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.
Highlights
Phakopsora pachyrhizi, the causal agent of Asian soybean rust (ASR), is a serious threat to soybean production worldwide and can cause yield losses greater than 80% if not controlled [1,2,3]
We identified a repertoire of candidate secreted effector proteins (CSEPs) of which a majority was expressed during the later stages of infection, and many that could be bioinformatically associated with haustoria
The de novo transcriptome assemblies of P. pachyrhizi during infection were performed to identify genes encoding putative effectors involved in compatible soybean-rust interactions
Summary
Phakopsora pachyrhizi, the causal agent of Asian soybean rust (ASR), is a serious threat to soybean production worldwide and can cause yield losses greater than 80% if not controlled [1,2,3]. Genome and transcriptome analyses of several rust fungi have proven to be efficient approaches for the discovery of genes predicted to encode candidate secreted effector proteins (CSEPs) [8,9]. The present study describes identification of several hundreds of novel CSEPs from long-read isoform and short-read RNA-Seq during P. pachyrhizi infection, and it more than doubles the list of previously published P. pachyrhizi haustorial effector candidates. These datasets derived from the LA04-1 isolate augment the P. pachyrhizi genome and transcriptome annotations, and provide a valuable resource for studying molecular mechanisms during P. pachyrhizi pathogenicity
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