title: Transcriptome analysis reveals long noncoding RNAs involved in fiber development in cotton (Gossypium arboreum).
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.
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
authors.forename: Changsong
authors.initials: C
authors.lastname: Zou
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
authors.forename: Qiaolian
authors.initials: Q
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
authors.forename: Cairui
authors.initials: C
authors.lastname: Lu
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
authors.forename: Wencui
authors.initials: W
authors.lastname: Yang
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
authors.forename: Youping
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
authors.forename: Hailiang
authors.initials: H
authors.lastname: Cheng
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
authors.forename: Xiaoxu
authors.initials: X
authors.lastname: Feng
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
authors.forename: Mtawa Andrew
authors.initials: MA
authors.lastname: Prosper
authors.affiliation: State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China. sglzms@163.com.
authors.forename: Guoli
authors.initials: G
authors.lastname: Song
mesh_terms: D017343:Genes, Plant; D003368:Gossypium / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics*; D059467:Transcriptome
chemical_list: D062085:RNA, Long Noncoding
keywords: expression; fiber; long noncoding RNAs; strand specific RNA sequencing; transcriptome