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2017 ; 34
(10
): 2716-2729
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Phenetic Comparison of Prokaryotic Genomes Using k-mers
#MMPMID28957508
Déraspe M
; Raymond F
; Boisvert S
; Culley A
; Roy PH
; Laviolette F
; Corbeil J
Mol Biol Evol
2017[Oct]; 34
(10
): 2716-2729
PMID28957508
show ga
Bacterial genomics studies are getting more extensive and complex, requiring new
ways to envision analyses. Using the Ray Surveyor software, we demonstrate that
comparison of genomes based on their k-mer content allows reconstruction of
phenetic trees without the need of prior data curation, such as core genome
alignment of a species. We validated the methodology using simulated genomes and
previously published phylogenomic studies of Streptococcus pneumoniae and
Pseudomonas aeruginosa. We also investigated the relationship of specific genetic
determinants with bacterial population structures. By comparing clusters from the
complete genomic content of a genome population with clusters from specific
functional categories of genes, we can determine how the population structures
are correlated. Indeed, the strain clustering based on a subset of k-mers allows
determination of its similarity with the whole genome clusters. We also applied
this methodology on 42 species of bacteria to determine the correlational
significance of five important bacterial genomic characteristics. For example,
intrinsic resistance is more important in P. aeruginosa than in S. pneumoniae,
and the former has increased correlation of its population structure with
antibiotic resistance genes. The global view of the pangenome of bacteria also
demonstrated the taxa-dependent interaction of population structure with
antibiotic resistance, bacteriophage, plasmid, and mobile element k-mer data
sets.
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