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Genome Sequencing and Assembly by Long Reads in Plants
Review

Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes

1
School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dong Chuan Road, Shanghai 200240, China
2
Institute of Biology/Plant Physiology, Martin-Luther-University of Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
*
Author to whom correspondence should be addressed.
Genes 2018, 9(1), 43; https://doi.org/10.3390/genes9010043
Received: 27 November 2017 / Revised: 30 December 2017 / Accepted: 15 January 2018 / Published: 18 January 2018
(This article belongs to the Special Issue Plant Genomics and Epigenomics for Trait Improvement)
Single-molecule real-time (SMRT) sequencing developed by PacBio, also called third-generation sequencing (TGS), offers longer reads than the second-generation sequencing (SGS). Given its ability to obtain full-length transcripts without assembly, isoform sequencing (Iso-Seq) of transcriptomes by PacBio is advantageous for genome annotation, identification of novel genes and isoforms, as well as the discovery of long non-coding RNA (lncRNA). In addition, Iso-Seq gives access to the direct detection of alternative splicing, alternative polyadenylation (APA), gene fusion, and DNA modifications. Such applications of Iso-Seq facilitate the understanding of gene structure, post-transcriptional regulatory networks, and subsequently proteomic diversity. In this review, we summarize its applications in plant transcriptome study, specifically pointing out challenges associated with each step in the experimental design and highlight the development of bioinformatic pipelines. We aim to provide the community with an integrative overview and a comprehensive guidance to Iso-Seq, and thus to promote its applications in plant research. View Full-Text
Keywords: isoform sequencing; genome annotation; novel genes; alternative splicing; long reads; single-molecule real-time sequencing; transcriptomics; plant; fusion genes isoform sequencing; genome annotation; novel genes; alternative splicing; long reads; single-molecule real-time sequencing; transcriptomics; plant; fusion genes
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MDPI and ACS Style

An, D.; Cao, H.X.; Li, C.; Humbeck, K.; Wang, W. Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes. Genes 2018, 9, 43. https://doi.org/10.3390/genes9010043

AMA Style

An D, Cao HX, Li C, Humbeck K, Wang W. Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes. Genes. 2018; 9(1):43. https://doi.org/10.3390/genes9010043

Chicago/Turabian Style

An, Dong, Hieu X. Cao, Changsheng Li, Klaus Humbeck, and Wenqin Wang. 2018. "Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes" Genes 9, no. 1: 43. https://doi.org/10.3390/genes9010043

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