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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 .

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