The clam Ruditapes philippinarum is an important species in the marine aquaculture industry in China. However, in recent years, the aquaculture of R. philippinarum has been negatively impacted by various bacterial pathogens. In this study, the transcriptome libraries of R. philippinarum showing different levels of resistance to challenge with Vibrio anguillarum were constructed and RNA-seq was performed using the Illumina sequencing platform. Host immune factors were identified that responded to V. anguillarum infection, including C-type lectin domain, glutathione S-transferase 9, lysozyme, methyltransferase FkbM domain, heat shock 70 kDa protein, Ras-like GTP-binding protein RHO, C1q, F-box and BTB/POZ domain protein zf-C2H2. Ten genes were selected and verified by RT-qPCR, and nine of the gene expression results were consistent with those of RNA-seq. The lectin gene in the phagosome pathway was expressed at a significantly higher level after V. anguillarum infection, which might indicate the role of lectin in the immune response to V. anguillarum. Comparing the results from R. philippinarum resistant and nonresistant to V. anguillarum increases our understanding of the resistant genes and key pathways related to Vibrio challenge in this species. The results obtained here provide a reference for future immunological research focusing on the response of R. philippinarum to V. anguillarum infection.

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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 were predicted in M. veneriformis. Construction of a genome-level phylogenetic tree demonstrated that M. veneriformis and R. 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 P. 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.