Dataset Information

Black pepper proteome - Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum-Phytophthora capsici Phytopathosystem

ABSTRACT: In this study, we have evaluated the proteomic changes that occur in Piper nigrum L.(black pepper) after infection by the pathogen Phytophthora capsici. We report novel leaf proteins from black pepper identified by an integrated transcriptome-assisted label-free quantitative proteomics pipeline. Several previously described methods were used to create this data set. Detached leaves were inoculated with either mock treatment, or the oomycete pathogen and small tissue samples only around the site of inoculation were collected for protein sample preparations. In order to quantify protein abundance in the samples being compared, we used a label free method of spiking samples with a known ratio of pre-digested peptide samples to normalize endogenous protein abundance in the MS detection. Our study attempts to explain the basal immune components of black pepper when challenged with P. capsici.

INSTRUMENT(S): Synapt MS

ORGANISM(S): Piper Nigrum

TISSUE(S): Leaf

SUBMITTER: Chidambareswaren Mahadevan

LAB HEAD: Manjula Sakuntala

PROVIDER: PXD003887 | Pride | 2016-07-07

REPOSITORIES: Pride

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Publications

Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum-Phytophthora capsici Phytopathosystem.

Mahadevan Chidambareswaren C Krishnan Anu A Saraswathy Gayathri G GG Surendran Arun A Jaleel Abdul A Sakuntala Manjula M

Frontiers in plant science 20160620

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. capsi ...[more]

PMID: 27379110

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Project description:To facilitate the functional annotation of the pepper genome, we generated 90.84 Gb of RNA-Seq data from 33 libraries representing all major tissue types and developmental stages of Zunla 1, as well as fruits from other accessions with significant phenotypic differences. Pepper ‘Zunla 1’ and other inbred lines were grown in a greenhouse as described in Table S1, with their different developmental stages Plants at full-bloom stage were harvested for roots, stems, and leaves as the same as the samples for phased small RNAs (see text S3.4.2 for details). Mature plants were harvested for unopened flower buds (buds) and fully open flowers (flowers). Additional flowers were allowed to self-pollinate and fruit was harvested at four pre-breaker stages (1-3cm, 3-4cm, 4-5cm fruit length, and mature green), the breaker stage (when the fruit was turning red) and three post-breaker stages (3, 5, and 7 days after breaker). These samples will respectively be referred to as Root, Stem, Leaf, Bud, Flower, F-Dev-1, F-Dev-2, F-Dev-3, F-Dev-4, F-Dev-5, F-Dev-6, F-Dev-7, F-Dev-8, and F-Dev-9. Similar roots, stems, leaves, immature fruit and red fruit were harvested from other inbred lines from domesticated Capsicum species. Meanwhile, chiltepin plants were grown under long days at controlled temperature and RNA was extracted from a mix of leaves from four stages (seedling, early blooming, full bloom, and fruit breaker phases), a mix of flowers from unopened flower buds (buds) and fully open flowers (flowers), and fruit at breaker and breaker plus five days respectively. All tissues were frozen in liquid nitrogen and then stored at -80℃. Total RNA was isolated from different samples by using the Trizol Reagent (Invitrogen) according to manufacturer’s instructions. Strand-specific RNA-Seq library preparations were performed as previously described (39) with 12 independently bar-coded samples sequenced on one lane of an Illumina HiSeq2000 system. The 200 bp paired-end libraries were sequenced using Illumina HiSeq 2000 (90 bp PE).

Dataset Information

Black pepper proteome - Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum-Phytophthora capsici Phytopathosystem

Publications

Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum-Phytophthora capsici Phytopathosystem.

Similar Datasets

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