49944
doi
10.5281/zenodo.49944
oai:zenodo.org:49944
Hamilton, Michael
Computer Science Department, Colorado State University, Fort Collins, CO, 80523
Jacobi, Jennifer
National Center for Genome Resources, 2935 Rodeo Park Dr. East, Santa Fe, NM 87505
Ngam, Peter
National Center for Genome Resources, 2935 Rodeo Park Dr. East, Santa Fe, NM 87505
Devitt, Nicholas
National Center for Genome Resources, 2935 Rodeo Park Dr. East, Santa Fe, NM 87505
Schilkey, Faye
National Center for Genome Resources, 2935 Rodeo Park Dr. East, Santa Fe, NM 87505
Ben-Hur, Asa
Computer Science Department, Colorado State University, Fort Collins, CO, 80523
Reddy, Anireddy
Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523
A survey of the sorghum transcriptome using single-molecule long reads
Abdel-Ghany, Salah
Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523
info:eu-repo/semantics/openAccess
Creative Commons Zero v1.0 Universal
https://creativecommons.org/publicdomain/zero/1.0/legalcode
sorghum
isoseq
<p>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 analyze 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 analyze Iso-Seq data from any organism.</p>
line21: control
line22: PEG treated
Zenodo
2016-04-18
info:eu-repo/semantics/other
632447
1579893852.338844
409992420
md5:ffa33d0703375ce3d0259d99cac98ae5
https://zenodo.org/records/49944/files/line22.fasta.gz
489504680
md5:139d816318c6c7c852122a21ed09b9a6
https://zenodo.org/records/49944/files/line21.fasta.gz
public
isVersionOf
doi