A research group led by Associate Professor Shotaro Hirase of the Graduate School of Agricultural and Life Sciences, the University of Tokyo has sequenced the complete genome of the western Pacific abalone (Haliotis gigantea), a large abalone species native to Japan, and constructed a high-quality diploid genome assembly. Their findings were published in Molecular Ecology Resources.
Diploid organisms have a pair of chromosomes derived from each parent, which are called homologous chromosomes. In constructing the complete genome sequence of such organisms, known as genome assembly, homologous chromosomes are assumed to share the same gene order (synteny). Based on this assumption, haploid genome sequences in which genome sequences of homologous chromosomes are mixed have traditionally been built. However, when genomes differ greatly between homologous chromosomes, the genomic diversity of the species may be overlooked.
Marine invertebrates account for a large portion of Earth's biodiversity. Previous studies have revealed that some marine invertebrates have substantially different genome structures between homologous chromosomes. To obtain a full picture of such genomic diversity, it is necessary to perform haplotype-phased genome assembly. This sequences the genomes of homologous chromosomes separately, and then directly compares them.
Approximately 60 species of abalones are known worldwide, and all species belong to the genus Haliotis. Abalones have significant cultural and historical value and are important as a fishery resource. But in recent years, wild populations have declined sharply due to overfishing, climate change, and the spread of disease.
As a result, many species are now at risk of extinction, and genome assemblies of the world's major abalone species have been carried out to support their conservation and breeding. However, no high-precision haplotype-phased genome assembly had previously been constructed for abalones.
By comparing the two genome assemblies derived from homologous chromosomes (the primary assembly and the alternative assembly) constructed in this study, three pairs of homologous chromosomes with large non-syntenic genomic regions—where synteny is not conserved—were identified. Such homologous chromosomes with non-syntenic regions were also found in other major abalone species worldwide, suggesting that the origin of these genomic regions may date back to the time when abalones first appeared.
Upon closer examination of these genomic regions, extensive segmental duplications were observed. Analysis of genes duplicated in these regions revealed they possess specific domains, including those related to immunity. Furthermore, when the proportion of duplicated genes in the genome was investigated across 46 invertebrate species, abalones included, it was found the Western Pacific abalone and other abalone species have particularly large numbers of duplicated genes.
It is generally believed that genes produced through duplication can acquire new capabilities when released from functional constraints, as well as increasing gene expression levels. Abalones are a very ancient group of organisms whose origins date back to the Cretaceous period. The non-syntenic regions discovered in this study may have led to the accumulation of duplicated genes in the genome, with such redundancy potentially having contributed to the prosperity of abalones.
In future studies on the evolution, conservation, and breeding of abalones, the large number of duplicated genes they possess will attract attention as an important genetic background.
Journal Information
Publication: Molecular Ecology Resources
Title: Ancestral Origin and Structural Characteristics of Non-Syntenic Homologous Chromosomes in Abalones (Haliotis)
DOI: 10.1111/1755-0998.70057
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