Single individual structural variant detection uncovers widespread hemizygosity in molluscs

Abstract

The advent of complete genomic sequencing has opened a window into genomic phenomena obscured by fragmented assemblies. A good example of these is the existence of hemizygous regions of autosomal chromosomes, which can result in marked differences in gene content between individuals within species. While these hemizygous regions, and presence/absence variation of genes that can result, are well known in plants, firm evidence has only recently emerged for their existence in metazoans. Here, we use recently published, complete genomes from wild-caught molluscs to investigate the prevalence of hemizygosity across a well-known and ecologically important clade. We show that hemizygous regions are widespread in mollusc genomes, not clustered in individual chromosomes, and often contain genes linked to transposition, DNA repair and stress response. With targeted investigations of HSP70-12 and C1qDC , we also show how individual gene families are distributed within pan-genomes. This work suggests that extensive pan-genomes are widespread across the conchiferan Mollusca, and represent useful tools for genomic evolution, allowing the maintenance of additional genetic diversity within the population. As genomic sequencing and re-sequencing becomes more routine, the prevalence of hemizygosity, and its impact on selection and adaptation, are key targets for research across the tree of life. This article is part of the Theo Murphy meeting issue ‘Molluscan genomics: broad insights and future directions for a neglected phylum’.

ADAR-Editing during Ostreid Herpesvirus 1 Infection in Crassostrea gigas : Facts and Limitations

“…Several bottlenecks currently limited the analysis of ADAR editing from bivalve RNA-seq data. Firstly, we rely only on a reference genome for the quantification of ADAR editing, not covering interindividual variability, which is extremely important in bivalves, compared to vertebrates, and involves presence–absence of hundreds to thousands of genes ( 19 ). Second, the different strategies adopted for the RNA library preparation likely biased the identification of ADAR edits, with the polyA depletion showing a lower efficiency than the ribosomal rRNA depletion in collecting key substrates such as ncRNAs ( 20 ).…”

Ancestral Physical Stress and Later Immune Gene Family Expansions Shaped Bivalve Mollusc Evolution

“…Exploring the evolution of these gene families requires high-quality bivalve reference genomes. Generating such genomes has been impeded by high levels of heterozygosity ( Plough 2016 ; Takeuchi 2017 ; Hollenbeck and Johnston 2018 ), repetitive regions ( Davison and Neiman 2021 ), and structural variations ( Calcino et al 2021 ). A pan-genome based on gene presence–absence variation has recently been suggested for the Mediterranean mussel ( Gerdol et al 2020 ).…”

Pearls of wisdom—a Theo Murphy issue on molluscan genomics

“…Such variation has led to an appreciation of the ‘pangenome', the complete set of genes present in a species, although still with relatively few studies in metazoans. Thus, work by Calcino et al [11] and others [12] using recently published complete genomes from representatives of eight wild-caught mollusc species to investigate the prevalence of hemizygous regions has implications for understanding genome dynamics across the other animal phyla. For similar benefit, Modak et al [13] assess copy number variation in oyster.…”

“…Although rigorous characterization of genomic architecture across all but model eukaryotes is at an early stage of cataloguing, it is likely that this is the beginning of a deluge as data generation becomes more straightforward. A note of caution, however, is that future comparative studies should use genome assemblies built with consistent assembly and annotation pipelines [11].…”