Phenetic Comparison of Prokaryotic Genomes Using k-mers.

ABSTRACT: 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 correlate

SUBMITTER: Deraspe M 

PROVIDER: S-EPMC5850840 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature