First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence

Campos Paola, Groot Crego Clara, Boyer Karine, Gaudeul Myriam, Baider Claudia, Richard Damien, Pruvost Olivier, Roumagnac Philippe, Szurek Boris, Becker Nathalie, Gagnevin Lionel, Rieux Adrien. 2021. First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence. PLoS Pathogens, 17 (7):e1009714, 25 p.

https://doi.org/10.1371/journal.ppat.1009714

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Url - autre : https://www.southgreen.fr/ / Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/sra/?term=SRR12792042 / Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/nuccore/CP072205 / Url - jeu de données - Entrepôt autre : https://www.ncbi.nlm.nih.gov/nuccore/CP072207

Quartile : Outlier, Sujet : PARASITOLOGY / Quartile : Q1, Sujet : MICROBIOLOGY / Quartile : Q1, Sujet : VIROLOGY

Résumé : Over the past decade, ancient genomics has been used in the study of various pathogens. In this context, herbarium specimens provide a precious source of dated and preserved DNA material, enabling a better understanding of plant disease emergences and pathogen evolutionary history. We report here the first historical genome of a crop bacterial pathogen, Xanthomonas citri pv. citri (Xci), obtained from an infected herbarium specimen dating back to 1937. Comparing the 1937 genome within a large set of modern genomes, we reconstructed their phylogenetic relationships and estimated evolutionary parameters using Bayesian tip-calibration inferences. The arrival of Xci in the South West Indian Ocean islands was dated to the 19th century, probably linked to human migrations following slavery abolishment. We also assessed the metagenomic community of the herbarium specimen, showed its authenticity using DNA damage patterns, and investigated its genomic features including functional SNPs and gene content, with a focus on virulence factors.

Mots-clés Agrovoc : agent pathogène, génome, herbier, Xanthomonas campestris citri, maladie bactérienne

Mots-clés géographiques Agrovoc : Maurice

Mots-clés complémentaires : Xanthomonas citri pv citri

Classification Agris : H20 - Maladies des plantes
H50 - Troubles divers des plantes

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

Agences de financement européennes : European Regional Development Fund

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