Data from: Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

The assembled genomic scaffolds of Bathymodiolus platifronsBpl_v1.0.zipThe assembled genomic scaffolds of Modiolus philippinarumMph_v1.0.zipBathymodiolus platifrons genome annotation file (gff3 format)Bpl_maker_v1.0.zipModiolus philippinarum genome annotation file (gff3 format)Mph_maker_v1.0.zipThe predicted transcript sequences of the MAKER v3.0 annotations for the genome of Bathymodiolus platifrons (fasta format)Bpl.maker_FilteredModels_transcripts_v1.0.zipThe predicted protein sequences of the MAKER v3.0 annotations for the genome of Bathymodiolus platifrons (fasta format)Bpl.maker_FilteredModels_proteins_v1.0.zipThe predicted transcript sequences of the MAKER v3.0 annotations for the genome of Modiolus philippinarum (fasta format)Mph.maker_FilteredModels_transcripts_v1.0.zipThe predicted protein sequences of the MAKER v3.0 annotations for the genome of Modiolus philippinarum (fasta format)Mph.maker_FilteredModels_proteins_v1.0.zipThe functional annotation and gene expression level file of the predicted Bathymodiolus platifrons gene modelsAbbreviations used in this excel table: tpm, Transcripts Per Kilobase Million; AM, adductor muscle; F, foot; O, ovary; G, gill; M, mantle; and VM, visceral mass.Bathymodiolus_FunAnno_FilteredGeneModels.xlsxThe functional annotation and gene expression level file of the predicted Modiolus philippinarum gene modelsAbbreviations used in this excel table: tpm, Transcripts Per Kilobase Million; AM, adductor muscle; F, foot; G, gill; M, mantle; and VM, visceral mass.Modiolus_FunAnno_FilteredGeneModels.xlsx

Hydrothermal vents and methane seeps are extreme deep-sea ecosystems that support dense populations of specialised macrobenthos such as mussels. But lack of genome information hinders understanding of the adaptation of these animals to such inhospitable environment. Here we report the genomes of a deep-sea vent/seep mussel Bathymodiolus platifrons and a shallow-water mussel Modiolus philippinarum. Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago. Many gene families, especially those for stabilising protein structures and removing toxic substances from the cells, are greatly expanded in B. platifrons, indicating adaptation to extreme environmental conditions. The B. platifrons innate immune system is considerably more complex than that of other lophotrochozoan species including M. philippinarum, with significant expansion and high expression of gene families related to immune recognition, endocytosis and caspase-mediated apoptosis in the gill, revealing presumed genetic adaptation of the deep-sea mussel to the presence of its chemoautotrophic endosymbionts. A follow-up metaproteomic analysis of the gill of B. platifrons found methanotrophy, assimilatory sulfate reduction, and ammonia metabolic pathways in the symbionts, providing energy and nutrients to allow the host to thrive. Our study of the genomic composition allowing symbiosis in extremophile molluscs gives wider insights into the mechanisms of symbiosis in other organisms such as deep-sea tubeworms and giant clams.