First historical genome of a crop bacterial pathogen from herbarium specimen: Insights into citrus canker emergence

Author summary Herbarium collections are a precious resource to plant pathologists, tracking crop diseases on specimens collected in the past centuries. In 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. Despite 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 Mauritius: Xanthomonas citri pv. citri, responsible for Asiatic citrus canker (ACC, an economically important agricultural disease controlled mostly through prophylactic and quarantine measures). Enhanced knowledge about the epidemiology and evolution of this bacterial pathogen is valuable to improve these measures. We 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. This forensic investigation informs us about how and when the disease developed in the South West Indian Ocean Islands. We hypothesize that there was a single (or a few related) introduction of ACC in Mauritius in the mid-19th century, followed by expansion to the neighbouring islands. 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.

Automated summary

By analyzing microbial DNA extracted from historical specimens, researchers successfully reconstructed the genome of the pathogenic bacterium Xanthomonas citri pv. citri from a 1937 citrus specimen. This study provides valuable information about the evolution and spread of the pathogen, contributing to improvements in agricultural disease control measures.