Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation.

BMC Genomics
Tim KahlkePeik Haugen

Abstract

The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genome sequence data is becoming available. However, it is still unclear how the new advances in genomics should be used most efficiently to address this question. In this study we identify genes that are common to any group of genomes in our dataset, to determine whether genes specific to a particular taxon exist and to investigate their potential role in adaptation of bacteria to their specific niche. These genes were named unique core genes. Additionally, we investigate the existence and importance of unique core genes that are found in isolates of phylogenetically non-coherent groups. These groups of isolates, that share a genetic feature without sharing a closest common ancestor, are termed genophyletic groups. The bacterial family Vibrionaceae was used as the model, and we compiled and compared genome sequences of 64 different isolates. Using the software orthoMCL we determined clusters of homologous genes among the investigated genome sequences. We used multilocus sequence analysis to build a host phylogeny and mapped the numbers of unique core genes of all d...Continue Reading

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Citations

Apr 16, 2013·Journal of Bacteriology·Evgeny N GordienkoMikhail S Gelfand
Oct 25, 2016·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·Julieta BonacinaLucila Saavedra
Mar 30, 2018·Frontiers in Microbiology·Mikhail A Moldovan, Mikhail S Gelfand
Jan 23, 2021·Microorganisms·Iliana Guardiola-AvilaLorena Noriega-Orozco
Feb 4, 2014·The Plant Cell·Candice N HirschC Robin Buell

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Software Mentioned

GenDB
RaxML
Glimmer
MrBayes
MAFFT
Epos
orthoMCL

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