P-592 - Proposal for two novel non-pathogenic Clavibacter species: Clavibacter seminis sp. nov. and Clavibacter quasicaliforniensis sp. nov.

Tuesday, August 5, 2025

10:15 AM - 11:00 AM HST

Location: Exhibit Hall 3

Presenting Author(s)

EA

Eduardo D. Arizala (he/him/his)

University of Hawaii at Manoa
Honolulu, HI, USA

Author(s)

SD

Shefali Dobhal

Assistant Researcher (Research Professor)
University of Hawaii at Manoa
Honolulu, Hawaii, United States
AA

Anne Alvarez

University of Hawaii at Manoa
Honolulu, Hawaii, United States
MA

Mohammad Arif

Associate Professor
University of Hawaii at Manoa
Honolulu, Hawaii, United States

Abstract Text: The genus Clavibacter is currently split into ten species, including C. michiganensis, C. nebraskensis, C. capsici, C. sepedonicus, C. tessellarius, C. insidiosus, C. californiensis, C. phaseoli, C. zhangzhiyongii, and C. lycopersici. These bacterial species have been isolated from different hosts, and some are reported as endophytes. In this study, we sequenced three new Clavibacter strains A6099, A4868, and A6308 isolated from tomato using Oxford Nanopore MinION and Illumina NovaSeq sequencing platforms. Based on different in silico approaches, including average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), alignment coverage (AP), multi-locus sequence analysis (MLSA) of eight housekeeping genes atpD, dnaA, dnaK, pgi, gyrB, ppk, recA and rpoB, and a phylogenomic analysis of 808 core genes of 97 Clavibacter strains, we identified two novel clades within the genus Clavibacter that are closely related to C. michiganensis and C. californiensis. The ANI and dDDH values were lower than the 96 and 70% cut-off values for species delineation, respectively; likewise, the phylogenies showed a clear differentiation of these two novel clades with respect to the other Clavibacter species. Therefore, we propose establishment of two new species: Clavibacter seminis sp. nov., type strain A6099^Tand Clavibacter quasicaliforniensis sp. nov., type strain A4868^T. These species were non-pathogenic on tomato and showed the absence of the major virulence-associated genes.