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

Abstract

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.

Keywords: Burkholderia; Burkholderia rhizoxinica; Caballeronia; Paraburkholderia; Robbsia andropogonis; phylogenomics.

FIGURE 1

A heat map depicting the sequence similarity of the concatenated sequence of the conserved 106 genes used for phylogenetic analysis. The cladogram indicating the various intra- and intergeneric relationships were inferred from the amino acid based ML topology. Nucleotide similarity values are indicated in the upper triangle of the map, with amino acid similarity values indicated in the lower triangle of the map. A summary of the similarity values for the 5 lineages of interest are indicated for each group (nucleotide/amino acid %), in the panel on the right. For specific values, refer to Supplementary File S1.

FIGURE 2

A maximum-likelihood phylogeny of the amino acid sequences of 106 concatenated genes for the 92 strains used in this study. A similar topology was obtained using the nucleotide sequences for these genes (Supplementary Figure S3). New combinations that have not yet been validated are indicated in inverted commas. General species substrates and origins are color coded according to the key provided. The majority of branches received 100% bootstrap in both the amino acid and nucleotide phylogenies and therefore only those branches in which 100% was not calculated for both analyses are indicated. Support is indicated in the order amino acid/nucleotide. The scale bar indicates the number of changes per site.