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

Authors: ELMORE, MANJULA - Iowa State University; BANERJEE, SAGNIK - Iowa State University; Pedley, Kerry; Wright, Amy; WHITHAM, STEVEN - Iowa State University

Submitted to: Physiological and Molecular Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/20/2020
Publication Date: 1/23/2020
Citation: Elmore, M.G., Banerjee, S., Pedley, K.F., Ruck, A.L., Whitham, S.A. 2020. De novo transcriptome of Phakopsora pachyrhizi uncovers putative effector repertoire during infection. Physiological and Molecular Plant Pathology. 110:101464. https://doi.org/10.1016/j.pmpp.2020.101464.
DOI: https://doi.org/10.1016/j.pmpp.2020.101464

Interpretive Summary: Asian soybean rust is a devastating disease that can cause soybean yield losses of 80% or greater. During infection, the fungal pathogen delivers proteins called “effectors” inside the host plant cell in order to subdue or subvert the plant immune system. Since the genome of the soybean rust pathogen has not been sequenced, our knowledge of the pathogen’s effector repertoire deployed during the infection process is quite limited. In this study, we employed two complimentary RNA sequencing technologies to identify candidate effector proteins produced at 3, 7, 10, and 14 days after inoculation of soybean plants with the pathogen. This comprehensive analysis led to the identification of hundreds of novel candidate effectors and substantially improves our current understanding of molecular soybean-rust interactions. The repertoire of candidate effectors identified here are valuable for future functional analyses of the pathogen that will assist in efforts to combat this disease.

Technical 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. Shortread 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.