title: Updated mitochondrial phylogeny of Pteriomorph and Heterodont Bivalvia, including deep-sea chemosymbiotic Bathymodiolus mussels, vesicomyid clams and the thyasirid clam Conchocele cf. bisecta.
abstract: The mitochondrial genomes of bivalves have often been used for comparative genomics and for resolving phylogenetic relationships. More than 100 bivalve complete mitochondrial genomes have been sequenced to date. However, few mitochondrial genomes have been reported for deep-sea chemosymbiotic bivalves, which belong to the subclasses Pteriomorphia and Heterodonta. In the present study, we sequenced the mitochondrial genomes of eight deep-sea chemosymbiotic bivalve species: three species of Bathymodiolus mussels (B. japonicus, B. platifrons, and B. septemdierum), four species of vesicomyid clams (Abyssogena mariana, A. phaseoliformis, Isorropodon fossajaponicum, and Phreagena okutanii, all of which were formerly classified in the genus Calyptogena), and one species of thyasirid clam (Conchocele cf. bisecta). With a few exceptions, these mitochondrial genomes contained genes that are typical of metazoans: 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. The major non-coding region with a high A+T content of each genome, which contained tandem repeats and hairpins, was hypothesized to function as a control region. The phylogenetic trees of Pteriomorphia and Heterodonta were reconstructed based on the concatenated sequences of 14 shared genes. Bathymodiolus formed a monophyletic clade with asymbiotic Mytilidae mussels, the vesicomyid clams formed a monophyly that was sister to the Veneridae, and C. cf. bisecta branched basally in the Heterodonta. It is known that the gene orders of mitochondrial genomes vary among bivalves. To examine whether gene order variation exhibits phylogenetic signals, tree topologies based on the minimum number of gene rearrangements were reconstructed for two clades (superfamily Tellinoidea, which includes the Psammobiidae, Semelidae, Solecurtidae, and Tellinidae; and the clade comprising the Myidae, Mactridae, Arcticidae, Vesicomyidae, and Veneridae) with high statistical support in sequence-based phylogenies. The resulting tree topologies were almost identical to those of the sequence-based trees. Our present findings suggest that the evolution of bivalves could be precisely traced back through the analysis of mitochondrial genomes, and that such an analysis could contribute to understanding bivalve evolution and diversity.
authors.affiliation: Department of Marine Biosciences, School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan; Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan. Electronic address: genki-ozawa@jamstec.go.jp.
authors.forename: Genki
authors.initials: G
authors.lastname: Ozawa
authors.affiliation: Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan. Electronic address: shimas@jamstec.go.jp.
authors.forename: Shigeru
authors.initials: S
authors.lastname: Shimamura
authors.affiliation: Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan. Electronic address: takakiy@jamstec.go.jp.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Takaki
authors.affiliation: Laboratory of Cellular Biochemistry, Department of Molecular Biology, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, 1432-1 Horinouchi, Hachioji, Tokyo 192-0392, Japan. Electronic address: yokobori@ls.toyaku.ac.jp.
authors.forename: Shin-Ichi
authors.initials: SI
authors.lastname: Yokobori
authors.affiliation: Hydrographic and Oceanographic Department of Japan, 3-1-1, Kasumigaseki, Chiyoda-ku, Tokyo 100-8932, Japan. Electronic address: ohara@jodc.go.jp.
authors.forename: Yasuhiko
authors.initials: Y
authors.lastname: Ohara
authors.affiliation: Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan. Electronic address: takishitak@jamstec.go.jp.
authors.forename: Kiyotaka
authors.initials: K
authors.lastname: Takishita
authors.affiliation: Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan. Electronic address: tadashim@jamstec.go.jp.
authors.forename: Tadashi
authors.initials: T
authors.lastname: Maruyama
authors.affiliation: Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan. Electronic address: fujikura@jamstec.go.jp.
authors.forename: Katsunori
authors.initials: K
authors.lastname: Fujikura
authors.affiliation: Department of Marine Biosciences, School of Marine Biosciences, Kitasato University, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan; Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan. Electronic address: tyoshida@jamstec.go.jp.
authors.forename: Takao
authors.initials: T
authors.lastname: Yoshida
mesh_terms: D000818:Animals; D049872:Bivalvia / Q000145:classification* / Q000235:genetics*; D023061:Gene Order; D020459:Genes, rRNA / Q000235:genetics; D054629:Genome, Mitochondrial; D060086:Hydrothermal Vents; D010802:Phylogeny; D012343:RNA, Transfer / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D012343:RNA, Transfer
keywords: Gene order arrangement; Mitochondrial genome; Non-coding region; Phylogenetic tree