Comparative Genomic and Phylogenomic Analyses Clarify Relationships Within and Between and : Proposal for the Recognition of Two Genomovars.

The present study was designed to clarify the taxonomic status of two species classified as , namely and . To this end, nearly 900 whole genome sequences of strains assigned to these taxa were the subject of comparative genomic and phylogenomic analyses. A phylogenomic tree based on core gene sequences showed that the type strains of and formed a well-supported monophyletic clade that was clearly separated from corresponding clades composed of the remaining validly published species classified as . However, since average nucleotide identity and digital DNA-DNA hybridization similarities between the two types of were slightly higher than the thresholds used to distinguish between closely related species we conclude that and should continue to be recognized as validly published species. The strains were assigned to two genomically distinct groups, we propose that these taxa be recognized as genomovars, that is, as gv. and gv. . The extensive comparative genomic data clearly show that the distribution of pesticidal genes is irregular as strains identified as were assigned to several polyphyletic groups/subclades within the - clade. Consequently, we recommend that genomic or equivalent molecular systematic features should be used to identify strains as the presence of pesticidal genes cannot be used as a diagnostic marker for this species. Comparative taxonomic studies are needed to find phenotypic properties that can be used to distinguish between the genomovars and between them and .