The scale bar indicates 0.05 expected substitutions per site.
d, Phylogenetic tree of Mytilidae based on transcriptome data from representative genera/species.
Comparisons among five molluscan genomes revealed 6,883 shared protein domains and 474 protein domains unique to B. 2a and Supplementary Table 14).a, Venn diagram showing the number of shared and unique Pfam functional domains in five molluscan species.
b, Divergence times of 11 lophotrochozoan species with error bars (purple lines) indicating the 95% confidence interval, and the event of gene family expansions (red) and contractions (blue) analysed by counting Pfam domains.
Phylogenetic analysis shows that these mussel species diverged approximately 110.4 million years ago.
Many gene families, especially those for stabilizing protein structures and removing toxic substances from cells, are highly expanded in B.This result supports the hypothesis that the ancestors of modern deep-sea mussels might have experienced an extinction event during the global anoxia period that has been associated with the Palaeocene–Eocene thermal maximum at around 57 Ma. The number of contracted domains in the deep-sea mussel is the smallest among all the species examined. platifrons to the deep-sea chemosynthetic environment was mainly mediated by gene family/domain expansion, and the deep-sea mussel has retained most genes of its shallow-water ancestors.Gene-family analysis among the 11 lophotrochozoans revealed the expansion of 111 protein domains and contraction of 39 domains in B. Among the most numerously expanded gene families in B.platifrons, indicating adaptation to extreme environmental conditions. platifrons is considerably more complex than that of other lophotrochozoan species, including M.philippinarum, with substantial expansion and high expression levels of gene families that are 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.Despite this hostile environment, these ecosystems support dense populations of macrobenthos which, with the help of chemoautotrophic endosymbionts, are fuelled by simple reduced molecules such as methane and hydrogen sulfide.Deep-sea mussels (Mytilidae, Bathymodiolinae) often dominate at hydrothermal vents and cold seeps around the world.1b) in the family Mytilidae using a whole-genome shotgun approach and compared their features ( Supplementary Note 1). The deep-sea and shallow-water mussel genome contained 96.3% and 93.7% complete and partial universal single-copy metazoan orthologous genes, respectively, indicating the completeness of the assembly and gene models ( Supplementary Note 6).Both assembled genomes were highly repetitive ( Supplementary Fig. As with other bilaterians, the two mussel genomes contained all the expected Hox and Para Hox genes, as well as similar numbers of micro RNAs, again suggesting that the assemblies encapsulate a nearly complete representation of genic information ( Supplementary Note 13 and 14). platifrons contain endosymbiotic methane-oxidizing bacteria (MOB), the host scaffolds did not contain bacterial nucleotide sequences, showing a lack of horizontal gene transfer from the symbiont. platifrons has a lower rate of heterozygosity compared to the other three bivalves with a sequenced genome ( Supplementary Fig.Ac, Aplysia californica; Bp, Bathymodiolus platifrons; Bg, Biomphalaria glabrata; Cg, Crassostrea gigas; Ct, Capitella teleta; Hr, Hellobdella robusta; La, Lingula anatina; Lg, Lottia gigantea; Mp, Modiolus philippinarum; Ob, Octopus bimaculoides; Pf, Pinctada fucata.A phylogenetic tree constructed using 375 single-copy orthologues from 11 lophotrochozoan species (Fig.