High throughput sequencing of small RNAs from black pepper (Piper nigrum L.)
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ABSTRACT:
ORGANISM(S): Piper nigrum
PROVIDER: GSE65782 | GEO | 2017/08/24
SECONDARY ACCESSION(S): PRJNA275003
REPOSITORIES: GEO
Similar Datasets
Project description:The experiments were performed to elucidate the enigmatic enzymatic formation of the pungent principle, piperine, from black pepper (Piper nigrum L.), the world´s most popular spice. Based a differential RNA-Seq approach including immature fruits, flowers, and leaves, the gene encoding piperine synthase, encoding a BAHD-type acyltransferase and several other candidate genes encoding various enzymatic functions in the biosynthetic pathway were identified. Recombinant piperine synthase and additional promiscuous piperamide synthases were used to facilitate the microbial production of a broad range of medicinally relevant piperamides. Subsequent investigations will also include the identification of enzymatic steps in the phenylpropanoid pathway and the amino acid derived biosynthesis of piperidine Based on the assumption that piperine encoding genes are highly expressed shortly before the slope of piperine accumulation reaches its maximum, RNA from greenhouse grown black pepper plants was extracted from young fruits at two different stages of development, flowers, and leaves were harvested for a differential RNA-Seq approach. Candidate transcripts associated with piperine biosynthesis were identified by comparative transcript abundance and sequence annotation tools.
2021-04-28 | E-MTAB-9029 | biostudies-arrayexpress
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
Project description:Drought is one of the major factor that limits crop production and reduces yield. To understand the early response of plants under nearly natural conditions, pepper plants were grown in a greenhouse and drought stressed by withholding water for one week. Plants adapted to the decreasing water content of the substrate by adjustment of their osmotic potential in roots by accumulation of raffinose, glucose, galactinol and proline. In contrast in leaves levels of fructose, sucrose and also galactinol increased. Due to the water deficit cadaverine, putrescine, spermidine and spermine accumulated in leaves whereas the concentration of polyamines was reduced in roots. These polyamines are suggested to rather act as stress protectants than for osmotic adjustment. To understand the molecular basis of the response to this early drought stress better, four suppression subtractive hybridisation libraries from leaves and roots were constructed. Microarray technique was used to identify differentially expressed genes. A total of 109 unique ESTs were detected. The diversity of the putative functions of all identified genes confirms the complexity of the plant response to drought stress. Keywords: Transcription profiling Two-condition experiment in roots and leaves, control leaves (CL) vs. drought-stressed leaves (DL) and control roots (CR) vs. drought-stressed roots (DR). Biological replicates: 4 control (1-4), drought-stressed (1-4), independently grown and harvested. One swap replicate per array.
2010-06-20 | E-GEOD-18627 | biostudies-arrayexpress
Project description:Drought is one of the major factor that limits crop production and reduces yield. To understand the early response of plants under nearly natural conditions, pepper plants were grown in a greenhouse and drought stressed by withholding water for one week. Plants adapted to the decreasing water content of the substrate by adjustment of their osmotic potential in roots by accumulation of raffinose, glucose, galactinol and proline. In contrast in leaves levels of fructose, sucrose and also galactinol increased. Due to the water deficit cadaverine, putrescine, spermidine and spermine accumulated in leaves whereas the concentration of polyamines was reduced in roots. These polyamines are suggested to rather act as stress protectants than for osmotic adjustment. To understand the molecular basis of the response to this early drought stress better, four suppression subtractive hybridisation libraries from leaves and roots were constructed. Microarray technique was used to identify differentially expressed genes. A total of 109 unique ESTs were detected. The diversity of the putative functions of all identified genes confirms the complexity of the plant response to drought stress. Keywords: Transcription profiling
2009-10-28 | GSE18627 | GEO
Project description:Piperine Biosythesis in Black Pepper
| PRJEB38192 | ENA
Project description:Phytophthora blight is a highly destructive soil borne disease caused by Phytophthora capsici Leonian, which seriously threatens global pepper production. Grafting is one of the important means to improve plant disease resistance and prevent soil borne diseases in vegetable production. However, the molecular mechanism by which grafting enhances the resistance of pepper to Phytophthora blight is still unclear. This study used Phytophthora capsici resistant strain ‘ZCM334’ and susceptible strain ‘Early Calwonder’ as rootstocks, and ‘Early Calwonder’ as scions for grafting. Phenotypic observation and cytological analysis showed that compared with the ‘Early Calwonder’ self rooted plants, the ‘ZCM334’ grafted plants had a later onset of disease, stronger resistance, and less damage to leaf cells, indicating that grafting can significantly improve the resistance of pepper to Phytophthora capsici. This study identified differentially expressed proteins (DEPs) in the leaves and roots of ‘ZCM334’ grafted plants and ‘Early Calwonder’ self rooted plants through proteomic analysis based on iTRAQ technology, and 478 and 349 DEPs were identified between their leaves and roots, respectively. These DEPs were mainly involved in metabolic process, cellular process, response to stimulus and catalytic activity processes. We identified and screened 12 DEPs with consistent expression trends in the leaves and roots of ‘ZCM334’ grafted plants and ‘Early Calwonder’ self rooted plants, including seven DEPs related to Phytophthora capsici resistance (CA01g31060, CA02g15780, CA02g30850, CA01g11410, CA05g12260, CA03g35150, and CA03g36980) and five proteins with unknown functions (CA01g26190, CA11g10620, CA12g02730, CA01g20890 and CA02g11340). Through qRT-PCR analysis, a significant correlation was observed between the protein and transcript levels of these 12 DEPs, and their expression characteristics were analyzed in the roots and leaves of ‘ZCM334’ grafted plants and ‘Early Calwonder’ self rooted plants at different stages (0h, 12h, 24h, and 36h) after inoculation with Phytophthora capsici. This study provides valuable information for exploring the molecular mechanisms by which grafting enhances the resistance of pepper to Phytophthora blight and the excavation of these key genes provides research ideas for studying the regulatory network of pepper resistance to Phytophthora capsici.
2024-05-24 | PXD045628 | Pride
Project description:ngs2013_07_pcapsici-effecaps-phytophthora capsici-The analysed RNAseq concerned the oomycete Phytophthora capsici in growth on pepper plants. 1/ How the adaptation of a pathogen to a host depends on its gene expression? 2/ How the plant host impacts the expression of pathogen genes at the very beginning of infection?-Two isolates of Phytophthora capsici were used: the Pc107 isolate (called A for adapted to pepper from INRAE GAFL Avignon), and the Pc273 isolate (N for non-adapted to pepper, collected on pumpkin in the USA). Two accessions of pepper (Capsicum annuum L., the host) were used: Yolo Wonder (YW, PM0031), susceptible (S) to Phytophthora capsici, and Criollo de Morelos 334 (CM334, PM0702), partially resistant (R). Inoculations were performed, as described in Lefebvre and Palloix (1996), by putting on the wounded stem a plug of mycelium. Inoculated plants were transferred to a growth chamber at 24°C/22°C temperature on a 12h/12h light/dark cycle. At 24 hours-post-inoculation, 12 total RNA samples were extracted from inoculated plants for the 4 host-isolate interactions: R_A, S_A, R_N and S_N. Each sample consisted of six pooled stem fragments. The stem fragments are the 5-mm region immediately under the visible stem necrosis. Samples were flash-frozen in liquid-nitrogen and stored at -80ºC. They were ground in liquid nitrogen with a cold mortar and pestle. Total RNA was extracted using QIAGEN Rneasy Plant Mini Kit. RNA-seq libraries were constructed at IPS2 POPS platform (France) by TruSeq_Stranded_mRNA_SamplePrep_Guide_15031047_D protocol (Illumina®, California, USA). Sequencing was conducted on an Illumina Hiseq2000 hosted by Genoscope (Evry, France). The RNA-seq samples have been sequenced in paired-end (PE) with a sizing of 260 bp and a read length of 100 bases, lane repartition and barcoding giving approximately 35 million of paired-end reads per sample.
2022-10-24 | GSE206447 | GEO
Project description:Black pepper rhizosphere mycobiome Raw sequence reads
| PRJNA942950 | ENA
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:A comparative study to determine the pepper leaf curl virus resistance machanism between resistant and susceptible genotypes at three leaf stage. To study the molecular mechanism of pepper leaf curl virus (PepLCV) resistance, pepper plants were exposed to PepLCV through artificial inoculation and hybridization on Agilent tomato microarrays. The expression analysis of PepLCV resistant and susceptible genotypes after artificial inoculation at three leaf stage showed that the resistance against PepLCV is due to sum of expression of hundreds of genes at a particular stage.
2012-10-11 | GSE41131 | GEO