@article{fdi:010082708,
  title = {{F}irst historical genome of a crop bacterial pathogen from herbarium specimen : insights into citrus canker emergence},
  author = {{C}ampos, {P}. {E}. and {C}rego, {C}. {G}. and {B}oyer, {K}. and {G}audeul, {M}. and {B}aider, {C}. and {R}ichard, {D}. and {P}ruvost, {O}. and {R}oumagnac, {P}. and {S}zurek, {B}oris and {B}ecker, {N}. and {G}agnevin, {L}. and {R}ieux, {A}.},
  editor = {},
  language = {{ENG}},
  abstract = {{A}uthor summary {H}erbarium collections are a precious resource to plant pathologists, tracking crop diseases on specimens collected in the past centuries. {I}n addition to indicating the presence of a disease at a specific time and locality, recent molecular technologies now allow extraction and microbial {DNA} sequencing from dead specimens. {D}espite challenges due to the degraded nature of {DNA} retrieved from historical samples, we were able to reconstruct the genome of a pathogenic bacterium from a 1937 herbarium specimen collected in {M}auritius: {X}anthomonas citri pv. citri, responsible for {A}siatic citrus canker ({ACC}, an economically important agricultural disease controlled mostly through prophylactic and quarantine measures). {E}nhanced knowledge about the epidemiology and evolution of this bacterial pathogen is valuable to improve these measures. {W}e compared the genome of this 1937 bacterial strain to a collection of modern strains, included it in a tree representing their genetic relationships, and calculated both evolutionary mutation rate and divergence times. {T}his "forensic investigation" informs us about how and when the disease developed in the {S}outh {W}est {I}ndian {O}cean {I}slands. {W}e hypothesize that there was a single (or a few related) introduction of {ACC} in {M}auritius in the mid-19th century, followed by expansion to the neighbouring islands. {O}ver the past decade, ancient genomics has been used in the study of various pathogens. {I}n 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. {W}e report here the first historical genome of a crop bacterial pathogen, {X}anthomonas citri pv. citri ({X}ci), obtained from an infected herbarium specimen dating back to 1937. {C}omparing the 1937 genome within a large set of modern genomes, we reconstructed their phylogenetic relationships and estimated evolutionary parameters using {B}ayesian tip-calibration inferences. {T}he arrival of {X}ci in the {S}outh {W}est {I}ndian {O}cean islands was dated to the 19(th) century, probably linked to human migrations following slavery abolishment. {W}e also assessed the metagenomic community of the herbarium specimen, showed its authenticity using {DNA} damage patterns, and investigated its genomic features including functional {SNP}s and gene content, with a focus on virulence factors.},
  keywords = {{OCEAN} {INDIEN} ; {MAURICE}},
  booktitle = {},
  journal = {{PL}o{S} {P}athogens},
  volume = {17},
  numero = {7},
  pages = {e1009714 [25 ]},
  ISSN = {1553-7366},
  year = {2021},
  DOI = {10.1371/journal.ppat.1009714},
  URL = {https://www.documentation.ird.fr/hor/fdi:010082708},
}