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Re-classification of Clavibacter michiganensis subspecies into multiple new species

Sean Li, James Tambong, Kat (Xiaoli) Yuan, H. Xu and Solke H. De Boer (2016)Re-classification of Clavibacter michiganensis subspecies into multiple new species. Annual Meeting of the Canadian Phytopathological Society Moncton, NB. June 12-15, 2016. Abstract.

Abstract

The bacterial genus Clavibacter is monospecific consisting of only one species, C. michiganensis, subdivided into five subspecies, each with specificity for a single host crop. C. michiganensis subsp. michiganensis (Cmm) causes bacterial canker of tomato (Solanum lycopersicum), C. m. sepedonicus (Cms) causes bacterial ring rot of potato (Solanum tuberosum), C. m. insidiosus (Cmi) causes bacterial wilt of alfalfa (Medicago sativa), C. m. nebraskensis (Cmn) causes the Goss’s bacterial wilt of maize (Zea mays), and C. m. tesselarius (Cmt) causes bacterial mosaic disease of wheat (Triticum spp.). The taxonomic position of the subspecies was evaluated using whole genome sequences of multiple strains of Cmm, Cms, Cmi, Cmn, and Cmt, including type strains. Genomes were decoded using either BacBio single molecule real-time sequencing (McGill University and Genome Quebec Innovation Centre, Montreal, QC) or paired-end Illumina HiSeq sequencing with True Seq version 3 chemistry (National Research Council Canada, Saskatoon, SK, Canada). The assembled sequences were annotated and compared with sequences of Cmm, Cmi and Cms, and other Clavibacter spp. deposited in GenBank. Average nucleotide identity (ANI) values ranged from 91-95% among subspecies while pair-wise comparison among strains of the same subspecies had ANI values of 99-100%. Based on ANI values, 16S rRNA sequences, multi-locus sequence typing of house-keeping genes, and phenotypic characteristics, the taxonomic position of the phytopathogenic clavibacter subspecies should be raised to species status within the genus Clavibacter as C. michiganensis sp. nov., C. sepedonicus sp. nov., C. insidiosus sp. nov., C. nebraskensis sp. nov., and C. tessellarius sp. nov.

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