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

(E-pub Ahead of Print)

Author(s): Yubang Gao, Feihu Xi, Hangxiao zhang, Xuqing Liu, Huiyuan Wang, Liangzhen zhao, Anireddy S.N. Reddy, Lianfeng Gu*.

Journal Name: Current Bioinformatics

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Abstract:

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 to be much superior in identifying full-length splice variants and other post-transcriptional events as compared 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 some of them are still being refined to address different aspects of transcriptome complexity. However, a comprehensive summary of the available tools and their utility is still lacking.

Objective: Here, we summarized the existing Iso-Seq analysis tools and presented an integrated bioinformatics pipeline for Iso-Seq analysis, which overcomes the limitations of NGS and generates long contiguous full-length non-chimeric (FLNC) reads for analysis of post-transcriptional events.

Results: In this review, we summarized recent applications of Iso-Seq in plants, which include improved genome annotations, identification of novel genes and lncRNAs, identification of full-length splice isoforms, detection of novel alternative splicing (AS) and alternative polyadenylation (APA) events. In addition, we also discussed the bioinformatics pipeline for comprehensive Iso-Seq data analysis, including how to reduce the error rate in the reads and how to identify and quantify post-transcriptional events. Furthermore, visualization approach of Iso-Seq was discussed as well. Finally, we discussed methods to combine Iso-Seq data with RNA-Seq for transcriptome quantification.

Conclusion: Overall, this review demonstrates that the Iso-Seq is pivotal for analyzing transcriptome complexity and this new method offers unprecedented opportunities to comprehensively understand transcripts diversity.

Keywords: Pacific Bioscience (PacBio), SMRT isoform sequencing (Iso-Seq), Next-generation sequencing (NGS), Alternative splicing (AS), Alternative polyadenylation (APA), Genome annotation, Novel genes

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Article Details

(E-pub Ahead of Print)
DOI: 10.2174/1574893614666190204151746
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