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 ofB11,000 expressed genes and more than 2,100 novel genes. Lastly, 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:
- Publication Date:
- Research Org.:
- Colorado State Univ., Fort Collins, CO (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1306471
- Grant/Contract Number:
- SC0010733
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 7; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES
Citation Formats
Abdel-Ghany, Salah E., Hamilton, Michael, Jacobi, Jennifer L., Ngam, Peter, Devitt, Nicholas, Schilkey, Faye, Ben-Hur, Asa, and Reddy, Anireddy S. N. A survey of the sorghum transcriptome using single-molecule long reads. United States: N. p., 2016.
Web. doi:10.1038/ncomms11706.
Abdel-Ghany, Salah E., Hamilton, Michael, Jacobi, Jennifer L., Ngam, Peter, Devitt, Nicholas, Schilkey, Faye, Ben-Hur, Asa, & Reddy, Anireddy S. N. A survey of the sorghum transcriptome using single-molecule long reads. United States. https://doi.org/10.1038/ncomms11706
Abdel-Ghany, Salah E., Hamilton, Michael, Jacobi, Jennifer L., Ngam, Peter, Devitt, Nicholas, Schilkey, Faye, Ben-Hur, Asa, and Reddy, Anireddy S. N. Fri .
"A survey of the sorghum transcriptome using single-molecule long reads". United States. https://doi.org/10.1038/ncomms11706. https://www.osti.gov/servlets/purl/1306471.
@article{osti_1306471,
title = {A survey of the sorghum transcriptome using single-molecule long reads},
author = {Abdel-Ghany, Salah E. and Hamilton, Michael and Jacobi, Jennifer L. and Ngam, Peter and Devitt, Nicholas and Schilkey, Faye and Ben-Hur, Asa and Reddy, Anireddy S. N.},
abstractNote = {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 ofB11,000 expressed genes and more than 2,100 novel genes. Lastly, 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.},
doi = {10.1038/ncomms11706},
journal = {Nature Communications},
number = ,
volume = 7,
place = {United States},
year = {Fri Jun 24 00:00:00 EDT 2016},
month = {Fri Jun 24 00:00:00 EDT 2016}
}
Web of Science
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Root Hair Single Cell Type Specific Profiles of Gene Expression and Alternative Polyadenylation Under Cadmium Stress
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PacBio Long-Read Sequencing Reveals the Transcriptomic Complexity and Aux/IAA Gene Evolution in Gnetum (Gnetales)
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Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins
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Dynamic Changes in Metabolite Accumulation and the Transcriptome during Leaf Growth and Development in Eucommia ulmoides
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Transcriptome Analysis of Drought-Resistant and Drought-Sensitive Sorghum (Sorghum bicolor) Genotypes in Response to PEG-Induced Drought Stress
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Transcriptome profiling for floral development in reblooming cultivar ‘High Noon’ of Paeonia suffruticosa
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A transcriptome atlas of rabbit revealed by PacBio single-molecule long-read sequencing
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The developmental dynamics of the Populus stem transcriptome
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Full-length transcriptome sequences of ephemeral plant Arabidopsis pumila provides insight into gene expression dynamics during continuous salt stress
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A survey of transcriptome complexity using PacBio single-molecule real-time analysis combined with Illumina RNA sequencing for a better understanding of ricinoleic acid biosynthesis in Ricinus communis
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Genome-wide profiling of the alternative splicing provides insights into development in Plutella xylostella
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Comparative transcriptome and coexpression network analysis of carpel quantitative variation in Paeonia rockii
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Single-molecule real-time transcript sequencing identified flowering regulatory genes in Crocus sativus
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Analysis of transcripts and splice isoforms in red clover (Trifolium pratense L.) by single-molecule long-read sequencing
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Full-length transcript sequencing and comparative transcriptomic analysis to evaluate the contribution of osmotic and ionic stress components towards salinity tolerance in the roots of cultivated alfalfa (Medicago sativa L.)
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Transcriptome analysis based on a combination of sequencing platforms provides insights into leaf pigmentation in Acer rubrum
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Reconstruction of the full-length transcriptome atlas using PacBio Iso-Seq provides insight into the alternative splicing in Gossypium australe
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Single-molecule real-time sequencing facilitates the analysis of transcripts and splice isoforms of anthers in Chinese cabbage (Brassica rapa L. ssp. pekinensis)
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Bridging the gap between reference and real transcriptomes
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Revealing the transcriptomic complexity of switchgrass by PacBio long-read sequencing
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SMRT Sequencing of a Full-length Transcriptome Reveals Transcript Variants Involved in C18 Unsaturated Fatty Acid Biosynthesis and Metabolism Pathways at Chilling Temperature in Pennisetum giganteum
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Long Non-coding RNAs in Endothelial Biology
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Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing Approach for In-depth Understanding of Genes in Secondary Metabolism Pathways of Camellia sinensis
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Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching
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Root Hair Single Cell Type Specific Profiles of Gene Expression and Alternative Polyadenylation Under Cadmium Stress
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Expanding Alternative Splicing Identification by Integrating Multiple Sources of Transcription Data in Tomato
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Investigation of RNA Editing Sites within Bound Regions of RNA-Binding Proteins
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Dynamic Changes in Metabolite Accumulation and the Transcriptome during Leaf Growth and Development in Eucommia ulmoides
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Full-Length Transcriptome Assembly of Italian Ryegrass Root Integrated with RNA-Seq to Identify Genes in Response to Plant Cadmium Stress
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Discovery of Geranylgeranyl Pyrophosphate Synthase (GGPPS) Paralogs from Haematococcus pluvialis Based on Iso-Seq Analysis and Their Function on Astaxanthin Biosynthesis
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Analyses of alternative polyadenylation: from old school biochemistry to high-throughput technologies
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