Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing
Abstract
Nanopore sequencing from Oxford Nanopore Technologies (ONT) and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) long-read isoform sequencing (Iso-Seq) are revolutionizing the way transcriptomes are analyzed. These methods offer many advantages over most widely used high-throughput short-read RNA sequencing (RNA-Seq) approaches and allow a comprehensive analysis of transcriptomes in identifying full-length splice isoforms and several other post-transcriptional events. In addition, direct RNA-Seq provides valuable information about RNA modifications, which are lost during the PCR amplification step in other methods. Here, we present a comprehensive summary of important applications of these technologies in plants, including identification of complex alternative splicing (AS), full-length splice variants, fusion transcripts, and alternative polyadenylation (APA) events. Furthermore, we discuss the impact of the newly developed nanopore direct RNA-Seq in advancing epitranscriptome research in plants. Additionally, we summarize computational tools for identifying and quantifying full-length isoforms and other co/post-transcriptional events and discussed some of the limitations with these methods. Sequencing of transcriptomes using these new single-molecule long-read methods will unravel many aspects of transcriptome complexity in unprecedented ways as compared to previous short-read sequencing approaches. Analysis of plant transcriptomes with these new powerful methods that require minimum sample processing is likely to become the norm and is expectedmore »
- Authors:
-
- Fujian Agricultural and Forestry Univ., Fuzhou (China)
- Colorado State Univ., Fort Collins, CO (United States)
- Publication Date:
- Research Org.:
- Colorado State Univ., Fort Collins, CO (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC)
- OSTI Identifier:
- 1611512
- Grant/Contract Number:
- SC0010733
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Genetics
- Additional Journal Information:
- Journal Volume: 10; Journal ID: ISSN 1664-8021
- Publisher:
- Frontiers
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; Genetics & Heredity; SMRT isoform sequencing; nanopore direct RNA sequencing; RNA modification; alternative splicing; alternative polyadenylation; epitranscriptome
Citation Formats
Zhao, Liangzhen, Zhang, Hangxiao, Kohnen, Markus V., Prasad, Kasavajhala V. S. K., Gu, Lianfeng, and Reddy, Anireddy S. N. Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing. United States: N. p., 2019.
Web. doi:10.3389/fgene.2019.00253.
Zhao, Liangzhen, Zhang, Hangxiao, Kohnen, Markus V., Prasad, Kasavajhala V. S. K., Gu, Lianfeng, & Reddy, Anireddy S. N. Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing. United States. https://doi.org/10.3389/fgene.2019.00253
Zhao, Liangzhen, Zhang, Hangxiao, Kohnen, Markus V., Prasad, Kasavajhala V. S. K., Gu, Lianfeng, and Reddy, Anireddy S. N. Thu .
"Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing". United States. https://doi.org/10.3389/fgene.2019.00253. https://www.osti.gov/servlets/purl/1611512.
@article{osti_1611512,
title = {Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing},
author = {Zhao, Liangzhen and Zhang, Hangxiao and Kohnen, Markus V. and Prasad, Kasavajhala V. S. K. and Gu, Lianfeng and Reddy, Anireddy S. N.},
abstractNote = {Nanopore sequencing from Oxford Nanopore Technologies (ONT) and Pacific BioSciences (PacBio) single-molecule real-time (SMRT) long-read isoform sequencing (Iso-Seq) are revolutionizing the way transcriptomes are analyzed. These methods offer many advantages over most widely used high-throughput short-read RNA sequencing (RNA-Seq) approaches and allow a comprehensive analysis of transcriptomes in identifying full-length splice isoforms and several other post-transcriptional events. In addition, direct RNA-Seq provides valuable information about RNA modifications, which are lost during the PCR amplification step in other methods. Here, we present a comprehensive summary of important applications of these technologies in plants, including identification of complex alternative splicing (AS), full-length splice variants, fusion transcripts, and alternative polyadenylation (APA) events. Furthermore, we discuss the impact of the newly developed nanopore direct RNA-Seq in advancing epitranscriptome research in plants. Additionally, we summarize computational tools for identifying and quantifying full-length isoforms and other co/post-transcriptional events and discussed some of the limitations with these methods. Sequencing of transcriptomes using these new single-molecule long-read methods will unravel many aspects of transcriptome complexity in unprecedented ways as compared to previous short-read sequencing approaches. Analysis of plant transcriptomes with these new powerful methods that require minimum sample processing is likely to become the norm and is expected to uncover novel co/post-transcriptional gene regulatory mechanisms that control biological outcomes during plant development and in response to various stresses.},
doi = {10.3389/fgene.2019.00253},
journal = {Frontiers in Genetics},
number = ,
volume = 10,
place = {United States},
year = {Thu Mar 21 00:00:00 EDT 2019},
month = {Thu Mar 21 00:00:00 EDT 2019}
}
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