Beukes Chrizelle W, Palmer Marike, Manyaka Puseletso, Chan Wai Y, Avontuur Juanita R, van Zyl Elritha, Huntemann Marcel, Clum Alicia, Pillay Manoj, Palaniappan Krishnaveni, Varghese Neha, Mikhailova Natalia, Stamatis Dimitrios, Reddy T B K, Daum Chris, Shapiro Nicole, Markowitz Victor, Ivanova Natalia, Kyrpides Nikos, Woyke Tanja, Blom Jochen, Whitman William B, Venter Stephanus N, Steenkamp Emma T
Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa.
DOE Joint Genome Institute, Walnut CreekCA, United States.
Front Microbiol. 2017 Jun 26;8:1154. doi: 10.3389/fmicb.2017.01154. eCollection 2017.
Although the taxonomy of has been extensively scrutinized, significant uncertainty remains regarding the generic boundaries and composition of this large and heterogeneous taxon. Here we used the amino acid and nucleotide sequences of 106 conserved proteins from 92 species to infer robust maximum likelihood phylogenies with which to investigate the generic structure of sensu lato. These data unambiguously supported five distinct lineages, of which four correspond to sensu stricto and the newly introduced genera , , and . The fifth lineage was represented by . Based on these findings, we propose 13 new combinations for those species previously described as members of but that form part of . These findings also suggest revision of the taxonomic status of as it is does not form part of any of the genera currently recognized in sensu lato. From a phylogenetic point of view, sensu stricto has a sister relationship with the + clade. Also, the lineages represented by and , respectively, emerged prior to the radiation of the sensu stricto++ clade. Our findings therefore constitute a solid framework, not only for supporting current and future taxonomic decisions, but also for studying the evolution of this assemblage of medically, industrially and agriculturally important species.
尽管对[该分类单元名称]的分类法已进行了广泛审查，但关于这个庞大且异质的分类单元的属界限和组成仍存在重大不确定性。在此，我们使用了来自92个物种的106种保守蛋白质的氨基酸和核苷酸序列，以推断出稳健的最大似然系统发育树，从而研究广义[该分类单元名称]的属结构。这些数据明确支持了五个不同的谱系，其中四个对应狭义[该分类单元名称]以及新引入的属[新属名称1]、[新属名称2]和[新属名称3]。第五个谱系由[相关物种名称]代表。基于这些发现，我们为那些先前被描述为[该分类单元名称]成员但实际属于[相关分类单元名称]的物种提出了13个新的组合。这些发现还表明应修订[该分类单元名称]的分类地位，因为它不属于目前广义[该分类单元名称]中认可的任何一个属。从系统发育的角度来看，狭义[该分类单元名称]与[相关分类单元名称] + 分支具有姐妹关系。此外，分别由[相关物种名称1]和[相关物种名称2]代表的谱系在狭义[该分类单元名称] ++ 分支辐射之前就已出现。因此，我们的发现构成了一个坚实的框架，不仅可支持当前和未来的分类决策，还可用于研究这一具有医学、工业和农业重要性的物种组合的进化。
