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BMC Genomics. 2018 Dec 27;19(1):965. doi: 10.1186/s12864-018-5245-1.

Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp.

Author information

1
Kharkevich Institute for Information Transmission Problems, Moscow, Russia. olga.bochkaryova@gmail.com.
2
Center of Life Sciences Skolkovo Institute of Science and Technology, Moscow, Russia. olga.bochkaryova@gmail.com.
3
Kharkevich Institute for Information Transmission Problems, Moscow, Russia.
4
Department of Ecology and Evolution & Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
5
Swiss Institute of Bioinformatics, Lausanne, Switzerland.
6
Center of Life Sciences Skolkovo Institute of Science and Technology, Moscow, Russia.
7
Faculty of Computer Science, Higher School of Economics, Moscow, Russia.

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

PMID:
30587126
PMCID:
PMC6307245
DOI:
10.1186/s12864-018-5245-1
[Indexed for MEDLINE]
Free PMC Article

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