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.

现代农业实践增加了植物病原体传播的可能性，而负担得起的全基因组测序的出现使对病原体运动的深入研究成为可能。由于复杂的农业生产系统，种群基因组研究可能会破译病原体运动和种群结构。我们使用在佛罗里达州和佐治亚州南部田地的一个番茄生产季节内收集的 281 种穿孔黄单胞菌菌株的全基因组序列来测试与番茄生产系统变量相关的种群遗传结构。我们确定了六个X. perforans集群来自与系统发育谱系对应的核心基因 SNP。使用全基因组 SNP，我们发现了农场、移植设施、品种、种子生产商、种植者经营、地区和县之间的遗传结构。总的来说，与从多个来源接受移植物的种植者操作相比，自己生产移植物的种植者操作与遗传上不同且多样性较低的菌株种群相关。佛罗里达州番茄生产系统各组成部分之间的遗传分化程度因集群而异，表明菌株的不同传播，例如通过种子或受污染的移植与农场内的本地移动。总的来说，我们表明细菌植物病原体的遗传变异是由植物生产系统的结构决定的。