title: A survey of the sorghum transcriptome using single-molecule long reads.
abstract: 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.
authors.affiliation: Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA.
authors.forename: Salah E
authors.initials: SE
authors.lastname: Abdel-Ghany
authors.affiliation: Department of Computer Science, Colorado State University, Fort Collins, Colorado 80523, USA.
authors.forename: Michael
authors.initials: M
authors.lastname: Hamilton
authors.affiliation: National Center for Genome Resources, 2935 Rodeo Park Dr East, Santa Fe, New Mexico 87505, USA.
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Jacobi
authors.affiliation: National Center for Genome Resources, 2935 Rodeo Park Dr East, Santa Fe, New Mexico 87505, USA.
authors.forename: Peter
authors.initials: P
authors.lastname: Ngam
authors.affiliation: National Center for Genome Resources, 2935 Rodeo Park Dr East, Santa Fe, New Mexico 87505, USA.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Devitt
authors.affiliation: National Center for Genome Resources, 2935 Rodeo Park Dr East, Santa Fe, New Mexico 87505, USA.
authors.forename: Faye
authors.initials: F
authors.lastname: Schilkey
authors.affiliation: Department of Computer Science, Colorado State University, Fort Collins, Colorado 80523, USA.
authors.forename: Asa
authors.initials: A
authors.lastname: Ben-Hur
authors.affiliation: Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, USA.
authors.forename: Anireddy S N
authors.initials: AS
authors.lastname: Reddy
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism*; D016133:Polymerase Chain Reaction; D020033:Protein Isoforms; D012326:RNA Splicing; D018749:RNA, Plant / Q000235:genetics; D022661:RNA, Untranslated; D017423:Sequence Analysis, RNA; D045868:Sorghum / Q000235:genetics* / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D020033:Protein Isoforms; D018749:RNA, Plant; D022661:RNA, Untranslated