A high-quality chromosome-level genome assembly of the bivalve mollusk Mactra veneriformis.

Abstract

Mactra veneriformis (Bivalvia: Mactridae) is a bivalve mollusk of major economic importance in China. Decreased natural yields of M. veneriformis have led to an urgent need for genomic resources. To address this problem and the currently limited knowledge of molecular evolution in this genus, we here report a high-quality chromosome-level genome assembly of M. veneriformis. Our approach yielded a 939.32 Mb assembled genome with an N50 contig length of 7,977.84 kb. Hi-C scaffolding of the genome resulted in assembly of 19 pseudochromosomes. Repetitive elements made up ∼51.79% of the genome assembly. A total of 29,315 protein-coding genes (PCGs) were predicted in M. veneriformis. Construction of a genome-level phylogenetic tree demonstrated that M. veneriformis and Ruditapes philippinarum diverged around 231 million years ago (MYA). Inter-species comparisons revealed that 493 gene families have undergone expansion and 449 have undergone contraction in the M. veneriformis genome. Chromosome-based macrosynteny analysis revealed a high degree of synteny between the 19 chromosomes of M. veneriformis and those of Patinopecten yessoensis. These results suggested that M. veneriformis has a similar karyotype to that of P. yessoensis, and that a highly conserved 19-chromosome karyotype was formed in the early differentiation stages of bivalves. In summary, the genomic resources generated in this work serve as a valuable reference for investigating the molecular mechanisms underlying biological functions in M. veneriformis and will facilitate future genetic improvement and disease treatment in this economically important species. Furthermore, the assembled genome greatly improves our understanding of early genomic evolution of the Bivalvia.