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:Alternative splicing and alternative polyadenylation (APA) of pre-mRNAs greatly contribute to transcriptome diversity, coding capacity of a genome and gene regulatory mechanisms in eukaryotes. Second-generation sequencing technologies have been extensively used to analyse transcriptomes. However, a major limitation of short-read data is that it is difficult to accurately predict full-length splice isoforms. Here we sequenced the sorghum transcriptome using Pacific Biosciences single-molecule real-time long-read isoform sequencing and developed a pipeline called TAPIS (Transcriptome Analysis Pipeline for Isoform Sequencing) to identify full-length splice isoforms and APA sites. Our analysis reveals transcriptome-wide full-length isoforms at an unprecedented scale with over 11,000 novel splice isoforms. Additionally, we uncover APA of ∼11,000 expressed genes and more than 2,100 novel genes. These results greatly enhance sorghum gene annotations and aid in studying gene regulation in this important bioenergy crop. The TAPIS pipeline will serve as a useful tool to analyse Iso-Seq data from any organism.
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:Examining RNA Transcript Changes in Stem Cells Undergoing Differentiation, Using Short and Long Reads Sequencing Technologies [Nanopore long reads]