Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history

Campos Paola, Pruvost Olivier, Boyer Karine, Chiroleu Frédéric, Cao Thuy Trang, Gaudeul Myriam, Baider Claudia, Utteridge Timothy M. A., Becker Nathalie, Rieux Adrien, Gagnevin Lionel. 2023. Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history. Nature Communications, 14:4306, 13 p.

Résumé : Herbarium collections are an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography can shed light on the emergence and evolutionary history of plant pathogens. Here, we reconstruct 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected Citrus herbarium specimens. Following authentication based on ancient DNA damage patterns, we compare them with a large set of modern genomes to estimate their phylogenetic relationships, pathogenicity-associated gene content and several evolutionary parameters. Our results indicate that Xci originated in Southern Asia ~11,500 years ago (perhaps in relation to Neolithic climate change and the development of agriculture) and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world (probably via human-driven expansion of citriculture through early East-West trade and colonization).

Mots-clés Agrovoc : Xanthomonas campestris citri, phylogénie, génome, désamination, herbier, diversification, pathotype, agent pathogène, Xanthomonas, Citrus, maladie des plantes, adn

Mots-clés libres : Bacterial evolution, Bacterial genomics, Pathogens, Phylogenetics

Classification Agris : H20 - Maladies des plantes

Champ stratégique Cirad : CTS 4 (2019-) - Santé des plantes, des animaux et des écosystèmes

Agences de financement européennes : European Commission, European Regional Development Fund

Agences de financement hors UE : Région Réunion, Agropolis Fondation, Centre de Coopération Internationale en Recherche Agronomique pour le Développement

Programme de financement européen : FP7

Projets sur financement : (FRA) MUSEOVIR, (EU) SYNTHESYS, (FRA) "Une nuit au musée": mieux reconstuire les emergences de bactéries pathogènes des cultures grâce à des échantillons historiques

Auteurs et affiliations

• Campos Paola, CIRAD-BIOS-UMR PVBMT (REU)
• Pruvost Olivier, CIRAD-BIOS-UMR PVBMT (REU)
• Boyer Karine, CIRAD-BIOS-UMR PVBMT (REU)
• Chiroleu Frédéric, CIRAD-BIOS-UMR PVBMT (REU) ORCID: 0000-0002-4874-5357
• Cao Thuy Trang, CIRAD-BIOS-UMR PVBMT (REU)
• Gaudeul Myriam, MNHN (FRA)
• Baider Claudia, MSIRI (MUS)
• Utteridge Timothy M. A., Royal Botanic Gardens (GBR)
• Becker Nathalie, CIRAD-BIOS-UMR PVBMT (REU)
• Rieux Adrien, CIRAD-BIOS-UMR PVBMT (REU) - auteur correspondant
• Gagnevin Lionel, CIRAD-BIOS-UMR PHIM (FRA) ORCID: 0000-0002-2943-0827 - auteur correspondant

Source : Cirad-Agritrop (https://agritrop.cirad.fr/607948/)

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