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

Author

Listed:
  • Paola E. Campos

    (CIRAD, UMR PVBMT
    EPHE, Université des Antilles)

  • 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
    Muséum national d’Histoire naturelle, CP39)

  • 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
    CIRAD, UMR PHIM)

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).

Suggested Citation

  • Paola E. Campos & Olivier Pruvost & Karine Boyer & Frederic Chiroleu & Thuy Trang Cao & Myriam Gaudeul & Cláudia Baider & Timothy M. A. Utteridge & Nathalie Becker & Adrien Rieux & Lionel Gagnevin, 2023. "Herbarium specimen sequencing allows precise dating of Xanthomonas citri pv. citri diversification history," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-39950-z
    DOI: 10.1038/s41467-023-39950-z
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    References listed on IDEAS

    as
    1. Guohong Albert Wu & Javier Terol & Victoria Ibanez & Antonio López-García & Estela Pérez-Román & Carles Borredá & Concha Domingo & Francisco R. Tadeo & Jose Carbonell-Caballero & Roberto Alonso & Fran, 2018. "Genomics of the origin and evolution of Citrus," Nature, Nature, vol. 554(7692), pages 311-316, February.
    2. A. C. R. da Silva & J. A. Ferro & F. C. Reinach & C. S. Farah & L. R. Furlan & R. B. Quaggio & C. B. Monteiro-Vitorello & M. A. Van Sluys & N. F. Almeida & L. M. C. Alves & A. M. do Amaral & M. C. Ber, 2002. "Comparison of the genomes of two Xanthomonas pathogens with differing host specificities," Nature, Nature, vol. 417(6887), pages 459-463, May.
    3. Michael D. Martin & Enrico Cappellini & Jose A. Samaniego & M. Lisandra Zepeda & Paula F. Campos & Andaine Seguin-Orlando & Nathan Wales & Ludovic Orlando & Simon Y. W. Ho & Fred S. Dietrich & Piotr A, 2013. "Reconstructing genome evolution in historic samples of the Irish potato famine pathogen," Nature Communications, Nature, vol. 4(1), pages 1-7, October.
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