DOI: 10.5061/dryad.h9942
title: Data from: Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes

description: 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.
description: 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