Abstract
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 19th 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.
Highlights
Since the origins of agriculture, humanity has struggled with the incessant, devastating impact of plant diseases on food production [1]
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)
Consensus historical genome reconstructed for chromosome, plasmids pXAC33 and pXAC64 have been deposited on GenBank database (CP072205-CP072207)
Summary
Since the origins of agriculture, humanity has struggled with the incessant, devastating impact of plant diseases on food production [1]. Whole genome sequencing of pathogens can confirm suspected cases of an infectious disease, discriminate between different strains, classify novel pathogens and reveal virulence mechanisms in a time- and cost-efficient manner [7,8]. Most studies were performed on field-sampled contemporary individuals over a time interval of maximum four decades. Such studies grant a good understanding of the population structure and recent emergences of pathogens, such small temporal differences between samples do neither allow a thorough detection of measurable amounts of evolutionary changes, nor a reconstruction of deeper evolutionary timelines [11], leaving many questions on crop pathogen emergence unanswered. With the first studies on ancient DNA (hereafter aDNA) obtained from historical or ancient samples such as archaeological tissue remains or museum specimens [12], it became possible to explore the past from a genetic perspective
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