Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov.
Updating the Vibrio clades defined by multilocus sequence phylogeny: proposal of eight new clades, and the description of Vibrio tritonius sp. nov.
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DOI：
10.3389/fmicb.2013.00414
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发表时间：
2013
影响因子：
5.2
通讯作者：
Hayashi T
中科院分区：
文献类型：
--
作者：
Sawabe T;Ogura Y;Matsumura Y;Feng G;Amin AR;Mino S;Nakagawa S;Sawabe T;Kumar R;Fukui Y;Satomi M;Matsushima R;Thompson FL;Gomez-Gil B;Christen R;Maruyama F;Kurokawa K;Hayashi T
迄今为止，在弧菌科细菌中已描述了142种，分为7属；alialivibrio，棘单胞菌，肠弧菌，Grimontia，光细菌，盐弧菌和弧菌。由于弧菌在海洋环境中广泛存在，具有多种代谢和生态功能，因此被认为是最多样化和最重要的海洋异养细菌类群之一，有助于阐明基因组进化与生态适应之间的关系。然而，在16S rRNA基因系统发育的基础上，我们没有在任何已知属中发现任何强大的单系谱系。我们需要进一步尝试基于多位点序列分析（MLSA）和/或所有已知物种群的全基因组分类来重建它们的进化史。在我们2007年的报告中，我们首次进行了广泛的多位点序列分析（MLSA），利用9个家政基因（16S rRNA基因，gapA, gyrB, ftsZ, mreB, pyrH, recA， rpoA和topA）推断弧菌的进化史，并在58种弧菌科中提出了14个不同的分支。由于很难设计出能够在所有弧菌科物种中扩增MLSA基因的通用引物，一些分支尚未确定。在这项研究中，我们使用8个管家基因序列，对86种已描述弧菌和10种弧菌科菌株的最新分子系统发育有了更好的了解。这项新的研究特别强调了(1)8个新发现的分支（Damselae, Mediterranei, Pectenicida, Phosphoreum, proundum, Porteresiae， Rosenbergii和Rumoiensis）；(2)自2007年提案以来，新描述的新种被修正；(3) F6和F10基因组种的孤儿枝；(4) 3个基因组测序菌株（N418、EX25和EJY3）的系统发育定位；(5) tritonius sp. nov.的描述，它是“Porteresiae”分支的成员。
To date 142 species have been described in the Vibrionaceae family of bacteria, classified into seven genera; Aliivibrio, Echinimonas, Enterovibrio, Grimontia, Photobacterium, Salinivibrio and Vibrio. As vibrios are widespread in marine environments and show versatile metabolisms and ecologies, these bacteria are recognized as one of the most diverse and important marine heterotrophic bacterial groups for elucidating the correlation between genome evolution and ecological adaptation. However, on the basis of 16S rRNA gene phylogeny, we could not find any robust monophyletic lineages in any of the known genera. We needed further attempts to reconstruct their evolutionary history based on multilocus sequence analysis (MLSA) and/or genome wide taxonomy of all the recognized species groups. In our previous report in 2007, we conducted the first broad multilocus sequence analysis (MLSA) to infer the evolutionary history of vibrios using nine housekeeping genes (the 16S rRNA gene, gapA, gyrB, ftsZ, mreB, pyrH, recA, rpoA, and topA), and we proposed 14 distinct clades in 58 species of Vibrionaceae. Due to the difficulty of designing universal primers that can amplify the genes for MLSA in every Vibrionaceae species, some clades had yet to be defined. In this study, we present a better picture of an updated molecular phylogeny for 86 described vibrio species and 10 genome sequenced Vibrionaceae strains, using 8 housekeeping gene sequences. This new study places special emphasis on (1) eight newly identified clades (Damselae, Mediterranei, Pectenicida, Phosphoreum, Profundum, Porteresiae, Rosenbergii, and Rumoiensis); (2) clades amended since the 2007 proposal with recently described new species; (3) orphan clades of genomospecies F6 and F10; (4) phylogenetic positions defined in 3 genome-sequenced strains (N418, EX25, and EJY3); and (5) description of V. tritonius sp. nov., which is a member of the “Porteresiae” clade.
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影响因子：
--
作者：
Auch AF;von Jan M;Klenk HP;Göker M
通讯作者：
Göker M
影响因子：
4.2
作者：
Haley BJ;Grim CJ;Hasan NA;Choi SY;Chun J;Brettin TS;Bruce DC;Challacombe JF;Detter JC;Han CS;Huq A;Colwell RR
通讯作者：
Colwell RR
影响因子：
3.2
作者：
Aujoulat, Fabien;Jumas-Bilak, Estelle;Teyssier, Corinne
通讯作者：
Teyssier, Corinne
DOI：
10.1073/pnas.0409727102
发表时间：
2005-02-15
影响因子：
11.1
作者：
Konstantinidis, KT;Tiedje, JM
通讯作者：
Tiedje, JM
影响因子：
5.8
作者：
Larkin, M. A.;Blackshields, G.;Higgins, D. G.
通讯作者：
Higgins, D. G.