Project description:In this study, we compared the transcriptome map of maize and sorghum using PacBio single-molecule long-read sequencing from multiple matched tissues in each species. Maize and sorghum are both important crops with similar overall plant architectures, but they have key differences, especially in regard to their inflorescences. To better understand these two organisms at the molecular level, we compared the transcriptional profiles of both protein-coding and non-coding transcripts in matched tissues using large-scale single-molecule sequencing from 130 RSII cells and 5 Sequel cells, as well as deep short-read RNA sequencing. The use of multiple size-fractionated libraries (<1 kb, 12 kb, 23 kb, 35 kb, and >5 kb) enhanced our capture of non-redundant transcripts in these tissues.
Project description:Maize and sorghum are both important crops with similar overall plant architectures, but they have key differences, especially in regard to their inflorescences. To better understand these two organisms at the molecular level, we compared the expression profiles of both protein-coding and non-coding transcripts in 11 matched tissues using single-molecule long-read and deep RNA sequencing. In this study, maize B73 line was planted at Cold Spring Harbor Laboratory upland farm, 11 tissues together with previously reported six tissues were collected, RNA was extracted, library was made and sequenced on the HiSeq 2500 PE125 platform at Woodbury Genome Center.
Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in sweet sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .
Project description:The present study is expected to reveal regulatory network of small RNAs under drought in Sorghum (Sorghum bicolor (L.) Moench). Sorghum genotype drought tolerant (DT) and drought susceptible (DS) were grown at 28-32 degrees C day/night temperature with 12/12 h light/dark period in the phytotron glass house. The fully opened uppermost leaves from control and drought stressed seedlings were sampled and stored at -80 degrees C, and used for generation of a small RNA library. Total RNA was isolated from the leaves using the TRIzol reagent (Invitrogen, USA). Small RNA sequencing libraries were prepared using Illumina Truseq small RNA Library preparation kit following manufacturer's protocol and these libraries were sequenced on GAIIx platform (Illumina Inc., USA). Small RNA reads contaminated with poor-quality and adaptor sequences were trimmed by using the UEA sRNA workbench 2.4- Plant version sequence file pre-processing (http://srna-tools.cmp.uea.ac.uk/). Then, all unique reads were submitted to the UEA sRNA toolkit-Plant version miRCat pipeline (http://srna-tools.cmp.uea.ac.uk/) to predict novel miRNAs from high-throughput small RNA sequencing data.
Project description:Parallel Analysis of RNA Ends (PARE) sequencing reads were generated to validate putative microRNAs and identify cleavage sites in Sorghum bicolor and Setaria viridis.
Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in grain sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .
Project description:We report transcriptome profiling of middle internode tissues from four development stages and three soil moisture readings representing progressive drought stress in sweet sorghum. Sequencing of 14 libraries (two biological replicates for each stage). Each replicate yielded an average of 86 million reads per sample for developmental stages and drought stressed samples yielded an average of 74 million reads per sample .
Project description:We report transcriptome profiling from three developing stages of middle internode in sweet sorghum. Sequencing of 6 libraries (two replicates from each stage) each stage yielded approximately 80 million reads.
Project description:Sorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilitate understanding of the molecular mechanisms of low-N tolerance, and also facilitate the genetic improvement of sorghum through marker-assisted selection or gene transformation. In this study we compared the transcriptomes of root tissues from seven sorghum genotypes having different genetic backgrounds with contrasting low-N tolerance by the RNAseq deep sequencing data. Several genes were found which are common differentially expressed genes between four low-N tolerant sorghum genotypes (San Chi San, China17, KS78 and high-NUE bulk) and three sensitive genotypes (CK60, BTx623 and low-NUE bulk).