A survey of the sorghum transcriptome using single-molecule long reads View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2016-06-24

AUTHORS

Salah E. Abdel-Ghany, Michael Hamilton, Jennifer L. Jacobi, Peter Ngam, Nicholas Devitt, Faye Schilkey, Asa Ben-Hur, Anireddy S. N. Reddy

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. More... »

PAGES

11706

References to SciGraph publications

Identifiers

URI

http://scigraph.springernature.com/pub.10.1038/ncomms11706

DOI

http://dx.doi.org/10.1038/ncomms11706

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1022255583

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/27339290


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