Transcriptome analysis reveals long noncoding RNAs involved in fiber development in cotton (Gossypium arboreum).

Changsong Zou,Xiaoxu Feng,Guoli Song,Hailiang Cheng,Cairui Lu,Wencui Yang,Youping Zhang,Qiaolian Wang,Mtawa Andrew Prosper

doi:10.1007/s11427-016-5000-2

Abstract

Long noncoding RNAs (lncRNAs) play important roles in various biological regulatory processes in yeast, mammals, and plants. However, no systematic identification of lncRNAs has been reported in Gossypium arboreum. In this study, the strand-specific RNA sequencing (ssRNA-seq) of samples from cotton fibers and leaves was performed, and lncRNAs involved in fiber initiation and elongation processes were systematically identified and analyzed. We identified 5,996 lncRNAs, of which 3,510 and 2,486 can be classified as long intergenic noncoding RNAs (lincRNAs) and natural antisense transcripts (lncNAT), respectively. LincRNAs and lncNATs are similar in many aspects, but have some differences in exon number, exon length, and transcript length. Expression analysis revealed that 51.9% of lincRNAs and 54.5% of lncNATs transcripts were preferentially expressed at one stage of fiber development, and were significantly highly expressed than protein-coding transcripts (21.7%). During the fiber and rapid elongation stages, rapid and dynamic changes in lncRNAs may contribute to fiber development in cotton. This work describes a set of lncRNAs that are involved in fiber development. The characterization and expression analysis of lncRNAs will facilitate future studies on their roles in fiber development in cotton.

Highlights

With the development of DNA sequencing technology and transcriptome analysis in recent years, the traditional view that protein-coding genes are the only effectors of gene function has been challenged
In order to systematically identify Long noncoding RNAs (lncRNAs) related to cotton fiber development, we performed whole transcriptome strand-specific RNA sequencing for immature ovules (1 day prior to anthesis, 1 days post anthesis (DPA)), fiber cell initials, young fiber-bearing ovules (1 day post-anthesis, 1 DPA), fiber (10, 15 DPA), and leaves in G
The following criteria were used to provide a strict definition for lncRNAs: (i) the transcript length must more than 200 nucleotides, and (ii) the transcript must contain no open reading frame (ORF) encoding more than 50 amino acids

Summary

Introduction

With the development of DNA sequencing technology and transcriptome analysis in recent years, the traditional view that protein-coding genes are the only effectors of gene function has been challenged. Long noncoding RNAs (lncRNAs) have been identified as a major component of the eukaryotic transcriptomes involved in the regulation of important biological processes (Derrien et al, 2012; Fabbri and Calin, 2010; Rinn and Chang, 2012; Zhang et al, 2010). Based on their relative positions with respect to protein-coding genes, those located in the intergenic regions were defined as long intergenic noncoding RNAs

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