Characterization and inference of gene gain/loss along burkholderia evolutionary history

Abstract

A comparative analysis of 60 complete Burkholderia genomes was conducted to obtain insight in the evolutionary history behind the diversity and pathogenicity at species level. A concatenated multiprotein phyletic pattern and a dataset with Burkholderia clusters of orthologous genes (BuCOGs) were constructed. The extent of horizontal gene transfer (HGT) was assessed using a Markov based probabilistic method. A reconstruction of the gene gains and losses history shows that more than half of the Burkholderia genes families are inferred to have experienced HGT at least once during their evolution. Further analysis revealed that the number of gene gain and loss was correlated with the branch length. Genomic islands (GEIs) analysis based on evolutionary history reconstruction not only revealed that most genes in ancient GEIs were gained but also suggested that the fraction of the genome located in GEIs in the small chromosomes is higher than in the large chromosomes in Burkholderia. The mapping of coexpressed genes onto biological pathway schemes revealed that pathogenicity of Burkholderia strains is probably mainly determined by the gained genes in its ancestor. Taken together, our results strongly support that gene gain and loss especially in ancient evolutionary history play an important role in strain divergence, pathogenicity determinants of Burkholderia and GEIs formation.

Keywords: Burkholderia; Markov model; coexpression; gene gain/loss; genomic island.

Figure 1.

Phylogenetic tree of Burkholderiaceae based on concatenated amino acid alignments of one homolog gene and rooted by using proteins from other Burkholderiaceae species as the outgroup. All the evolutionary nodes in this tree were supported by bootstrap values higher than 90%. Reconstruction of gene content evolution based on BuCOGs in Burkholderia is shown. For each species and each internal node of a tree, the inferred number of BuCOGs present (numbers in black), and the numbers of BuCOGs lost (numbers in blue) or gained (numbers in red) along the branch leading to a given node (species) are indicated.

Figure 2.

Taxonomic distribution of candidate donors for putatively transferred Burkholderia genes. The taxonomy is sorted by the percentages representing numbers of hits relative to the BuCOGs total number (white bars). The percentages relative to the number of phylum-specific proteins in Genbank are shown as black bars. No matches were detected for Dictyoglomi, Elusimicrobia, Synergistetes and Tenericutes (data from 2, 2, 1, and 26 genomes, respectively). Data for Caldiserica, Chrysiogenetes were not available at the time of analysis.

Figure 3.

Profiling of the B. mallei SAVP1 and ATCC 23344 lost genes and regions. (A) Graphs represent the best protein hits scatter plot (black dots) and B. mallei SAVP1 chromosome 2 recent lost genes (blue dots under x axis) in B. mallei ATCC 23344 chromosome 2. (B) Graphs represent the best protein hits scatter plot (black dots) and B. mallei ATCC 23344 chromosome 2 B. mallei lost genes (blue dots under x axis) in B. pseudomallei K96243 chromosome 2. Black scatter plot represents the best protein hits of two genomes chromosome according to the Pathema Scatter Plot Results. The lost gene homologues were plotted onto the another genome’s chromosome under the bar with blue dots. The shaded regions represent the lost regions. The black rectangle region represents the T3SS location.