Genome Data Provides High Support for Generic Boundaries in Burkholderia Sensu Lato

被引:83
作者
Beukes, Chrizelle W. [1 ]
Palmer, Marike [1 ]
Manyaka, Puseletso [1 ]
Chan, Wai Y. [1 ]
Avontuur, Juanita R. [1 ]
van Zyl, Elritha [1 ]
Huntemann, Marcel [2 ]
Clum, Alicia [2 ]
Pillay, Manoj [2 ]
Palaniappan, Krishnaveni [2 ]
Varghese, Neha [2 ]
Mikhailova, Natalia [2 ]
Stamatis, Dimitrios [2 ]
Reddy, T. B. K. [2 ]
Daum, Chris [2 ]
Shapiro, Nicole [2 ]
Markowitz, Victor [2 ]
Ivanova, Natalia [2 ]
Kyrpides, Nikos [2 ]
Woyke, Tanja [2 ]
Blom, Jochen [3 ]
Whitman, William B. [4 ]
Venter, Stephanus N. [1 ]
Steenkamp, Emma T. [1 ]
机构
[1] Univ Pretoria, Forestry & Agr Biotechnol Inst, Dept Microbiol & Plant Pathol, Pretoria, South Africa
[2] DOE Joint Genome Inst, Walnut Creek, CA USA
[3] Justus Liebig Univ Giessen, Bioinformat & Syst Biol, Giessen, Germany
[4] Univ Georgia, Dept Microbiol, Athens, GA 30602 USA
基金
美国能源部; 新加坡国家研究基金会;
关键词
Burkholderia; Paraburkholderia; Caballeronia; phylogenomics; Robbsia andropogonis; Burkholderia rhizoxinica; SP-NOV; BACTERIAL; TAXONOMY; GENUS; RECONSTRUCTION; PHYLOGENOMICS; REASSESSMENT; ALGORITHMS; DIVERSITY; EVOLUTION;
D O I
10.3389/fmicb.2017.01154
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
Although the taxonomy of Burkholderia 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 Burkholderia sensu lato. These data unambiguously supported five distinct lineages, of which four correspond to Burkholderia sensu stricto and the newly introduced genera Paraburkholderia, Caballeronia, and Robbsia. The fifth lineage was represented by P. rhizoxinica. Based on these findings, we propose 13 new combinations for those species previously described as members of Burkholderia but that form part of Caballeronia. These findings also suggest revision of the taxonomic status of P. rhizoxinica as it is does not form part of any of the genera currently recognized in Burkholderia sensu lato. From a phylogenetic point of view, Burkholderia sensu stricto has a sister relationship with the Caballeronia C Paraburkholderia clade. Also, the lineages represented by P. rhizoxinica and R. andropogonis, respectively, emerged prior to the radiation of the Burkholderia sensu stricto C Caballeronia C Paraburkholderia 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.
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页数:11
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