Project description:We sought to investigate the scope of transcriptome analyses of peppers subjected to four major phytohormones. For this, At the 6-true-leaf stage, pepper plants were sprayed at underside of leaves with 5 mM sodium salicylate (SA), 100 μM methyl jasmonate (JA), 5 mM ethephone (ET), 100 μM (±)-ABA, or distilled water (mock). For RNA-seq library construction, the third or fourth leaves from four plants were harvested per replicate at 0, 1, 3, 6, 12, and 24 h after treatment. A total of 187.8 Gb of transcriptome data were generated using transcriptome analysis pipelines consisting of quality control, quantification, and differential gene expression analyses. The extensive transcriptome data obtained will provide valuable information for future studies of crops exposed to responsive of phytohormones.

2020-06-07 | GSE149037 | GEO

High-throughput sequencing of small RNAs in Capsicum annuum

Project description:Small RNAs (21-24 nt) are pivotal regulators of gene expression that guide both transcriptional and post-transcriptional silencing mechanisms in diverse eukaryotes, including most if not all plants. MicroRNAs (miRNAs) and short interfering RNAs (siRNAs) are the two major types, both of which have a demonstrated and important role in plant development, stress responses and pathogen resistance. In this work, we used a deep sequencing approach (Sequencing-By-Synthesis, or SBS) to develop sequence resources of small RNAs from different Capsicum annuum tissues (including leaves, flowers and fruit). The high depth of the resulting datasets enabled us to examine in detail critical small RNA features, such as size distribution, tissue-specific regulation and sequence conservation between different organs in this species. We also developed database resources and a dedicated website (http://smallrna.udel.edu/) with computational tools for allowing other users to identify new miRNAs or siRNAs involved in specific regulatory pathways, verify the degree of conservation of these sequences in other plant species and map small RNAs on genes or larger regions of the maize genome under study. Small RNA libraries were derived from leaves, flowers and fruit of Capsicum annuum. Total RNA was isolated using the TriReagent (Molecular Research Center) for leaves and flowers and the Plant RNA Purification Reagent (Invitrogen) for fruit, and submitted to Illumina (Hayward, CA, http://www.illumina.com) for small RNA library construction using approaches described in (Lu et al., 2007) with minor modifications. The small RNA libraries were sequenced with the Sequencing-By-Synthesis (SBS) technology by Illumina. PERL scripts were designed to remove the adapter sequences and determine the abundance of each distinct small RNA. We thank Barbara Baker for providing the plant material, as well as Kan Nobuta and Gayathri Mahalingam for assistance with the computational methods.

2011-04-29 | E-GEOD-28751 | biostudies-arrayexpress

Capsicum annuum

Project description:Identification and characterization of conserved microRNAs in pepper by high-throughput sequencing

| PRJNA167034 | ENA

Capsicum annuum

Project description:Early drought-responsive changes in pepper leaves and roots

| PRJNA121467 | ENA