Dataset Information

Analysis of microsatellites from transcriptome sequences of Phytophthora capsici and applications for population studies.

ABSTRACT: Phytophthora capsici is a devastating oomycete that affects solanaceous, cucurbitaceous, fabaceous, and other crops in the United States (US) and worldwide. The release of the P. capsici genome allows for design of robust markers for genetic studies. We identified and characterized microsatellites in the P. capsici transcriptome. A subset of 50 microsatellites were assayed in a diverse set of P. capsici isolates and evaluated for polymorphism. Polymorphic microsatellites were confirmed by fragment analysis, and 12 were used for population characterization of 50 P. capsici isolates from different states, hosts, and mating types. Analysis of genetic relationship among isolates revealed significant geographic structure by state. Our findings highlight the usefulness of these 12 microsatellites to characterize the population structure of P. capsici and potential transferability to closely-related Phytophthora spp. since markers are located in coding regions. Our markers will facilitate genetic characterization and complement phenotypic studies of P. capsici populations, which may assist in deployment of disease management strategies.

SUBMITTER: Parada-Rojas CH

PROVIDER: S-EPMC5980080 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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Analysis of microsatellites from transcriptome sequences of Phytophthora capsici and applications for population studies.

Parada-Rojas C H CH Quesada-Ocampo L M LM

Scientific reports 20180326 1

Phytophthora capsici is a devastating oomycete that affects solanaceous, cucurbitaceous, fabaceous, and other crops in the United States (US) and worldwide. The release of the P. capsici genome allows for design of robust markers for genetic studies. We identified and characterized microsatellites in the P. capsici transcriptome. A subset of 50 microsatellites were assayed in a diverse set of P. capsici isolates and evaluated for polymorphism. Polymorphic microsatellites were confirmed by fragme ...[more]

PMID: 29581516

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Project description:Black pepper (Piper nigrum L.), a tropical spice crop of global acclaim, is susceptible to Phytophthora capsici, an oomycete pathogen which causes the highly destructive foot rot disease. A systematic understanding of this phytopathosystem has not been possible owing to lack of genome or proteome information. In this study, we explain an integrated transcriptome-assisted label-free quantitative proteomics pipeline to study the basal immune components of black pepper when challenged with P. capsici. We report a global identification of 532 novel leaf proteins from black pepper, of which 518 proteins were functionally annotated using BLAST2GO tool. A label-free quantitation of the protein datasets revealed 194 proteins common to diseased and control protein datasets of which 22 proteins showed significant up-regulation and 134 showed significant down-regulation. Ninety-three proteins were identified exclusively on P. capsici infected leaf tissues and 245 were expressed only in mock (control) infected samples. In-depth analysis of our data gives novel insights into the regulatory pathways of black pepper which are compromised during the infection. Differential down-regulation was observed in a number of critical pathways like carbon fixation in photosynthetic organism, cyano-amino acid metabolism, fructose, and mannose metabolism, glutathione metabolism, and phenylpropanoid biosynthesis. The proteomics results were validated with real-time qRT-PCR analysis. We were also able to identify the complete coding sequences for all the proteins of which few selected genes were cloned and sequence characterized for further confirmation. Our study is the first report of a quantitative proteomics dataset in black pepper which provides convincing evidence on the effectiveness of a transcriptome-based label-free proteomics approach for elucidating the host response to biotic stress in a non-model spice crop like P. nigrum, for which genome information is unavailable. Our dataset will serve as a useful resource for future studies in this plant. Data are available via ProteomeXchange with identifier PXD003887.

Dataset Information

Analysis of microsatellites from transcriptome sequences of Phytophthora capsici and applications for population studies.

Publications

Analysis of microsatellites from transcriptome sequences of Phytophthora capsici and applications for population studies.

Similar Datasets

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