De novo transcriptome of Phakopsora pachyrhizi uncovers putative effector repertoire during infection
Manjula G. Elmore, Sagnik Banerjee, Kerry F. Pedley, Amy Ruck, Steven A. Whitham
Abstract
Phakopsora pachyrhizi , 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 P. pachyrhizi 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 de novo 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 P. pachyrhizi effectorome, and these CSEPs are expected to be a valuable resource for future studies of P. pachyrhizi- soybean interactions.