Comparative genomic analysis of Ralstonia solanacearum reveals candidate genes for host specificity

Autor: Tiffany M. Lowe, David Roche, Gilles Cellier, Caitilyn Allen, Philippe Prior, Florent Ailloud
Přispěvatelé: Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Laboratoire de santé des végétaux (LSV Angers), Laboratoire de la santé des végétaux (LSV), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)-Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Department of Plant Pathology, University of Wisconsin-Madison, Institut de Génomique, Département Santé des Plantes et Environnement (DPT SPE), Institut National de la Recherche Agronomique (INRA), European Union (ERDF), Conseil Regional de La Reunion, French Agence Nationale de la Recherche, CIRAD, ANSES [11-237/BSL], Laboratoire de la Santé des Végétaux, Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES)
Rok vydání: 2015
Předmět:
Phylogénie
[SDV]Life Sciences [q-bio]
Medical and Health Sciences
Hôte
Solanum lycopersicum
Cucumis melo
2.2 Factors relating to the physical environment
Aetiology
Phylogeny
2. Zero hunger
Genetics
0303 health sciences
Ralstonia solanacearum
Virulence
biology
Ecotype
U10 - Informatique
mathématiques et statistiques
Bacterial
food and beverages
Genomics
Plants
Biological Sciences
Musa paradisiaca
Plante ornementale
Host adaptation
Infection
Research Article
Biotechnology
Flétrissement
Species complex
Virulence Factors
Bioinformatics
Relation hôte pathogène
Host Specificity
génomique
03 medical and health sciences
Bioinformatique
Genetic
Phylogenetics
Information and Computing Sciences
Polymorphism
Adaptation
Plant Diseases
H20 - Maladies des plantes
Écotype
030304 developmental biology
Génie génétique
Comparative genomics
Polymorphism
Genetic
Génome
génomique comparative
030306 microbiology
Human Genome
Musa
biology.organism_classification
Pourriture des racines
Genes
Genes
Bacterial
pseudomonas solanacearum
Zdroj: BMC Genomics
BMC Genomics, 2015, 16, ⟨10.1186/s12864-015-1474-8⟩
BMC Genomics, BioMed Central, 2015, 16, ⟨10.1186/s12864-015-1474-8⟩
BMC Genomics (16), . (2015)
BMC genomics, vol 16, iss 1
ISSN: 1471-2164
DOI: 10.1186/s12864-015-1474-8
Popis: Background Ralstonia solanacearum is a vascular soil-borne plant pathogen with an unusually broad host range. This economically destructive and globally distributed bacterium has thousands of distinct lineages within a heterogeneous and taxonomically disputed species complex. Some lineages include highly host-adapted strains (ecotypes), such as the banana Moko disease-causing strains, the cold-tolerant potato brown rot strains (also known as R3bv2) and the recently emerged Not Pathogenic to Banana (NPB) strains. Results These distinct ecotypes offer a robust model to study host adaptation and the emergence of ecotypes because the polyphyletic Moko strains include lineages that are phylogenetically close to the monophyletic brown rot and NPB strains. Draft genomes of eight new strains belonging to these three model ecotypes were produced to complement the eleven publicly available R. solanacearum genomes. Using a suite of bioinformatics methods, we searched for genetic and evolutionary features that distinguish ecotypes and propose specific hypotheses concerning mechanisms of host adaptation in the R. solanacearum species complex. Genome-wide, few differences were identified, but gene loss events, non-synonymous polymorphisms, and horizontal gene transfer were identified among type III effectors and were associated with host range differences. Conclusions This extensive comparative genomics analysis uncovered relatively few divergent features among closely related strains with contrasting biological characteristics; however, several virulence factors were associated with the emergence of Moko, NPB and brown rot and could explain host adaptation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1474-8) contains supplementary material, which is available to authorized users.
Databáze: OpenAIRE
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