Campus Units

Plant Pathology and Microbiology, Statistics, Bioinformatics and Computational Biology

Document Type

Article

Publication Version

Published Version

Publication Date

2020

Journal or Book Title

Physiological and Molecular Plant Pathology

Volume

110

First Page

101464

DOI

10.1016/j.pmpp.2020.101464

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.

Comments

This article is published as Elmore, Manjula G., Sagnik Banerjee, Kerry F. Pedley, Amy Ruck, and Steven A. Whitham. "De novo transcriptome of Phakopsora pachyrhizi uncovers putative effector repertoire during infection." Physiological and Molecular Plant Pathology 110 (2020): 101464. doi: 10.1016/j.pmpp.2020.101464.

Rights

Works produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted.

Language

en

File Format

application/pdf

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