Transcriptome and Degradome of microRNAs and Their Targets in Response to Drought Stress in the Plants of a Diploid and Its Autotetraploid Paulownia australis

Suyan Niu; Yuanlong Wang; Zhenli Zhao; Minjie Deng; Lin Cao; Lu Yang; Guoqiang Fan

doi:10.1371/journal.pone.0158750

Transcriptome and Degradome of microRNAs and Their Targets in Response to Drought Stress in the Plants of a Diploid and Its Autotetraploid Paulownia australis

PLoS One. 2016 Jul 7;11(7):e0158750. doi: 10.1371/journal.pone.0158750. eCollection 2016.

Authors

Suyan Niu^{1

2}, Yuanlong Wang^{1

2}, Zhenli Zhao^{1

2}, Minjie Deng^{1

2}, Lin Cao^{1

2}, Lu Yang^{1

2}, Guoqiang Fan^{1

2}

Affiliations

¹ Institute of Paulownia, Henan Agricultural University, 95 Wenhua Road, Jinsui District, 450002, Zhengzhou, Henan, P.R. China.
² College of Forestry, Henan Agricultural University, 95 Wenhua Road, Jinsui District, 450002, Zhengzhou, Henan, P.R. China.

Abstract

MicroRNAs (miRNAs) are small, non-coding RNAs that play vital roles in plant growth, development, and stress response. Increasing numbers of studies aimed at discovering miRNAs and analyzing their functions in plants are being reported. In this study, we investigated the effect of drought stress on the expression of miRNAs and their targets in plants of a diploid and derived autotetraploid Paulownia australis. Four small RNA (sRNA) libraries and four degradome libraries were constructed from diploid and autotetraploid P. australis plants treated with either 75% or 25% relative soil water content. A total of 33 conserved and 104 novel miRNAs (processing precision value > 0.1) were identified, and 125 target genes were identified for 36 of the miRNAs by using the degradome sequencing. Among the identified miRNAs, 54 and 68 were differentially expressed in diploid and autotetraploid plants under drought stress (25% relative soil water content), respectively. The expressions of miRNAs and target genes were also validated by quantitative real-time PCR. The results showed that the relative expression trends of the randomly selected miRNAs were similar to the trends predicted by Illumina sequencing. And the correlations between miRNAs and their target genes were also analyzed. Furthermore, the functional analysis showed that most of these miRNAs and target genes were associated with plant development and environmental stress response. This study provided molecular evidence for the possible involvement of certain miRNAs in the drought response and/or tolerance in P. australis, and certain level of differential expression between diploid and autotetraploid plants.

MeSH terms

China
Diploidy
Droughts*
Gene Expression Profiling
Gene Expression Regulation, Plant
Gene Library
Genes, Plant
Genotype
High-Throughput Nucleotide Sequencing
Lamiales / genetics*
MicroRNAs / metabolism*
RNA, Plant / genetics
RNA, Small Untranslated / metabolism
Real-Time Polymerase Chain Reaction
Stress, Physiological
Tetraploidy
Transcriptome*

Substances

MicroRNAs
RNA, Plant
RNA, Small Untranslated

Grants and funding

This study was funded by the National Natural Science Foundation of China (grant number 30271082, 30571496, U1204309), by the Outstanding Talents Project 347 of Henan Province (grant number 122101110700), by the Transformation Project of the National Agricultural Scientific and Technological Achievement of China (grant number 2012GB2D000271), and by the Science and Technology Innovation Team Project of Zhengzhou City, China (grant number 121PCXTD515). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.