Phylomark, a tool to identify conserved phylogenetic markers from whole-genome alignments.

Applied and Environmental Microbiology
Jason W SahlDavid A Rasko

Abstract

The sequencing and analysis of multiple housekeeping genes has been routinely used to phylogenetically compare closely related bacterial isolates. Recent studies using whole-genome alignment (WGA) and phylogenetics from >100 Escherichia coli genomes has demonstrated that tree topologies from WGA and multilocus sequence typing (MLST) markers differ significantly. A nonrepresentative phylogeny can lead to incorrect conclusions regarding important evolutionary relationships. In this study, the Phylomark algorithm was developed to identify a minimal number of useful phylogenetic markers that recapitulate the WGA phylogeny. To test the algorithm, we used a set of diverse draft and complete E. coli genomes. The algorithm identified more than 100,000 potential markers of different fragment lengths (500 to 900 nucleotides). Three molecular markers were ultimately chosen to determine the phylogeny based on a low Robinson-Foulds (RF) distance compared to the WGA phylogeny. A phylogenetic analysis demonstrated that a more representative phylogeny was inferred for a concatenation of these markers compared to all other MLST schemes for E. coli. As a functional test of the algorithm, the three markers (genomic guided E. coli markers, or GIG-...Continue Reading

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Citations

Feb 25, 2014·International Journal of Biological Macromolecules·Urmila Saha, Kalyan K Mukherjea
Feb 26, 2014·Emerging Infectious Diseases·Hervé TettelinAdrian M Zelazny
Jan 22, 2013·Trends in Microbiology·Sebastien MatamorosMarie-France de La Cochetiere
Dec 3, 2014·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Debra E BessenHervé Tettelin
Jan 30, 2013·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Marcos Pérez-LosadaKeith A Crandall
Sep 25, 2014·Frontiers in Immunology·Marie-Claire ArrietaBrett Finlay
Jan 16, 2015·Journal of Clinical Microbiology·Jason W SahlDavid A Rasko
Jun 27, 2019·Proceedings. Biological Sciences·Tatiana DimitriuBen Raymond
May 10, 2017·BMC Genomics·Andreas LeimbachUlrich Dobrindt
Apr 22, 2017·Genome Announcements·Aruna PandaLouis J DeTolla
Oct 6, 2015·EcoSal Plus·Seth T Walk

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