Although the genus Clavibacter was originally proposed to accommodate all phytopathogenic coryneform bacteria containing B2g diaminobutyrate in the peptidoglycan, reclassification of all but one species into other genera has resulted in the current monospecific status of the genus. The single species in the genus, Clavibacter michiganensis, has multiple subspecies, which are all highly host-specific plant pathogens. Whole genome analysis based on average nucleotide identity and digital DNA– DNA hybridization as well as multi-locus sequence analysis (MLSA) of seven housekeeping genes support raising each of the C. michiganensis subspecies to species status. On the basis of whole genome and MLSA data, we propose the establishment of two new species and three new combinations: Clavibacter capsici sp. nov., comb. nov. and Clavibacter tessellarius sp. nov., comb. nov., and Clavibacter insidiosus comb. nov., Clavibacter nebraskensis comb. nov. and Clavibacter sepedonicus comb. nov
The genus Clavibacter was originally proposed by Davis et al.  to accommodate all phytopathogenic coryneform bacteria containing B2g diaminobutyrate in the peptidoglycan. This genus originally included six plant pathogenic species: Clavibacter michiganensis, Clavibacter iranicum, Clavibacter rathayi, Clavibacter toxicus, Clavibacter tritici and Clavibacter xyli. Subsequently, the grass-specific pathogens, C. iranicum, C. rathayi, C. toxicus and C. tritici, were reclassified into the genus Rathayibacter on the basis of DNA–DNA hybridization and their unique menaquinone structures . The two subspecies of C. xyli were placed in the genus, Leifsonia [3, 4]. Currently, the genus Clavibacter consists of only one species, C. michiganensis, which is subdivided into seven subspecies of plant pathogenic bacteria with narrow host specificities and two subspecies with close association with tomato and pepper seeds. Five of the subspecies comprise well-known pathogens, namely, C. michiganensis subsp. michiganensis (Cmm; bacterial canker and wilt of tomato), C. michiganensis subsp. sepedonicus (Cms; bacterial ring rot of potato), C. michiganensis subsp. insidiosus (Cmi; wilting and stunting in alfalfa), C. michiganensis subsp. nebraskensis (Cmn; wilt and blight of maize), and C. michiganensis subsp. tessellarius (Cmt; leaf freckles and leaf spots in wheat). More importantly, the first three subspecies are quarantine or regulated pathogens of important agricultural crops in many countries. Recently, C. michiganensis subsp. phaseoli was described as the causal agent of bacterial leaf yellowing on bean  and C. michiganensis subsp. capsici (Cmc) as the causal agent of bacterial canker on pepper . Another two subspecies, C. michiganensis subsp. californiensis and C. michiganensis subsp. chilensis were named to include bacterial isolates from tomato and pepper seeds produced in California and Chile, respectively . Among these newly established subspecies, only C. michiganensis subsp. capsici with available genome sequence data (Table 1) was used in this study. The other three recently named subspecies were not included in this study.
To better define the taxonomic position of the subspecies of C. michiganensis, whole-genome sequences of two strains of Cms, six strains of Cmn, two strains of Cmt, and the type strains of Cmm, Cmi, and Cmt were decoded using PacBio single molecule real-time (SMRT) sequencing at Genome Quebec (McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada). The assembled sequences were compared with published sequences of C. michiganensis subsp. michiganensis and subsp. insidiosus, and other clavibacter sequences in GenBank (Table 1). Currently available genome sequences for most type strains of each subspecies of Clavibacter michiganensis were included in this study. The genome sequences generated in this study were deposited in Genbank with accession numbers of MZMQ00000000 (Cmt ATCC 33566), MZMM00000000 (Cms CFIA-Cs3N), MZMN00000000 (Cms CFIA-CsR14), MZMO00000000 (Cmi LMG 3663) and MZMP00000000 (Cmm LMG 7333).