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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+Paraburkholderia clade. Also, the lineages represented by P. rhizoxinica and R. andropogonis, respectively, emerged prior to the radiation of the Burkholderia sensu stricto+Caballeronia+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.

尽管伯克霍尔德菌属（Burkholderia）的分类学已得到详尽梳理，但这一庞大且异质的类群的属级界限与组成仍存在显著不确定性。本研究利用92个物种的106个保守蛋白的氨基酸及核苷酸序列，构建稳健的最大似然系统发育树，以探究广义伯克霍尔德菌属（Burkholderia sensu lato）的属级结构。该数据明确支持五个独立演化支：其中四个分别对应狭义伯克霍尔德菌属（Burkholderia sensu stricto），以及新确立的副伯克霍尔德菌属（Paraburkholderia）、卡瓦勒氏菌属（Caballeronia）与罗布茨菌属（Robbsia）；第五个演化支以P. rhizoxinica为代表。基于上述发现，我们为此前被归类为伯克霍尔德菌属但实际隶属于卡瓦勒氏菌属的13个物种提出13个新组合。本研究结果同时提示需重新审视P. rhizoxinica的分类地位，因其并不隶属于当前广义伯克霍尔德菌属中已被认可的任一属。从系统发育视角来看，狭义伯克霍尔德菌属与卡瓦勒氏菌属+副伯克霍尔德菌属单系群构成姊妹群关系。此外，分别以P. rhizoxinica和R. andropogonis为代表的两个演化支，均早于狭义伯克霍尔德菌属+卡瓦勒氏菌属+副伯克霍尔德菌属单系群的辐射演化事件出现。综上，本研究结果不仅为当前及未来的分类学决策提供了坚实的分类框架，也为研究这一类兼具医学、工业与农业重要价值的物种的演化历程奠定了基础。