Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp

Abstract

Background: The genus Burkholderia consists of species that occupy remarkably diverse ecological niches. Its best known members are important pathogens, B. mallei and B. pseudomallei, which cause glanders and melioidosis, respectively. Burkholderia genomes are unusual due to their multichromosomal organization, generally comprised of 2-3 chromosomes.

Results: We performed integrated genomic analysis of 127 Burkholderia strains. The pan-genome is open with the saturation to be reached between 86,000 and 88,000 genes. The reconstructed rearrangements indicate a strong avoidance of intra-replichore inversions that is likely caused by selection against the transfer of large groups of genes between the leading and the lagging strands. Translocated genes also tend to retain their position in the leading or the lagging strand, and this selection is stronger for large syntenies. Integrated reconstruction of chromosome rearrangements in the context of strains phylogeny reveals parallel rearrangements that may indicate inversion-based phase variation and integration of new genomic islands. In particular, we detected parallel inversions in the second chromosomes of B. pseudomallei with breakpoints formed by genes encoding membrane components of multidrug resistance complex, that may be linked to a phase variation mechanism. Two genomic islands, spreading horizontally between chromosomes, were detected in the B. cepacia group.

Conclusions: This study demonstrates the power of integrated analysis of pan-genomes, chromosome rearrangements, and selection regimes. Non-random inversion patterns indicate selective pressure, inversions are particularly frequent in a recent pathogen B. mallei, and, together with periods of positive selection at other branches, may indicate adaptation to new niches. One such adaptation could be a possible phase variation mechanism in B. pseudomallei.

Keywords: Burkholderia; Comparative genomics; Genome rearrangements; Multi-chromosome bacteria; Pan-genome; Positive selection; Strain phylogeny.

Fig. 1

Number of genes as a function of the number of sequenced Burkholderia genomes. (a) The pan-genome size, that is, the number of all genes in sequenced strains. The number of new genes decreases with each new genome n at the rate N(n)=2557n^−0,56 confirming that the pan-genome is open. As the numbers of genomes n→∞, the pan-genome size converges to 88,080 and the core-genome size converges to 457 genes. (b) The core-genome size, that is, the number of common genes in sequenced strains. The core-genome for a single strain (n=1) is defined as the number of genes in the strain

Fig. 2

Distribution of ortholog groups by the number of strains in which they are present. For each number of strains x, the number of genes y present in exactly x strains is given. The blue line corresponds to the approximation by a sum of three exponents y=e^−0.2x+8.4+e^−1.8x+11.6+e^{0.85x−100.1}; the red line corresponds to the approximation by a sum of two power functions y=21648.4x^−1.8+1182.8(128−x)^−1.2. Based on the Akaike information criterion (AIC), the approximation by the sum of three exponents recapitulates the U-shape slightly better

Fig. 3

Translocations in Burkholderia spp. The phylogenetic tree of Burkholderia is constructed based on the protein sequence similarity of single-copy universal genes. The bootstrap support is shown for branches where it is <100. The red numbers above the arrows show the number of genes translocated between chromosomes on the tree branches; the black numbers mark chromosomes that have been involved in the transfer, the arrows show the direction of the transfer

Fig. 4

Phyletic patterns of two genomic islands detected in the B. cepacia group. Strains with the genomic island in the first chromosome are marked by green; strains with the genomic island in the second chromosome are marked by blue; red indicates location on plasmids. Strains with an incomplete cassette are marked by stars. Phyletic patterns are shown on the basic tree

Fig. 5

Inversions in the B. mallei clade. The numbers of inversions on branches are shown in squares on the basic tree. Yellow and blue color marks inversions in the first and second chromosomes, respectively

Fig. 6

The rearrangements rate as a function of the mutation rate for B. mallei. Each dot corresponds to a branch in the basic phylogenetic tree (Fig. 5)

Fig. 7

Inversions in B. pseudomallei. (a) The numbers of inversions on branches are shown in squares on the basic tree. Yellow color corresponds to inversions in the first chromosomes, blue color corresponds to the second chromosomes. The parallel inversion is marked by triangles. (b) The breakpoint composition of the parallel inversion in the second chromosomes in B. pseudomallei

Fig. 8

Inversions in B. thailandensis. The number of inversions on branches are shown in squares on the basic tree. The area indicated by the gray triangle at the left panel is zoomed in the right panel. Yellow and blue colors mark inversions in the first and second chromosomes, respectively. Parallel inversions are marked by colored triangles

Fig. 9

Phylogenetic species tree with detected events of positive selection. The phylogenetic tree is constructed based on the nucleotide sequence similarity of single-copy universal genes. The branch lengths are transformed using the square root. The bootstrap support is shown only for branches where it is <90. The branch thickness reflects the number of positive selection tests mapped on this branch. Color indicates the fraction of significant tests (blue=0; green, low rate; red, high rate), this number and the total number of tests are indicated on branches were positive selection has been detected. Branches with detected episodes of positive selection are marked by IDs in green squares that correspond to branches ID in Table 2. The tree with full strain names is shown in Additional file 9: Figure S9

Fig. 10

Histograms of lenghts of rearranged synteny blocks. (a) Blocks inverted in the first chromosomes in B. mallei; (b) blocks translocated between chromosomes in Burkholderia spp. Blue color corresponds to synteny blocks that have retained their position with respect to the leading/lagging strand; red color corresponds to synteny blocks that changed the strand