Genome-level homology and phylogeny of Vibrionaceae (Gammaproteobacteria: Vibrionales) with three new complete genome sequences

Background: Phylogenetic hypotheses based on complete genome data are presented for the Gammaproteobacteria family Vibrionaceae. Two taxon samplings are presented: one including all those taxa for which the genome sequences are complete in terms of arrangement (chromosomal location of fragments; 19 taxa) and one for which the genome sequences contain multiple contigs (44 taxa). Analyses are presented under the Maximum Parsimony and Maximum Likelihood optimality criteria for total evidence datasets, the two chromosomes separately, and individual analyses of locally collinear blocks. Three of the genomes included in the 44 taxon dataset, those of Vibrio gazogenes, Salinivibrio costicola, and Aliivibrio logei have been newly sequenced and their genome sequences are documented here. Results: Phylogenetic results for the 19-taxon datasets show similar levels of collinear subset of dataset incongruence as a previous study of 22 taxa from the sister family Shewanellaceae, while also echoing th...

背景：本研究基于全基因组数据构建了γ-变形菌纲（Gammaproteobacteria）弧菌科（Vibrionaceae）的系统发育假说。本研究设置两类类群采样方案：其一涵盖所有基因组序列在片段排布（片段的染色体位置）上完成的类群（共19个类群）；其二涵盖基因组序列包含多个重叠群（contig）的类群（共44个类群）。本研究基于最大简约法（Maximum Parsimony）与最大似然法（Maximum Likelihood）两项最优性准则，分别针对全证据数据集、两条染色体各自的数据集以及局部共线性区块（locally collinear blocks）开展单独分析。本研究新测序了44个类群数据集内的3个基因组，分别为产黄弧菌（Vibrio gazogenes）、嗜盐盐弧菌（Salinivibrio costicola）以及洛氏异弧菌（Aliivibrio logei）的基因组序列，并在此处对其基因组序列进行了记载。结果：针对19个类群数据集的系统发育分析结果显示，其共线性子集数据集的不一致性水平与此前一项针对姐妹群希瓦氏菌科（Shewanellaceae）22个类群的研究结果相近，同时也呼应了……