Open AccessFirst historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence
Author(s) -
Paola Campos,
Clara Groot Crego,
Karine Boyer,
Myriam Gaudeul,
Cláudia Baider,
Damien Richard,
Olivier Pruvost,
Philippe Roumagnac,
Boris Szurek,
Norbert Becker,
Lionel Gagnevin,
Adrien Rieux
Publication year - 2021
Publication title -
plos pathogens
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.719
H-Index - 206
eISSN - 1553-7374
pISSN - 1553-7366
DOI - 10.1371/journal.ppat.1009714
Subject(s) - canker , herbarium , biology , citrus canker , genome , pathogen , crop , botany , microbiology and biotechnology , genetics , bacteria , ecology , gene
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 19 th 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.