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

Wang, M. and Yuan, D. and Tu, L. and Gao, W. and He, Y. and Hu, H. and Wang, P. and Liu, N. and Lindsey, K. and Zhang, X. (2015) 'Long non-coding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.).', New phytologist., 207 (4). pp. 1181-1197.


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.

Item Type:Article
Keywords:Cotton (Gossypium spp.), Fibre development, Long noncoding RNAs (lncRNAs), Methylation, Polyploidization.
Full text:(AM) Accepted Manuscript
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Publisher statement:This is the accepted version of the following article: Wang, M., Yuan, D., Tu, L., Gao, W., He, Y., Hu, H., Wang, P., Liu, N., Lindsey, K. and Zhang, X. (2015), Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.). New Phytologist, 207(4): 1181-1197, which has been published in final form at This article may be used for non-commercial purposes in accordance With Wiley Terms and Conditions for self-archiving.
Date accepted:22 March 2015
Date deposited:09 June 2016
Date of first online publication:28 April 2015
Date first made open access:No date available

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