Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.)

Publication Overview
TitleLong noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.)
AuthorsWang M, Yuan D, Tu L, Gao W, He Y, Hu H, Wang P, Liu N, Lindsey K, Zhang X
TypeJournal Article
Journal NameThe New phytologist
Year2015
CitationWang M, Yuan D, Tu L, Gao W, He Y, Hu H, Wang P, Liu N, Lindsey K, Zhang X. Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.). The New phytologist. 2015 Apr 28.

Abstract

Long noncoding RNAs (lncRNAs) are transcripts of at least 200 bp in length, possess no apparent coding capacity and are involved in various biological regulatory processes. Until now, no systematic identification of lncRNAs has been reported in cotton (Gossypium spp.). Here, we describe the identification of 30 550 long intergenic noncoding RNA (lincRNA) loci (50 566 transcripts) and 4718 long noncoding natural antisense transcript (lncNAT) loci (5826 transcripts). LncRNAs are rich in repetitive sequences and preferentially expressed in a tissue-specific manner. The detection of abundant genome-specific and/or lineage-specific lncRNAs indicated their weak evolutionary conservation. Approximately 76% of homoeologous lncRNAs exhibit biased expression patterns towards the At or Dt subgenomes. Compared with protein-coding genes, lncRNAs showed overall higher methylation levels and their expression was less affected by gene body methylation. Expression validation in different cotton accessions and coexpression network construction helped to identify several functional lncRNA candidates involved in cotton fibre initiation and elongation. Analysis of integrated expression from the subgenomes of lncRNAs generating miR397 and its targets as a result of genome polyploidization indicated their pivotal functions in regulating lignin metabolism in domesticated tetraploid cotton fibres. This study provides the first comprehensive identification of lncRNAs in Gossypium.

Properties
Additional details for this publication include:
Property NameValue
Copyright© 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.
eISSN1469-8137
Elocation10.1111/nph.13429
ISSN1469-8137
Journal AbbreviationNew Phytol.
LanguageEnglish
Language AbbrENG
Publication Date2015 Apr 28
Publication ModelPrint-Electronic
Publication TypeJournal Article
URLhttp://onlinelibrary.wiley.com/doi/10.1111/nph.13429/full
Cross References
This publication is also available in the following databases:
DatabaseAccession
PMID: PubMedPMID:25919642