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Open AccessArticle

Single-Molecule Long-Read Sequencing Reveals the Diversity of Full-Length Transcripts in Leaves of Gnetum (Gnetales)

by Nan Deng 1,2,†, Chen Hou 3,†, Fengfeng Ma 1, Caixia Liu 1,* and Yuxin Tian 1,2,*
1
Institute of Ecology, Hunan Academy of Forestry, Changsha 410004, China
2
Hunan Cili Forest Ecosystem State Research Station, Cili 417100, China
3
School of life Sciences, Sun Yat-sen University, Guangzhou 510275, China
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Int. J. Mol. Sci. 2019, 20(24), 6350; https://doi.org/10.3390/ijms20246350
Received: 12 October 2019 / Revised: 1 December 2019 / Accepted: 11 December 2019 / Published: 17 December 2019
(This article belongs to the Section Molecular Biology)
The limitations of RNA sequencing make it difficult to accurately predict alternative splicing (AS) and alternative polyadenylation (APA) events and long non-coding RNAs (lncRNAs), all of which reveal transcriptomic diversity and the complexity of gene regulation. Gnetum, a genus with ambiguous phylogenetic placement in seed plants, has a distinct stomatal structure and photosynthetic characteristics. In this study, a full-length transcriptome of Gnetum luofuense leaves at different developmental stages was sequenced with the latest PacBio Sequel platform. After correction by short reads generated by Illumina RNA-Seq, 80,496 full-length transcripts were obtained, of which 5269 reads were identified as isoforms of novel genes. Additionally, 1660 lncRNAs and 12,998 AS events were detected. In total, 5647 genes in the G. luofuense leaves had APA featured by at least one poly(A) site. Moreover, 67 and 30 genes from the bHLH gene family, which play an important role in stomatal development and photosynthesis, were identified from the G. luofuense genome and leaf transcripts, respectively. This leaf transcriptome supplements the reference genome of G. luofuense, and the AS events and lncRNAs detected provide valuable resources for future studies of investigating low photosynthetic capacity of Gnetum. View Full-Text
Keywords: Gnetum; full-length transcriptome; high throughout-put sequencing; bHLH gene; leaf Gnetum; full-length transcriptome; high throughout-put sequencing; bHLH gene; leaf
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Deng, N.; Hou, C.; Ma, F.; Liu, C.; Tian, Y. Single-Molecule Long-Read Sequencing Reveals the Diversity of Full-Length Transcripts in Leaves of Gnetum (Gnetales). Int. J. Mol. Sci. 2019, 20, 6350.

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