A chromosome-length genome assembly for the Pismo clam, Tivela stultorum, a long-lived bivalve species severely impacted by overfishing.

Abstract

The Pismo clam, Tivela stultorum, is an ecologically and economically important species that inhabiting sandy beaches and subtidal zones in central and southern California, USA, and northern Baja California, Mexico. This long lived venerid clam species is of great management, cultural and conservation interest in California where it was harvested for centuries by indigenous people and then nearly extirpated by intense commercial and recreational overfishing in the mid 1900's. A recreational fishery continues today in California, however T. stultorum faces pressure from poaching, overharvest, and the loss of sandy beaches from rising sea levels and beach erosion. Understanding the susceptibility and resilience of Pismo clams to these pressures is essential for their conservation. We used Pacific Biosciences HiFi long sequencing reads and Dovetail Omni-C proximity reads to assemble a highly contiguous genome of 763 Mb. The genome had a contig N50 of 13 Mb and a scaffold N50 of 38 Mb with a BUSCO completeness score of 95%. Most of the genome sequences (96%) were contained in 19 scaffolds at least 10MB long, consistent with prior evidence that venerid clam genomes are composed of 19 autosomes. This reference genome will enable a more complete understanding of the ecology and evolutionary dynamics of T. stultorum via population genomic analyses, which will help assess risks from climate, fishing, environmental change, and susceptibilities due to life history. Our goal is to better support the continued recovery, informed management and conservation, and future persistence of T. stultorum, a long lived and highly valued clam species.