Peering into the gaps: Long-read sequencing illuminates structural variants and genomic evolution in the Australasian snapper

Abstract

Even before genome sequencing, genetic resources have supported species management and breeding programs. Current technologies, such as long-read sequencing, resolve complex genomic regions, like those rich in repeats or high in GC content. Improved genome contiguity enhances accuracy in identifying structural variants (SVs) and transposable elements (TEs). We present an improved genome assembly and SV catalogue for the Australasian snapper (Chrysophrys auratus). The new assembly is more contiguous, allowing for putative identification of 14 centromeres and transfer of 26,115 gene annotations from yellowfin seabream. Compared to the previous assembly, 35,000 additional SVs, including larger and more complex rearrangements, were annotated. SVs and TEs exhibit a distribution pattern skewed towards chromosome ends, likely influenced by recombination. Some SVs overlap with growth-related genes, underscoring their significance. This upgraded genome serves as a foundation for studying natural and artificial selection, offers a reference for related species, and sheds light on genome dynamics shaped by evolution.