this genus, we studied 12 species and found that while the Amhr2 locus likely determines sex in the majority of Takifugu species, three species have acquired sex-determining loci at different chromosomal locations. Nevertheless, the generation of genome assemblies for the three species revealed that they share a portion of the male-specific supergene that contains a candidate sex-determining gene, GsdfY, along with genes that potentially play a role in male fitness. The shared supergene span approximately 100 kb and are flanked by two duplicated regions characterized by CACTA transposable elements. These results suggest that the shared supergene has taken over the role of sex-determining locus from Amhr2 in lineages leading to the three species, and repeated translocations of the supergene underlie the turnover of sex chromosomes in these lineages. These findings highlight the underestimated role of a mobile supergene in the turnover of sex chromosomes in vertebrates. SignificanceAlthough turnover of sex chromosomes is very common in many vertebrate lineages, the transition process is still elusive. We studied the sex-determining region (SDR) of 12 congeneric fish species. We found that while nine species retained their ancestral SDR, three species had acquired derived SDRs. Although the derived SDRs resided in three different chromosomes, they harbored a shared supergene flanked by two putative transposable elements. The results highlight the underestimated role of a mobile supergene in turnover of sex chromosomes in vertebrates.

genomics↗