Identification of drought-responsive and novel Populus trichocarpamicroRNAs by high-throughput sequencing and their targets using degradome analysis

Abstract

BackgroundMicroRNAs (miRNAs) are endogenous small RNAs (sRNAs) with a wide range of regulatory functions in plant development and stress responses. Although miRNAs associated with plant drought stress tolerance have been studied, the use of high-throughput sequencing can provide a much deeper understanding of miRNAs. Drought is a common stress that limits the growth of plants. To obtain more insight into the role of miRNAs in drought stress, Illumina sequencing of Populus trichocarpa sRNAs was implemented.ResultsTwo sRNA libraries were constructed by sequencing data of control and drought stress treatments of poplar leaves. In total, 207 P. trichocarpa conserved miRNAs were detected from the two sRNA libraries. In addition, 274 potential candidate miRNAs were found; among them, 65 candidates with star sequences were chosen as novel miRNAs. The expression of nine conserved miRNA and three novel miRNAs showed notable changes in response to drought stress. This was also confirmed by quantitative real time polymerase chain reaction experiments. To confirm the targets of miRNAs experimentally, two degradome libraries from the two treatments were constructed. According to degradome sequencing results, 53 and 19 genes were identified as targets of conserved and new miRNAs, respectively. Functional analysis of these miRNA targets indicated that they are involved in important activities such as the regulation of transcription factors, the stress response, and lipid metabolism.ConclusionsWe discovered five upregulated miRNAs and seven downregulated miRNAs in response to drought stress. A total of 72 related target genes were detected by degradome sequencing. These findings reveal important information about the regulation mechanism of miRNAs in P. trichocarpa and promote the understanding of miRNA functions during the drought response.

MicroRNA dynamics in a wild and cultivated species of Convolvulaceae exposed to drought stress

“…by targeting LEAF CURLING RESPONSIVENESS {LCR} gene). It is known to be drought responsive in Arabidopsis and other species (Song et al 2012;Liu et al 2008;Kantar et al 2011;Shuai et al 2013). Upregulation of miR394 in J. pentantha is comparable to those reported in cotton (0.87 fold increase) exposed to drought stress (Xie et al 2014).…”

“…In Arabidopsis, miR160 appears to regulate auxin-ABA crosstalk, playing crucial role in seed germination (Liu et al 2007). Drought mediated downregulation of miR160 was reported in Cassava, Populus trichocarpa and Sorghum bicolor (Ballen-Taborda et al 2013;Shuai et al 2013;Hamza et al 2016). Contrary to this, miR160 was reported to accumulate in Prunus persica and Sugarcane under drought (Eldem et al 2012;Gentile et al 2015).…”

Comparative miRNAome Analysis Revealed Numerous Conserved and Novel Drought Responsive miRNAs in Cotton (<i>Gossypium spp.</i>)

“…Up regulation of miR156 in rice shoot and root tissues in response to heat (Sailaja et al, 2014) and drought (Zhou et al, 2010) stresses was also reported as it found in KC3-WS in this study. Further, high-throughput sequencing and expression analysis of microRNAs and their targets under salt stress in Caragana intermedia has shown that the miR156 family exhibited the highest abundance among all of the miRNA families Shuai et al (2013) shown that the expression patterns and RT-qPCR results of drought-responsive miRNAs in Populus were consistent and both indicating that miR159 members were up-regulated after drought treatment. Similar kind of up regulation of miR159 under drought was also reported in legumes (Mantri et al, 2013), finger millet (Nageshbabu et al, 2013) and in cotton .…”

“…Similarly, more than two fold down regulation of miR394 was noticed in KC3-WS. Downregulated miR394 was noticed in Populus, whose predicted targets are annotated as dehydration-responsive protein and F-box proteins, which were reported to play significant roles in the abiotic stress-response pathway (Shuai et al, 2013).…”

“…Up regulation of miR482 under drought was reported in finger millet (Nageshbabu et al, 2013). Four UDP-glucosyltransferases (UDPGs) were found to be targeted by miR482 (Shuai et al, 2013). The UDPGs are enzymes that attach a sugar molecule to a specific acceptor in plants.…”