Data from: Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes
Sun, Jin, The Hong Kong University of Science and Technology
Zhang, Yu, Research Center for Eco-Environmental Sciences
Xu, Ting, Hong Kong Baptist University
Zhang, Yang, South China Sea Institute Of Oceanology
Mu, Huawei, Hong Kong Baptist University
Zhang, Yanjie
Lan, Yi, The Hong Kong University of Science and Technology
Fields, Christopher J., University of Illinois at Urbana Champaign
Hui, Jerome H. L., Chinese University of Hong Kong
Zhang, Wei-Peng, The Hong Kong University of Science and Technology
Li, Runsheng, Hong Kong Baptist University
Nong, Wenyan, Chinese University of Hong Kong
Cheung, Fiona K. M., Chinese University of Hong Kong
Qiu, Jian-Wen, Hong Kong Baptist University
Qian, Pei-Yuan, The Hong Kong University of Science and Technology
Citation
Sun, Jin et al. (2017), Data from: Adaptation to deep-sea chemosynthetic environments as revealed by mussel genomes, Dryad, Dataset, https://doi.org/10.5061/dryad.h9942
Abstract
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.
Usage Notes
The assembled genomic scaffolds of Bathymodiolus platifrons
Bpl_v1.0.zip
The assembled genomic scaffolds of Modiolus philippinarum
Mph_v1.0.zip
Bathymodiolus platifrons genome annotation file (gff3 format)
Bpl_maker_v1.0.zip
Modiolus philippinarum genome annotation file (gff3 format)
Mph_maker_v1.0.zip
The predicted transcript sequences of the MAKER v3.0 annotations for the genome of Bathymodiolus platifrons (fasta format)
Bpl.maker_FilteredModels_transcripts_v1.0.zip
The predicted protein sequences of the MAKER v3.0 annotations for the genome of Bathymodiolus platifrons (fasta format)
Bpl.maker_FilteredModels_proteins_v1.0.zip
The predicted transcript sequences of the MAKER v3.0 annotations for the genome of Modiolus philippinarum (fasta format)
Mph.maker_FilteredModels_transcripts_v1.0.zip
The predicted protein sequences of the MAKER v3.0 annotations for the genome of Modiolus philippinarum (fasta format)
Mph.maker_FilteredModels_proteins_v1.0.zip
The functional annotation and gene expression level file of the predicted Bathymodiolus platifrons gene models
Abbreviations 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.xlsx
The functional annotation and gene expression level file of the predicted Modiolus philippinarum gene models
Abbreviations 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