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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 chilensis sp. nov. based on complete genome in-silico analyses

Dario Arizala, View ORCID ProfileShefali Dobhal, Anne M. Alvarez, View ORCID ProfileMohammad Arif
doi: https://doi.org/10.1101/2022.01.17.476658
Dario Arizala
Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822
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Shefali Dobhal
Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822
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Anne M. Alvarez
Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822
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Mohammad Arif
Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI 96822
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  • For correspondence: arif@hawaii.edu
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ABSTRACT

The Gram-positive Clavibacter genus is currently divided into seven species (C. michiganensis, C. nebraskensis, C. capsici, C. sepedonicus, C. tessellarius, C. insidiosus and C. zhangzhiyongii) and three subspecies (C. michiganensis subsp. californiensis, C. michiganensis subsp. chilensis and C. michiganensis subsp. phaseoli). Recent studies have indicated that the taxonomic rank of the subspecies must be re-evaluated. In this research, we assessed the taxonomy position of the three C. michiganensis subspecies and clarified the taxonomic nomenclature of other 75 Clavibacter strains. The complete genomes of the type strains of the three Clavibacter subspecies, type strain of C. tessellarius and C. nebraskensis A6096 were sequenced using PacBio RSII technology. Application of whole-genome-based computational approaches such as average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), multi-locus sequence analysis (MLSA) of seven housekeeping genes (acnA, atpD, bipA, icdA, mtlD, recA and rpoB), phylogenomic tree reconstructed from 1,028 core genes, and ANI-based phylogeny pinpointed conclusive evidence to raise C. michiganensis subsp. californiensis to the species status. These results led us to propose the establishment of C. californiensis sp. nov. as a species with its type strain C55ᵀ (=CFBP 8216ᵀ=ATCC BAA-2691ᵀ). Moreover, the orthologous and in-silico dot plot analyses, along with the aforementioned bioinformatic strategies, revealed a high degree of homology between C. michiganensis subsp. chilensis and C. michiganensis subsp. phaseoli. Based on these outcomes, we proposed to combine both subspecies into a single taxon and elevate its rank to the species level as C. chilensis sp. nov., with ZUM3936ᵀ (= ATCC BAA-2690ᵀ = CFBP 8217ᵀ) as the type strain.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Repositories: CP040786-CP040787; CP040788-CP040791; CP040792-CP040794; CP040795-CP040796; CP040797

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted January 18, 2022.
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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…
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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 chilensis sp. nov. based on complete genome in-silico analyses
Dario Arizala, Shefali Dobhal, Anne M. Alvarez, Mohammad Arif
bioRxiv 2022.01.17.476658; doi: https://doi.org/10.1101/2022.01.17.476658
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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 chilensis sp. nov. based on complete genome in-silico analyses
Dario Arizala, Shefali Dobhal, Anne M. Alvarez, Mohammad Arif
bioRxiv 2022.01.17.476658; doi: https://doi.org/10.1101/2022.01.17.476658

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