Abstract
BackgroundLncRNAs are extensively involved in plant biological processes. However, the lack of a comprehensive lncRNA landscape in moso bamboo has hindered the molecular study of lncRNAs. Moreover, the role of lncRNAs in secondary cell wall (SCW) biosynthesis of moso bamboo is elusive.ResultsFor comprehensively identifying lncRNA throughout moso bamboo genome, we collected 231 RNA-Seq datasets, 1 Iso-Seq dataset, and 1 full-length cDNA dataset. We used a machine learning approach to improve the pipeline of lncRNA identification and functional annotation based on previous studies and identified 37,009 lncRNAs in moso bamboo. Then, we established a network of potential lncRNA-coding gene for SCW biosynthesis and identified SCW-related lncRNAs. We also proposed that a mechanism exists in bamboo to direct phenylpropanoid intermediates to lignin or flavonoids biosynthesis through the PAL/4CL/C4H genes. In addition, we identified 4 flavonoids and 1 lignin-preferred genes in the PAL/4CL/C4H gene families, which gained implications in molecular breeding.ConclusionsWe provided a comprehensive landscape of lncRNAs in moso bamboo. Through analyses, we identified SCW-related lncRNAs and improved our understanding of lignin and flavonoids biosynthesis.
Highlights
LncRNAs are extensively involved in plant biological processes
We identified 37,009 potential Long non-coding RNAs (lncRNAs), including 36,032 from RNA-Seq datasets, 418 from cDNA dataset, and 559 from isoform sequencing (Iso-Seq) dataset (Fig. 1)
A comprehensive lncRNA map from the datasets covering multi tissues and treatments would promote the processing of lncRNA functional analysis and researches
Summary
LncRNAs are extensively involved in plant biological processes. the lack of a comprehensive lncRNA landscape in moso bamboo has hindered the molecular study of lncRNAs. LncRNAs can be produced in a sense or antisense direction from intergenic, intronic, or coding sequences of the genome. Depending on their location in the genome, they can be classified into different categories: long intergenic ncRNAs (lincRNAs), intronic ncRNAs (incRNAs), and natural antisense transcripts (NATs) [2]. LncRNAs can regulate gene expression at different levels through various mechanisms. They act by sequence complementarity or homology with RNA or DNA, and/or by structure, forming molecular frameworks and scaffolds for the assembly of macromolecular complexes [2]. The functions of lncRNAs in flowering regulation, reproductive developmental mediation, and stress response have been demonstrated [3, 4]
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