Use of whole genome sequences to develop a molecular phylogenetic framework for Rhodococcus fascians and the Rhodococcus genus.

Allison L Creason,Jeff H Chang,Melodie L Putnam,Edward W Davis,Olivier M Vandeputte

doi:10.3389/fpls.2014.00406

Allison L Creason, Jeff H Chang + Show 3 more

Open Access

https://doi.org/10.3389/fpls.2014.00406

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Abstract

The accurate diagnosis of diseases caused by pathogenic bacteria requires a stable species classification. Rhodococcus fascians is the only documented member of its ill-defined genus that is capable of causing disease on a wide range of agriculturally important plants. Comparisons of genome sequences generated from isolates of Rhodococcus associated with diseased plants revealed a level of genetic diversity consistent with them representing multiple species. To test this, we generated a tree based on more than 1700 homologous sequences from plant-associated isolates of Rhodococcus, and obtained support from additional approaches that measure and cluster based on genome similarities. Results were consistent in supporting the definition of new Rhodococcus species within clades containing phytopathogenic members. We also used the genome sequences, along with other rhodococcal genome sequences to construct a molecular phylogenetic tree as a framework for resolving the Rhodococcus genus. Results indicated that Rhodococcus has the potential for having 20 species and also confirmed a need to revisit the taxonomic groupings within Rhodococcus.

Highlights

Defining bacteria into stable and coherent genetically similar species has many practical implications
Multi-locus sequence analysis (MLSA) and trees based on whole genome sequences are powerful methods for inferring evolutionary relationships (Staley, 2009)
Average nucleotide identity (ANI), for example, is a simple measure of genetic relatedness based on sequences conserved among compared genomes and has gained acceptance as a method for defining bacterial species (Konstantinidis et al, 2006; Chan et al, 2012; Kim et al, 2014)

Summary

Introduction

Defining bacteria into stable and coherent genetically similar species has many practical implications. Traditional polyphasic approaches define bacterial species as a monophyletic group with at least one discriminative phenotypic trait. With major advances in contemporary methods in sequencing, operational criteria based on whole genome sequences have been developed and adopted to assist in resolving bacterial phylogeny (Konstantinidis et al, 2006). Average nucleotide identity (ANI), for example, is a simple measure of genetic relatedness based on sequences conserved among compared genomes and has gained acceptance as a method for defining bacterial species (Konstantinidis et al, 2006; Chan et al, 2012; Kim et al, 2014). ANI has been developed as a method for codifying bacteria based on genome similarity (Marakeby et al, 2014)

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