期刊
FRONTIERS IN GENETICS
卷 10, 期 -, 页码 -出版社
FRONTIERS MEDIA SA
DOI: 10.3389/fgene.2019.00253
关键词
SMRT isoform sequencing; nanopore direct RNA sequencing; RNA modification; alternative splicing; alternative polyadenylation; epitranscriptome
资金
- National Natural Science Foundation of China [31570674]
- National Key R&D Program of China [2016YFD0600106, 2018YFD0600101]
- International Science and Technology Cooperation and Exchange Fund from Fujian Agriculture and Forestry University [KXGH17016]
- Natural Science Foundation of Fujian Province of China [2018J01608]
- Department of Energy Office of Science, Office of Biological and Environmental Research [DE-SC0010733]
- U.S. Department of Energy (DOE) [DE-SC0010733] Funding Source: U.S. Department of Energy (DOE)
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.
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