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

Abstract

Red abalone, Haliotis rufescens, 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, United States, to Baja California, MEX. Recently, red abalone have been in decline as a consequence of overharvesting, 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.

Keywords: CCGP; California Conservation Genomics Project; conservation genomics; red abalone.

Fig. 1.

(A) Adult red abalone, Haliotis rufescens. Photo taken by Jackson Gross. (B) Red abalone larvae 74 d postfertilization at 1.6× magnification. Photo taken by Sara Boles.

Fig. 2.

Visual overview of genome assembly metrics. (A) K-mer spectrum output generated from PacBio HiFi data without adapters using GenomeScope2.0. The bimodal pattern observed corresponds to a diploid genome. K-mers covered at lower coverage and high frequency correspond to differences between haplotypes, whereas the higher coverage and slightly lower frequency k-mers correspond to the similarities between haplotypes. (B) BlobToolKit Snail plot showing a graphical representation of the quality metrics presented in Table 2 for the Haliotis rufescens primary assembly (xgHalRufe1). The plot circle represents the full size of the assembly. From the inside-out, the central plot covers length-related metrics. The red line represents the size of the longest scaffold; all other scaffolds are arranged in size-order moving clockwise around the plot and drawn in gray starting from the outside of the central plot. Dark and light orange arcs show the scaffold N50 and scaffold N90 values. The central light gray spiral shows the cumulative scaffold count with a white line at each order of magnitude. White regions in this area reflect the proportion of Ns in the assembly. The dark versus light blue area around it shows mean, maximum, and minimum GC versus AT content at 0.1% intervals (Challis et al. 2020). Omni-C contact maps for the primary (C) and alternate (D) genome assembly generated with PretextSnapshot. Hi-C contact maps translate proximity of genomic regions in 3D space to contiguous linear organization. Each cell in the contact map corresponds to sequencing data supporting the linkage (or join) between 2 of such regions.