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Alternative Splicing in the Obligate Biotrophic Oomycete Pathogen Pseudoperonospora cubensis

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  • Pseudoperonospora cubensis is an obligate pathogen and causative agent of cucurbit downy mildew. To help advance our understanding of the pathogenicity of P. cubensis, we used RNA-Seq to improve the quality of its reference genome sequence. We also characterized the RNA-Seq dataset to inventory transcript isoforms and infer alternative splicing during different stages of its development. Almost half of the original gene annotations were improved and nearly 4,000 previously unannotated genes were identified. We also demonstrated that approximately 24% of the expressed genome and nearly 55% of the intron-containing genes from P. cubensis had evidence for alternative splicing. Our analyses revealed that intron retention is the predominant alternative splicing type in P. cubensis, with alternative 5′- and alternative 3′-splice sites occurring at lower frequencies. Representatives of the newly identified genes and predicted alternatively spliced transcripts were experimentally validated. The results presented herein highlight the utility of RNA-Seq for improving draft genome annotations and, through this approach, we demonstrate that alternative splicing occurs more frequently than previously predicted. In total, the current study provides evidence that alternative splicing plays a key role in transcriptome regulation and proteome diversification in plantpathogenic oomycetes.
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  • Burkhardt, A., Buchanan, A., Cumbie, J. S., Savory, E. A., Chang, J. H., & Day, B. (2015). Alternative splicing in the obligate biotrophic oomycete pathogen Pseudoperonospora cubensis. Molecular Plant-Microbe Interactions, 28(3), 298-309. doi:10.1094/MPMI-09-14-0300-FI
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  • 28
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  • 3
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  • E. A.Savory is supported by United States Department of Agriculture NIFA postdoctoral fellowship number 2013-67012-21139. Work in the laboratory of J. H. Chang is supported by funding from the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R01GM104977. Research in the laboratory of B. Day is supported by funding from the Michigan State University Rackham Foundation, Michigan State University Project GREEN (GR13-007), and a grant from the United States Department of Agriculture Specialty Crops Research Initiative (2011-51181-30661).
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