Single-molecule Real-time (SMRT) Isoform Sequencing (Iso-Seq) in Plants: The Status of the Bioinformatics Tools to Unravel the Transcriptome Complexity

Gao, Yubang; Xi, Feihu; zhang, Hangxiao; Liu, Xuqing; Wang, Huiyuan; zhao, Liangzhen; Reddy, Anireddy S. N.; Gu, Lianfeng

doi:10.2174/1574893614666190204151746

Title: Single-molecule Real-time (SMRT) Isoform Sequencing (Iso-Seq) in Plants: The Status of the Bioinformatics Tools to Unravel the Transcriptome Complexity

Journal Article · Tue Sep 17 00:00:00 EDT 2019 · Current Bioinformatics

DOI:https://doi.org/10.2174/1574893614666190204151746· OSTI ID:1611511

Gao, Yubang ^[1]; Xi, Feihu ^[1]; zhang, Hangxiao ^[1]; Liu, Xuqing ^[1]; Wang, Huiyuan ^[1]; zhao, Liangzhen ^[1]; Reddy, Anireddy S. N. ^[2]; Gu, Lianfeng ^[1]

Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States

Background:The advent of the Single-Molecule Real-time (SMRT) Isoform Sequencing(Iso-Seq) has paved the way to obtain longer full-length transcripts. This method was found tobe much superior in identifying full-length splice variants and other post-transcriptional events ascompared to the Next Generation Sequencing (NGS)-based short read sequencing (RNA-Seq).Several different bioinformatics tools to analyze the Iso-Seq data have been developed and someof them are still being refined to address different aspects of transcriptome complexity. However, acomprehensive summary of the available tools and their utility is still lacking. Objective:Here, we summarized the existing Iso-Seq analysis tools and presented an integratedbioinformatics pipeline for Iso-Seq analysis, which overcomes the limitations of NGS and generateslong contiguous Full-Length Non-Chimeric (FLNC) reads for the analysis of posttranscriptionalevents. Results:In this review, we summarized recent applications of Iso-Seq in plants, which include improvedgenome annotations, identification of novel genes and lncRNAs, identification of fulllengthsplice isoforms, detection of novel Alternative Splicing (AS) and Alternative Polyadenylation(APA) events. In addition, we also discussed the bioinformatics pipeline for comprehensiveIso-Seq data analysis, including how to reduce the error rate in the reads and how to identify andquantify post-transcriptional events. Furthermore, the visualization approach of Iso-Seq was discussedas well. Finally, we discussed methods to combine Iso-Seq data with RNA-Seq for transcriptomequantification. Conclusion:Overall, this review demonstrates that the Iso-Seq is pivotal for analyzing transcriptomecomplexity and this new method offers unprecedented opportunities to comprehensively understandtranscripts diversity.

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Research Organization:: Colorado State Univ., Fort Collins, CO (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

DOE Contract Number:: SC0010733

OSTI ID:: 1611511

Journal Information:: Current Bioinformatics, Vol. 14, Issue 7; ISSN 1574-8936

Publisher:: Bentham Science Publishers

Country of Publication:: United States

Language:: English

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