Pathogenomics Characterization of an Emerging Fungal Pathogen, f. sp. in Greenhouse Tomato Production Systems.

In recent years, greenhouse-grown tomato () plants showing vascular wilt and yellowing symptoms have been observed between 2015 and 2018 in North Carolina (NC) and considered as an emerging threat to profitability. In total, 38 putative isolates were collected from symptomatic tomatoes in 12 grower greenhouses and characterized to infer pathogenic and genomic diversity, and mating-type () idiomorphs distribution. Morphology and polymerase chain reaction (PCR) markers confirmed that all isolates were f. sp. (FOL) and most of them were race 3. Virulence analysis on four different tomato cultivars revealed that virulence among isolates, resistance in tomato cultivars, and the interaction between the isolates and cultivars differed significantly ( < 0.001). Cultivar 'Happy Root' (, and genes for resistance) was highly resistant to FOL isolates tested. We sequenced and examined for the presence of 15 pathogenicity genes from different classes (, , , , , , , , , , , , , and ), and 14 () genes to use as genetic markers to identify and differentiate pathogenic isolates of FOL. Sequence data analysis showed that five pathogenicity genes, , , , and were present in all isolates while , , , , , , , and genes were dispersed among isolates. Two genes, and , were absent in all isolates. Of the 14 genes assessed, , and were identified in most isolates while the remaining genes varied among isolates. All isolates harbored one of the two mating-type ( or ) idiomorphs, but not both. The gene was present only in race 1 isolates. Diversity assessments based on sequences of the effector SIX3 and the translation elongation factor 1-α encoding genes and α, respectively were the most informative to differentiate pathogenic races of FOL and resulted in race 1, forming a monophyletic clade while race 3 comprised multiple clades. Furthermore, phylogeny-based on and α gene sequences showed that the predominant race 3 from greenhouse production systems significantly overlapped with previously designated race 3 isolates from various regions of the globe.