Transcriptome sequencing analysis of pepper
Ontology highlight
ABSTRACT:
ORGANISM(S): Capsicum chinense Capsicum annuum var. glabriusculum Capsicum annuum
PROVIDER: GSE45037 | GEO | 2014/03/14
SECONDARY ACCESSION(S): PRJNA193077
REPOSITORIES: GEO
Similar Datasets
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: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.
2014-03-14 | GSE45040 | GEO
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:Twelve chili pepper accessions, six domesticated, four wild and two F1 crosses were studied. RNA-Seq experiments were performed with fruits from each accession at 7 different times after anthesis. Additionally, samples of seedlings from two accessions were evaluated. The data set is comprised by 179 samples, that in total have more than 3 billion reads map to the Capsicum annuum genome.
2021-03-16 | GSE165448 | GEO
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:Background The set of all mRNA molecules present in a cell constitute the transcriptome. The transcriptome varies depending on cell type as well as in response to internal and external stimuli during development. Chili pepper is an economically and culturally important horticultural crop as well as a good model for the study of secondary metabolism during fruit development. Here we present a study of the changes that occur in the transcriptome of chili pepper fruit during development and ripening. Results RNA-Seq was used to obtain transcriptomes of whole Serrano-type chili pepper fruits (Capsicum annuum L.; 'Tampiqueno 74') collected at 10, 20, 40 and 60 days after anthesis (DAA). 15,550,468 Illumina MiSeq reads were assembled de novo into 34,066 chili genes. We classified the expression patterns of individual genes as well as genes grouped into Biological Process ontologies and Metabolic Pathway categories using statistical criteria. For the analyses of gene groups we added the weighted expression of individual genes. This method was effective in interpreting general patterns of expression changes and increased the statistical power of the analyses. Subsets of genes were expressed only at a single time point sampled (1,278, 1,596, 1,519 and 1,583 genes at 10, 20, 40 and 60 DAA, respectively). We also estimated the variation in diversity and specialization of the transcriptome during chili pepper development. Approximately 17% of genes exhibited a significant change of expression in at least one of the intervals sampled. In contrast, significant differences in approximately 63% of the Biological Processes and 80% of the Metabolic Pathways studied were detected in at least one interval. Confirming previous reports, genes related to capsaicinoid and ascorbic acid biosynthesis were significantly upregulated at 20 DAA while those related to carotenoid biosynthesis were highly expressed in the last period of fruit maturation (40-60 DAA). Our RNA-Seq data was validated by examining the expression of nine genes involved in carotenoid biosynthesis by qRT-PCR. Conclusions In general, more profound changes in the chili fruit transcriptome were observed in the intervals between 10 to 20 and 40 to 60 DAA. The last interval, between 40 to 60 DAA, included 49% of all significant changes detected, and was characterized predominantly by a global decrease in gene expression. This period signals the end of maturation and the beginning of senescence of chili pepper fruit. The transcriptome at 60 DAA was the most specialized and least diverse of the four states sampled. RNA-seq libraries of whole chili pepper (Capsicum annuum Serrano 'Tampiqueno 74' landrace) were prepared from fruits at 10, 20, 40 and 60 days after anthesis (DAA). Two biological replicates of each fruit state were prepared (8 libraries in total). Libraries were sequenced in the Illumina MiSeq platform. The title of the libraries are: <DAA>repbio<#> where <DAA> are the days after anthesis (10, 20, 40 or 60) and <#> is the number of biological replicate, 1 or 2. Details follow. Biological material and RNA extraction Capsicum annuum Serrano 'Tampiqueno 74' seeds were germinated and the seedlings were cultivated until maturity under greenhouse conditions in a completely randomized experimental design at Cinvestav-Unidad Irapuato (Guanajuato, Mexico). The plants were grown during the spring and summer, and individual flowers were tagged at anthesis. Chili pepper fruits were randomly collected from different plants at 10, 20, 40 and 60 DAA. After sampling, the fruits were cleaned with ethanol immediately frozen in liquid nitrogen and stored at -80C until further use. For total RNA extractions, 10 fruits at the 10 DAA developmental stage and 5 fruits from each of the 20, 40 and 60 DAA stages were randomly selected from the pool of all harvested fruits. Whole fruits (pericarp, placenta and seeds) were ground in liquid nitrogen with a mortar and pestle to form a fine uniform powder. Samples were mixed vigorously and 100 mg aliquots were measured for each RNA extraction. The process was repeated with different sets of fruits in order to obtain two independent biological replicates at each developmental stage. A NucleoSpin RNA Plant kit (Macherey-Nagel) was used for total RNA extraction and contaminating genomic DNA was removed by DNase I (Macherey-Nagel) treatment following the manufacturers' protocols. Total RNA concentration was quantified using a NanoDrop ND-1000 spectrophotometer (Nano-Drop, Wilmington, DE, USA) and RNA quality was evaluated by gel electrophoresis on 1.0% denaturing agarose gels. In addition, aliquots of RNA were run on an Agilent 2100 Bioanalyzer using RNA 6000 chips (Agilent, Santa Clara, CA, USA) to test the RNA integrity number (RIN). All eight samples had RIN values higher than 8.7. Thirty ?g of total RNA from each of the eight samples (two biological replicates of four fruit developmental stages) was used for cDNA library preparation. Library construction and sequencing The eight total RNA samples (two biological replicates from chili pepper fruits at 10, 20, 40 and 60 DAA) were prepared for RNA-Seq using the Illumina TruSeq RNA Sample Preparation v2 Guide following the manufacturer's instructions. Briefly, mRNA was purified from 20?g of total RNA using poly-T oligo- attached magnetic beads using two rounds of purification. During the second elution of the poly-A RNA, mRNA was fragmented using divalent cations under elevated temperature and primed for cDNA synthesis. The cleaved RNA fragments were primed with random hexamers and reverse transcribed into single-stranded cDNA using reverse transcriptase. In the next step, the RNA template was removed and the complementary cDNA strand was synthesized using RNAse H and DNA polymerase I, respectively. The overhangs that resulted from fragmentation were polished into blunt ends using an End Repair Mix (consisting of T4 DNA polymerase, Klenow fragment and T4 polynucleotide kinase). A single T nucleotide was added on the 3' end of the adapter for ligating the adapter to the cDNA fragments. Indexing adapters were ligated to the ends of the cDNAs using T4 DNA ligase, preparing them for hybridization onto a flow cell. Finally, the DNA fragments with adapter molecules at both ends were amplified by PCR to enrich the amount of DNA in the library. PCR was performed with a PCR primer cocktail that anneals to the ends of the adapters. Quantity and quality of the DNA libraries was assessed using Agilent DNA-1000 chips on an Agilent 2100 Bioanalyzer. The 8 cDNA libraries were pooled and simultaneously sequenced from both 5’ and 3’ ends using the Illumina MiSeq System platform according to the manufacturer's instructions. We performed three sequencing runs (technical replicates) with the aim of increase the sequencing depth. 150 bp paired-end reads were obtained in each sequencing run. Fluorescent image processing, base-calling and quality value calculations for each of the three runs were performed using Illumina MiSeq Control Software. Data were deposited at the NCBI (GEO database under series record GSE54123).
2014-02-21 | E-GEOD-54123 | biostudies-arrayexpress
Project description:Two fruit development stages of the wild chiltepin pepper (Capsicum annuum var. glabriusculum) were studied. RNA-Seq data was obtained from fruits at 20 and 68 days after anthesis with two biological replicates for a total of 4 samples. 260 million raw reads were sequenced and over 80% of them mapped back to the Capsicum annuum genome.
2021-08-05 | GSE171889 | GEO
Project description:TMT-labled proteome of pepper fruits treated with Heat stress was performed in this experiment
2022-02-11 | PXD031599 | iProX
Project description:In this study, we used the illumina high throughput sequencing approach (Sequencing-By-Synthesis, or SBS) to develop the sequence resource of black pepper. To identify micro RNAs functioning in stress response of the black pepper plant, small RNA libraries were prepared from the leaf and root of Phytophthora capsici infected plants, leaves from drought stressed and control plants.
2017-08-24 | GSE65782 | GEO
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