RT Journal Article
SR Electronic
T1 Herbarium Specimen Sequencing Allows Precise Datation of Xanthomonas citri pv. citri Diversification History
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2022.12.08.519547
DO 10.1101/2022.12.08.519547
A1 PE Campos
A1 O Pruvost
A1 K Boyer
A1 F Chiroleu
A1 TT Cao
A1 M Gaudeul
A1 C Baider
A1 TMA Utteridge
A1 S Dominick
A1 N Becker
A1 A Rieux
A1 L Gagnevin
YR 2022
UL http://biorxiv.org/content/early/2022/12/12/2022.12.08.519547.abstract
AB Over the past decade, the field of ancient genomics has triggered considerable progress in the study of various pathogens, including those affecting crops. In this context, herbarium collections have been an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography may shed light into the emergence and evolutionary history of plant pathogens. In this study, we reconstructed 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected citrus herbarium specimens using a shotgun-based deep sequencing strategy. Following authentication of the historical genomes based on ancient DNA damage patterns, we compared them to a large set of modern genomes to reconstruct their phylogenetic relationships, pathogeny-associated genes content and estimate several evolutionary parameters, using Bayesian tip-dating calibration and phylogeography inferences. Our results reveal that Xci originated in Southern Asia ~11,500 years ago and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world. This updated scenario links Xci specialization to Neolithic climatic change and the development of agriculture, and its diversification to the human-driven expansion of citriculture through the early East-West trade and later colonization. The analysis of data obtained from such historical specimens is challenging and must undergo adapted treatment before being compared to modern samples. Nevertheless, we confirm here that herbarium collections are a precious tool to improve the knowledge of the evolutionary history of plant pathogens.Competing Interest StatementThe authors have declared no competing interest.