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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 72, Issue 9

Elevation of subsp. to species level as sp. nov., merging and re-classification of subsp. and subsp. as sp. nov. based on complete genome analyses No Access

Abstract

The Gram-positive genus is currently divided into seven species (, , , , , and ) and three subspecies ( subsp. , subsp. and subsp. ). Recent studies have indicated that the taxonomic rank of the subspecies must be re-evaluated. In this research, we assessed the taxonomic position of the three subspecies and clarified the taxonomic nomenclature of other 75 strains. The complete genomes of the type strains of the three subspecies, the type strain of and A6096 were sequenced using PacBio RSII technology. Application of whole-genome-based computational approaches such as average nucleotide identity (ANI), digital DNA–DNA hybridization, multi-locus sequence analysis of seven housekeeping genes (, , , , , and ), a phylogenomic tree reconstructed from 1 028 core genes, and ANI-based phylogeny provided sufficient justification for raising subsp. to the species level. These results led us to propose the establishment of sp. nov. as a species with its type strain C55 (=CFBP 8216=ATCC BAA-2691). Moreover, the orthologous and dot plot analyses, along with the above described bioinformatic strategies, revealed a high degree of similarity between subsp. and subsp. . Based on these analyses, we propose that both subspecies be combined into a single taxon and elevated to the species level as sp. nov., with LPPA 982 (= CECT 8144= LMG 27667) as the type strain.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): phylogenomics , ANI , Clavibacter , dDDH , MLSA , taxonomy and whole genome
© 2022 The Authors
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2022-09-15
2024-05-02
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Elevation of Clavibacter michiganensis subsp. californiensis to species level as Clavibacter californiensis sp. nov., merging and re-classification of Clavibacter michiganensis subsp. chilensis and Clavibacter michiganensis subsp. phaseoli as Clavibacter phaseoli sp. nov. based on complete genome in silico analyses
Int J Syst Evol Microbiol 72, 005427 (2022); https://doi.org/10.1099/ijsem.0.005427
/content/journal/ijsem/10.1099/ijsem.0.005427
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