Título:
Comparative genomics of Pantoea allii lineages and distribution of ecologically relevant traits
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Autor:
Shin, Gi Yoon
De Armas, Stefanie
Galván, Guillermo A.
Siri, María I.
Rojas, Mariah
Vinatzer, Boris A.
Asselin, Jo Ann E.
Stodghill, Paul
Zhao, Mei
Dutta, Bhabesh
Tambong, James
Kvitko, Brian H.
De Armas, Stefanie
Galván, Guillermo A.
Siri, María I.
Rojas, Mariah
Vinatzer, Boris A.
Asselin, Jo Ann E.
Stodghill, Paul
Zhao, Mei
Dutta, Bhabesh
Tambong, James
Kvitko, Brian H.
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Tipo de documento:
Artículo
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Palabras clave:
Patógenos
Genómica
Cebolla
Enfermedades de las plantas
Genómica
Cebolla
Enfermedades de las plantas
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Año de publicación:
2026
Contenido:
Resumen:
Pantoea allii, one of four Pantoea species known to cause onion centre rot, is infrequently isolated from onion compared to its closely related onion-pathogenic species in the same genus. To better understand the genomic diversity and genetic determinants of pathogenicity in this species, we analysed a collection of 38 P. allii strains isolated from 2 primary ecological niches, plants and rainwater, across North and South American and African continents using comparative genomics and phylogenetic approaches. Core-genome phylogeny, average nucleotide identity and gene presence–absence analyses revealed three genetically distinct lineages. All strains harboured conserved biosynthetic gene clusters (BGCs) for quorum sensing, carotenoid production, siderophores and thiopeptides. In contrast, two phosphonate BGCs, key determinants of onion pathogenicity, exhibited lineage-specific distributions. Onion-associated strains from lineages 1 and 2 carried the Halophos BGC responsible for onion tissue necrosis and also encoded the alt gene cluster that confers tolerance to thiosulfinates. Lineage 3 strains, isolated from both onion and rainwater, either lacked a phosphonate BGC entirely or possessed the HiVir phosphonate BGC. In addition, lineage 3 strains lacked the alt cluster altogether. The localization of these virulence genes in the genome varied, with Halophos integrated in the chromosome, HiVir encoded on the conserved Large Pantoea Plasmid, and alt located on small, variable plasmids (plasmid B). The type IV secretion system (T4SS) and type VI secretion system (T6SS) showed variable genomic architectures, with plasmid-borne T4SSs and two chromosomal T6SS loci differing in conservation and gene content. Additionally, conserved Pantailocin phage islands were detected in most genomes. Overall, this study reveals that while core metabolic and competitive traits are conserved across P. allii, virulence-associated loci display lineage-specific distribution, reflecting ecological differentiation and evolutionary plasticity within the species.
Descripción:
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Microbiology Society
EN:
Microbial Genomics, v. 12, n°2, 2026. -- e001624
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Citación:
Shin, G., De Armas, S., Galván, G. y otros. "Comparative genomics of Pantoea allii lineages and distribution of ecologically relevant traits". Microbial Genomics [en línea], v. 12, n°2, 2026. -- e001624. 17 p.
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Licencia Creative Commons Atribución (CC - By 4.0)
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| Ficheros | Descripción | Tamaño | Formato | ||
|---|---|---|---|---|---|
| Texto completo.pdf | — | 4.34 MB | Adobe PDF |