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bioRxiv · 10.1101/2025.04.02.641744

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

Hirase, S.·Makino, T.·Takeuchi, T.·Kadota, M.·Kuraku, S.·Kikuchi, K.
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Abstract

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.

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Hirase, S., Makino, T., Takeuchi, T., Kadota, M., Kuraku, S., Kikuchi, K.. 2025-04-03. Ancestral origin and structural characteristics of non-syntenic homologous chromosomes in abalones. https://doi.org/10.1101/2025.04.02.641744

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