ITRAQ-based quantitative proteomic analysis of heat stress-induced mechanisms in pepper seedlings
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Capsicum Annuum
TISSUE(S): Leaf
SUBMITTER: 
Jing Wang
LAB HEAD: Jing Wang
PROVIDER: PXD019556 | Pride | 2021-05-06
REPOSITORIES: Pride
Similar Datasets
Project description:Upon virus infections, the transcriptomic profile of host plants markedly changes. The rapid and comprehensive transcriptional reprogramming is critical to ward off virus attack. To learn more about transcriptional reprogramming in tobamovirus-infected pepper leaves, we carried out transcriptome-wide RNA-Seq analyses of pepper leaves following Obuda pepper virus (ObPV) and Pepper mild mottle virus (PMMoV)-inoculations.
2021-07-23 | E-MTAB-10769 | biostudies-arrayexpress
Project description:To facilitate the functional annotation of the pepper genome, analysis of miRNAs was performed for the sequenced data from five small RNA libraries described above, representing five different tissues. Starting with a set of 5,436 plant mature miRNA sequences available in miRBase, we annotated with high confidence 176 pepper miRNAs from 64 families, of which 30 families are computationally predicted to target TFs, suggesting important roles of these miRNA families in post-transcriptional gene regulation and transcription networks consistent with previous findings. To identify genomic regions generating small RNAs, we applied previously described analytical strategies to five small RNA libraries from different tissues. Developing roots, stems and mature leaves were collected from plants grown in soil in a green house at 22 °C with a 16 hr light cycle and harvested from plants at full-bloom stage. Mature plants were harvested for fully open flowers. Additional flowers were allowed to self-pollinate and fruit was harvested in the breaker stage (thirty days after pollination when the fruit was turning red). Total RNA for different tissues was isolated from the frozen root samples by using the Trizol Reagent (Invitrogen) according to manufacturer’s instructions, and libraries were constructed using the Small RNA Sample Prep Kit (Illumina, San Diego, CA) as previously described, then sequenced on an Illumina HiSeq2000 system.
2014-03-14 | E-GEOD-45040 | biostudies-arrayexpress
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).
2014-03-14 | E-GEOD-45037 | biostudies-arrayexpress
Project description:Pepper(Capsicum annuum L.) fruit development is a complex and genetically programmed process, a comparative study of transcriptome and proteome changes during two varieties of pepper development（IMG, MG, Br and MR） has been carried out by using RNA-Seq and Lable-free quantitation technology.
2019-01-21 | PXD010746 | Pride
Project description:Transcriptome analysis in response to infestation of whitefly in peppr leaf and root Microarry study using total RNA from whitefly infestation, BTH, whitefly + BTH, and control in both leaf and root of pepper
2014-01-01 | E-GEOD-52661 | biostudies-arrayexpress
Project description:This project presents the raw data about pretomic of two clematis seedings in response to heat stress at 38 oC for 3 h
2020-06-04 | PXD018192 | Pride
Project description:Lysine acetylation in proteins is a dynamic and reversible Post-translational modification and plays an important role in diverse cellular processes, but limited knowledge is available for acetylation modifications in pepper (Capsicum annuum L.) resistance of cold stress. In this study, the proteome and acetylome of two peppers with different cold resistance under different cold stress and recovery treatment were investigated. In total, 6213 proteins groups and 4574 lysine acetylation sites of 2261 protein groups were identified. Cold stress and recovery treatment results in 3008 differentially expressed proteins (DEPs) and 768 differentially expressed acetylated proteins (DEAPs). Further analysis found a total 1988 proteins were both identifed in the proteome and acetylome data and elucidated the functional differences between the up-regulated and down-regulated proteins in these co-identified proteins through GO enrichment. Twenty acetylation motifs were defined on 3934 unique lysine acetylation sites and motifs *KS*, *KY*, and *KH* occupied the highest proportion of all the identified peptides. Subcellular distribution predictions showed that acetylated proteins in pepper leaves distributed predominantly in chloroplast, cytoplasm and nuclear. KEGG analysis showed 397 identified acetylated proteins were involved in 93 different metabolic pathways. Then the dynamic changes of acetylated proteins in photosynthesis and carbon fixation in photosynthetic organisms pathways under cold stress were further analyzed and many key acetylated proteins regulating cold resistance of pepper were found in these two metabolic pathways. This study is the first to identify the acetylome in pepper, expands greatly the catalog of lysine acetylation substrates and sites in Solanaceae crops and provide a new insight for the post-translational modification study.
2022-02-15 | PXD021024 | Pride
Project description:Nanotechnology has the potential to revolutionize agriculture by developing engineered nanomaterials to be used as biostimulants, fertilizers, pesticides or smart sensors. Seed priming may represent an opportunity for nano-enabled plant technology to match economic, agronomic and environmental needs. This study investigates the effects of seed priming mediated by iron oxide magnetic nanoparticles (MNPs) in plants. We performed a multilevel integrated study to understand the basic interactions between MNPs and seeds in pepper (Capsicum annuum). Moreover, phenotypic, physiological and molecular analyses were performed to elucidate the biological impact of MNPs from seed to plant development. Interestingly, our findings show positive effects of MNPs on vegetative growth and a profound impact on pepper gene expression patterns. Indeed, we found 2,204 differentially expressed transcripts in nanoprimed seeds, most of them involved in plant defence mechanisms, potentially establishing a seed memory that might enhance the plant's capacity to counteract diverse forms of stress. In conclusion, this work provides a comprehensive investigation about nanoparticle-seed interactions with interesting implications for agricultural technology.
2023-11-08 | E-MTAB-13087 | biostudies-arrayexpress
Project description:Comprehensive Phosphoproteomic Analysis of Pepper Fruit Development Provides Insight into Plant Signaling Transduction
2020-05-27 | PXD017648 | Pride
Project description: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.
2016-07-07 | PXD003887 | Pride