Genome-wide identification and functional prediction of novel and drought-responsive lincRNAs in Populus trichocarpa

J Exp Bot. 2014 Sep;65(17):4975-83. doi: 10.1093/jxb/eru256. Epub 2014 Jun 19.


Protein-coding genes are considered to be a dominant component of the eukaryotic transcriptome; however, many studies have shown that intergenic, non-coding transcripts also play an important role. Long intergenic non-coding RNAs (lincRNAs) were found to play a vital role in human and Arabidopsis. However, lincRNAs and their regulatory roles remain poorly characterized in woody plants, especially Populus trichocarpa (P. trichocarpa). A large set of Populus RNA-Seq data were examined with high sequencing depth under control and drought conditions and a total of 2542 lincRNA candidates were identified. In total, 51 lincRNAs and 20 lincRNAs were identified as putative targets and target mimics of known Populus miRNAs, respectively. A total of 504 lincRNAs were found to be drought responsive, eight of which were confirmed by RT-qPCR. These findings provide a comprehensive view of Populus lincRNAs, which will enable in-depth functional analysis.

Keywords: Drought; Populus trichocarpa; lincRNA; miRNA; non-coding RNA; target mimicry..

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Droughts
  • Gene Expression Regulation, Plant*
  • High-Throughput Nucleotide Sequencing
  • MicroRNAs / genetics
  • Populus / genetics*
  • Populus / metabolism
  • RNA, Long Noncoding / genetics*
  • RNA, Long Noncoding / metabolism
  • Transcriptome


  • MicroRNAs
  • RNA, Long Noncoding