isoform sequencing and state-of-art applications for unravelling complexity of plant transcriptomes

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ID: 249324
2018
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Abstract
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.
Reference Key
an2018genesisoform Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors ;Dong An;Hieu X. Cao;Changsheng Li;Klaus Humbeck;Wenqin Wang
Journal thermal science and engineering progress
Year 2018
DOI
10.3390/genes9010043
URL
http://www.mdpi.com/2073-4425/9/1/43
Keywords
genome annotation transcriptomics plant alternative splicing

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