A draft reference genome of the red abalone, Haliotis rufescens, for conservation genomics

Abstract

Red abalone, Haliotis rufencens, are herbivorous marine gastropods that primarily feed on kelp. They are the largest and longest-lived of abalone species with a range distribution in North America from central Oregon, USA, to Baja California, MEX. Recently, red abalone have been in decline as a consequence of over-harvesting, disease, and climate change, resulting in the closure of the commercial fishery in the 1990s and the recreational fishery in 2018. Protecting this ecologically and economically important species requires an understanding of their current population dynamics and connectivity. Here, we present a new red abalone reference genome as part of the California Conservation Genomics project (CCGP). Following the CCGP genome strategy, we used Pacific Biosciences HiFi long-reads and Dovetail Omni-C data to generate a scaffold-level assembly. The assembly comprises 616 scaffolds for a total size of 1.3 Gb, a scaffold N50 of 45.7 Mb, and a BUSCO complete score of 97.3 %. This genome represents a significant improvement over a previous assembly and will serve as a powerful tool for investigating seascape genomic diversity, local adaptation to temperature and ocean acidification, and informing management strategies.

Chromosome-scale genome assembly the tropical abalone (Haliotis asinina)

“…Retroelements (Class I) comprised 13.25%, DNA transposons (Class II) were 5.37%, and 1.30% were simple repeats. The proportion of repeats found in H. asinina genome is relatively similar to other abalone species 17,[43][44][45] and other marine invertebrates 46,47 such as Aplysia californica 48 and Crassostrea virginica 49 . isoforms and to obtain the longest isoform per gene.…”