Transcriptome analysis of Phakopsora pachyrhizi uncovers putative effector repertoire during infection

Phakopsora pachyrhizi is an obligate biotrophic fungal pathogen of soybean that causes Asian soybean rust (ASR), a devastating disease that can cause yield losses of 80% or greater. P. pachyrhizi secretes an arsenal of effector proteins to manipulate host immunity and promote disease. Current knowledge of the P. pachyrhizi genome is limited and only a small number of the total P. pachyrhizi effectors have been identified. We therefore sequenced the transcriptome of P. pachyrhizi during infection to identify P. pachyrhizi Candidate Secreted Effector Proteins (CSEPs). Total RNA was extracted from P. pachyrhizi infected soybean leaf tissue collected at 3, 7, 10, and 14 days after inoculation (dai). cDNA libraries were prepared and RNA sequencing was performed using Illumina HiSeq3000 and MiSeq (Illumina, https://www.illumina.com/) to generate paired-end reads (HiSeq: 2 × 150 bp, 2 lanes per time point; MiSeq: 2 × 300 bp; 3 lanes per time point). After removal of soybean reads, the short-reads were de novo assembled using the Trinity assembler. We identified a repertoire of CSEPs including haustorial effectors associated with pathogenicity during P. pachyrhizi infection. A significant number of the predicted effectors were expressed during the later stages of P. pachyrhizi infection. This comprehensive P. pachyrhizi transcriptome profiling substantially improves our current understanding of molecular soybean-rust interactions. The repertoire of candidate effectors identified here are valuable for future functional analysis of P. pachyrhizi virulence and pathogenicity.