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

Paola E. Campos, Olivier Pruvost, Karine Boyer, Frederic Chiroleu, Thuy Trang Cao, Myriam Gaudeul, Cláudia Baider, Timothy M. A. Utteridge, Nathalie Becker, Adrien Rieux () and Lionel Gagnevin ()
Additional contact information
Paola E. Campos: CIRAD, UMR PVBMT
Olivier Pruvost: CIRAD, UMR PVBMT
Karine Boyer: CIRAD, UMR PVBMT
Frederic Chiroleu: CIRAD, UMR PVBMT
Thuy Trang Cao: CIRAD, UMR PVBMT
Myriam Gaudeul: EPHE, Université des Antilles
Cláudia Baider: R.E. Vaughan Building (MSIRI Compound)
Timothy M. A. Utteridge: Royal Botanic Gardens
Nathalie Becker: EPHE, Université des Antilles
Adrien Rieux: CIRAD, UMR PVBMT
Lionel Gagnevin: CIRAD, INRAE, Institut Agro, IRD

Nature Communications, 2023, vol. 14, issue 1, 1-13

Abstract: Abstract 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).

Date: 2023
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DOI: 10.1038/s41467-023-39950-z

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