Exome capture of 86 field samples of Phakopsora pachyrhizi from different geographic regions
Asian soybean rust (ASR), caused by the obligate biotrophic rust fungus, Phakopsora pachyrhizi, was first reported in the continental United States in 2004 and over the years has been of concern to soybean production in the United States (US). The current working hypothesis is that fungal spores got introduced into the US with hurricanes from South America, specifically hurricane Ivan. Using exome-capture based sequencing, we interrogated the genetic diversity of 84 P. pachyrhizi infected field populations collected from different geographic regions around the world. We compared the gene encoding regions from all the field populations samples and found that four major haplotypes are prevalent worldwide. Here, we provided evidence supporting multiple incursions have led to the currently established US P. pachyrhizi population. Phylogenetic analysis of mitochondrial genes further supports this hypothesis. Nevertheless, we observed a limited genetic diversity in Brazilian P. pachyrhizi populations, which suggests a strong selection pressure compared to field populations from other geographic regions, as US and Africa. This is the first report of P. pachyrhizi population structures defined by the genetic evidence from populations across different geographic region.