Iowa State University
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Phakopsora pachyrhizi transcriptome from PacBio Isoform Sequencing

posted on 2019-09-30, 21:54 authored by Manjula ElmoreManjula Elmore, Sagnik BanerjeeSagnik Banerjee, Kerry F. Pedley, Amy Ruck, Steven WhithamSteven Whitham
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 7, and 10 days after inoculation (dai). cDNA libraries were prepared according to the Iso-Seq protocol using Clontech SMARTer PCR cDNA synthesis kit with no size selection. Sequencing was performed on a PacBio RS II ( For each time point, final libraries composed of transcripts with no size selection were sequenced on six SMRT cells. The subreads generated from six SMRT cells were pooled together for each time point and processed following the RS_IsoSeq protocol ( available in SMRT analysis package v2.3.0. Each time point contains two fasta files: (1) The error-corrected transcripts of P. pachyrhizi, and (2) High quality and low quality consensus transcripts before error correction. The error-corrected transcripts were used for CSEP prediction.

M.G.Elmore, S.Banerjee, K.F.Pedley, A.Ruck, S.A.Whitham. De novo transcriptome of Phakopsora pachyrhizi uncovers putative effector repertoire during infection. Physiological and Molecular Plant Pathology, 110 (2020),101464, 10.1016/j.pmpp.2020.101464