Evidence map›Paper›PMID 42092757›Full record

ArticleBMC genomics2026

Unlocking the genetic arsenal of Xanthomonas arboricola: new insights into taxonomic classification, pathogenicity and adaptation beyond the effectorome.

Renata de A B Assis, Alessandro M Varani, Aidan C Shands, Cintia H D Sagawa, José S L Patané, João C Setubal, Paulo A Zaini, Nalvo F Almeida, Robson F de Souza, Camila C M Garcia and 4 more

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Article in BMC genomics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

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4 · The record

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5 · Who and what money

Authors and funding

14 authors.

Renata de A B AssisCenter of Research in Biological Science, Federal University of Ouro Preto, Ouro Preto, MG, Brazil.
Alessandro M VaraniDepartment of Agricultural and Environmental Biotechnology, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, SP, Brazil.
Aidan C ShandsMicrobiology & Plant Pathology Department, University of California, Riverside, CA, USA.
Cintia H D SagawaDepartment of Plant Sciences, University of California, Davis, CA, USA.
José S L PatanéLaboratório Especial de Ciclo Celular, Instituto Butantan, São Paulo, SP, Brazil.
João C SetubalDepartment of Biochemistry, Chemistry Institute, University of Sao Paulo, Sao Paulo, SP, Brazil.
Paulo A ZainiDepartment of Plant Sciences, University of California, Davis, CA, USA.
Nalvo F AlmeidaSchool of Computing, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, MS, Brazil.
Robson F de SouzaDepartment of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
Camila C M GarciaCenter of Research in Biological Science, Federal University of Ouro Preto, Ouro Preto, MG, Brazil.
Elena G OrellanoInstituto de Biología Molecular y Celular de Rosario, Facultad de Ciencias Bioquímicas y Farmacéuticas, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Rosario, Rosario, Argentina.
James E AdaskavegMicrobiology & Plant Pathology Department, University of California, Riverside, CA, USA.
Abhaya M DandekarDepartment of Plant Sciences, University of California, Davis, CA, USA.
Leandro M MoreiraCenter of Research in Biological Science, Federal University of Ouro Preto, Ouro Preto, MG, Brazil. lmmorei@gmail.com.

Funding

Conselho Nacional de Desenvolvimento Científico e Tecnológico LMM, AMV, NFA, JCS
6 · The paper itself

Abstract

backgroundXanthomonas arboricola (Xar) is a phytopathogenic bacterial species responsible for economically significant diseases in a wide range of plants, including agricultural, ornamental, and forest species. This study aimed to investigate the genomic basis of host specificity, adaptation, and virulence in Xar through comprehensive comparative genomics.

resultsA total of 177 genomes from nine Xar pathovars were analyzed for evolutionary relationships and effector repertoires. From these, 30 genetically diverse genomes were selected for in-depth comparison. Core, unique, and shared genes were identified and functionally annotated, focusing on their potential roles in adaptation and pathogenicity. Nineteen of the genomes were originally misclassified and did not belong to the Xar species. The remaining 158 genomes clustered into three major clades: I (Xar. pv. juglandis), II (Xar. pv. pruni + Xar. pv. corylina), and III (miscellaneous Xar). Clades I and II exhibited high effector diversity, ranging from 38 to 54 genes, with Xar. pv. corylina harboring the most. In contrast, Clade III genomes had significantly fewer effectors, with subclade IIIa containing only 5 and IIIb up to 15. Only one TAL effector was found in nine Xar. pv. corylina strains (with no conserved RVD patterns) and in both Xar. pv. guizotiae strains (up to 31 RVDs identified). Phylogenomic and effectorome analyses revealed potential genomic islands acquired via horizontal gene transfer, encoding metal metabolism genes, type II/IV secretion systems, and DNA modification enzymes. Additionally, several gene losses were observed: 19 genomes lacked flagellar assembly genes, 15 lacked nitrate metabolism genes, and 9 lacked cellulose biosynthesis and secretion genes. In contrast, all genomes possessed a lasso peptide biosynthetic cluster, highlighting recurrent genomic rearrangements through insertions and deletions.

conclusionsThis study provides a refined understanding of the genetic diversity and adaptive mechanisms in X. arboricola, emphasizing gene gain/loss events as central to pathovar-specific metabolic and virulence traits. These findings identify novel molecular markers with potential applications in diagnostics and targeted disease control strategies. In particular, the characterization of conserved and lineage-specific effector repertoires provides a framework to inform strategies for breeding resistance through the identification of candidate targets for durable host immunity.

Indexed as

Adaptation, PhysiologicalGenome, BacterialGenomicsXanthomonasBacterial ProteinsEvolution, MolecularGenetic VariationGene Transfer, HorizontalPhylogenyPlant DiseasesVirulenceBacterial ProteinsAdaptationComparative genomicsEffectoromeHorizontal gene transferPathogen-host interactionVirulenceXanthomonas arboricola

Identifiers

PMID42092757
PMCPMC13312709

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.