Whole genome sequences reveal the Xanthomonas perforans population is shaped by the tomato production system

Jeannie M Klein-Gordon,Karen A Garrett,Erica M Goss,Yanru Xing,Peter Abrahamian,Jeffrey B Jones,Gary E Vallad,Sujan Timilsina

doi:10.1038/s41396-021-01104-8

Abstract

Modern agricultural practices increase the potential for plant pathogen spread, while the advent of affordable whole genome sequencing enables in-depth studies of pathogen movement. Population genomic studies may decipher pathogen movement and population structure as a result of complex agricultural production systems. We used whole genome sequences of 281 Xanthomonas perforans strains collected within one tomato production season across Florida and southern Georgia fields to test for population genetic structure associated with tomato production system variables. We identified six clusters of X. perforans from core gene SNPs that corresponded with phylogenetic lineages. Using whole genome SNPs, we found genetic structure among farms, transplant facilities, cultivars, seed producers, grower operations, regions, and counties. Overall, grower operations that produced their own transplants were associated with genetically distinct and less diverse populations of strains compared to grower operations that received transplants from multiple sources. The degree of genetic differentiation among components of Florida’s tomato production system varied between clusters, suggesting differential dispersal of the strains, such as through seed or contaminated transplants versus local movement within farms. Overall, we showed that the genetic variation of a bacterial plant pathogen is shaped by the structure of the plant production system.

Highlights

Human activities have accelerated long-distance movement of microbes, changing global distributions of microbes as well as genetic variation within and among local populations
A progression of studies looking at Xanthomonas perforans (Xp) populations since that time has revealed the diversity and change in type III secretion system effector content over time despite lack of any commercially deployed resistant cultivars [23, 28,29,30,31,32]. These results suggest that the complex tomato production system may be contributing to the diversity and structure of Xp populations
The core gene single nucleotide polymorphisms (SNPs) that were used to create the ClonalFrameML multilocus tree were analyzed with Rhierbaps (v. 1.1.3) [53, 54] with one level of clustering to assign strains to core gene clusters. iTOL (v. 5.6.3) [55] was used to visualize the multilocus trees generated with RAxML and ClonalFrameML, overlaid with colors indicating Rhierbaps cluster assignments

Summary

Introduction

Human activities have accelerated long-distance movement of microbes, changing global distributions of microbes as well as genetic variation within and among local populations. The repeated, inadvertent introduction of pathogens to plant production systems has the potential to cause genetic shifts in local and regional pathogen populations within each production cycle. Whole genome sequencing has enabled in-depth study of microbial populations in medical settings and surveillance of bacterial pathogens affecting human health [6,7,8,9,10,11,12]. Genomic variation of bacterial plant pathogens can be used to decipher pathogen movement in complex agricultural production systems [19] and the role of production systems in structuring regional populations

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Results

Conclusion