De novo transcriptome of Phakopsora pachyrhizi uncovers putative effector repertoire during infection

Abstract

<p><em>Phakopsora pachyrhizi</em>, which causes Asian soybean rust (ASR), secretes effector proteins to manipulate host immunity and promote disease. To date, only a small number of effectors have been identified from transcriptome studies. To obtain a more comprehensive understanding of <em>P. pachyrhizi</em> candidate secreted effector proteins (CSEPs), we sequenced the transcriptome using two next-generation sequencing technologies. Short-read Illumina RNA-Seq data was used for reducing base-calling errors for long-read PacBio Iso-Seq. After initial <em>de novo</em> assemblies for RNA-seq and error correction of transcripts for Iso-Seq followed by filtering, we obtained 8,528, 27,647, 26,895, and 17,141 non-plant, non-soybean transcripts at 3, 7, 10, and 14 days after inoculation, respectively. We identified a repertoire of CSEPs of which a majority was expressed during the later stages of infection, and many that could be bioinformatically associated with haustoria. This approach for identifying CSEPs improves our current understanding of the <em>P. pachyrhizi</em> effectorome, and these CSEPs are expected to be a valuable resource for future studies of <em>P. pachyrhizi-</em>soybean interactions.</p>