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

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. H...

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Bibliographic Details
Published in:Journal of experimental botany Vol. 65; no. 17; p. 4975
Main Authors: Shuai, Peng, Liang, Dan, Tang, Sha, Zhang, Zhoujia, Ye, Chu-Yu, Su, Yanyan, Xia, Xinli, Yin, Weilun
Format: Journal Article
Language:English
Published: England 01.09.2014
Subjects:
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
target mimicry
lincRNA
miRNA
Populus trichocarpa
non-coding RNA
Drought
ISSN:1460-2431, 1460-2431
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Summary: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.
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ISSN:1460-2431
1460-2431
DOI:10.1093/jxb/eru256