4.7 Article

Whole-Genome Resources and Species-Level Taxonomic Validation of 89 Plant-Pathogenic Xanthomonas Strains Isolated from Various Host Plants

期刊

PLANT DISEASE
卷 106, 期 6, 页码 1558-1565

出版社

AMER PHYTOPATHOLOGICAL SOC
DOI: 10.1094/PDIS-11-21-2498-SC

关键词

average nucleotide identity; bacteria; bacterial spot disease; genome-based DNA-DNA hybridization; genome sequencing; pepper; prokaryotes; taxonomy; whole-genome sequencing; Xanthomonas; X; euvesicatoria; X; gardneri; X; hortorum; X; perforans; X; vesicatoria

资金

  1. Agriculture and Agri-Food Canada through the Biological Collections Data Mobilization Initiative project (BioMob) [J-001564]
  2. [J-002272]
  3. [J-001577]
  4. [J-000409]

向作者/读者索取更多资源

This study reports whole-genome resources of 89 Xanthomonas strains, providing valuable insights into the global population structure and evolution of these pathogens.
Bacterial spot disease caused by Xanthomonas spp. is a global threat to tomato and pepper plants. A recent classification of these pathogens indicated the need for a diverse dataset of whole-genome resources. We report whole-genome resources of 89 Xanthomonas strains isolated from Canada (n = 44), the United States (n = 29), Argentina (n = 4), Brazil (n = 3), Costa Rica (n = 3), New Zealand (n = 1), Australia (n = 1), Mexico (n = 1), Taiwan (n = 1), Thailand (n = 1), and unknown (n = 1). Of these strains, 48 were previously identified to species-level based on nongenome-based approaches while 41 strains were classified only at the genus level. The average coverage of the sequencing reads was 103x. The draft genome sizes ranged from 4.53 to 5.46 Mbp with a G + C content of 63.53 to 67.78% and comprised 4,233-5,178 protein-coding sequences. Using average nucleotide identity (ANI) and genome-based DNA-DNA hybridization (gDDH) values, the taxonomic classifications were validated for 38 of the 48 strains previously assigned to species level using other methods. Ten strains previously identified as Xanthomonas campestris, X. axonopodis, X. vasicola, and X. arboricola were incorrectly assigned, and new species-level delineations are proposed. Data from ANI, gDDH, and pangenome phylogeny of shared protein families were used to assign the 41 strains, previously identified only to genus level, into five distinct species: X. euvesicatoria (pv. euvesicatoria or pv. perforans), X. hortorum pv. gardneri, X. vesicatoria, X. campestris, and X. arboricola. These 89 whole-genome sequences of Xanthomonas strains, the majority (49.4%) of which are from Canada, could be useful resources in our understanding of the global population structure and evolution of these pathogens.

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