Ozawa Genki, Shimamura Shigeru, Takaki Yoshihiro, Yokobori Shin-Ichi, Ohara Yasuhiko, Takishita Kiyotaka, Maruyama Tadashi, Fujikura Katsunori, Yoshida Takao
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.
Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa 237-0061, Japan.
Mar Genomics. 2017 Feb;31:43-52. doi: 10.1016/j.margen.2016.09.003. Epub 2016 Oct 6.
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.
双壳贝类的线粒体基因组常被用于比较基因组学和解析系统发育关系。迄今为止，已测序了100多个双壳贝类的完整线粒体基因组。然而，关于深海化学共生双壳贝类（属于翼形亚纲和异齿亚纲）的线粒体基因组报道较少。在本研究中，我们对8种深海化学共生双壳贝类的线粒体基因组进行了测序：3种深海贻贝（日本深海贻贝、宽额深海贻贝和七鳃深海贻贝）、4种泡蛤科蛤类（玛丽安娜深渊蛤、菜豆形深渊蛤、日本化石等鳃蛤和奥库塔尼深海蛤，它们以前都被归类于潜泥蛤属）以及1种海笋科蛤类（双分海笋蛤）。除少数例外，这些线粒体基因组包含后生动物典型的基因：13个蛋白质编码基因、2个rRNA基因和22个tRNA基因。每个基因组中A+T含量高的主要非编码区包含串联重复序列和发夹结构，推测其具有控制区的功能。基于14个共享基因的串联序列重建了翼形亚纲和异齿亚纲的系统发育树。深海贻贝与非共生的贻贝科贻贝形成一个单系类群，泡蛤科蛤类形成一个单系类群，是帘蛤科的姐妹群，双分海笋蛤在异齿亚纲中基部分支。已知双壳贝类线粒体基因组的基因顺序存在差异。为了检验基因顺序变异是否表现出系统发育信号，针对在基于序列的系统发育中具有高统计支持的两个类群（包含沙蛤科、樱蛤科、索氏蛤科和海螂科的海螂超科；以及包含海月蛤科、蛤蜊科、北极蛤科、泡蛤科和帘蛤科的类群），基于最小基因重排数量重建了树形拓扑结构。得到的树形拓扑结构与基于序列的树形结构几乎相同。我们目前的研究结果表明，通过线粒体基因组分析可以精确追溯双壳贝类的进化，并且这种分析有助于理解双壳贝类的进化和多样性。
