Genome-Wide Identification of miRNAs Responsive to Drought in Peach (Prunus persica) by High-Throughput Deep Sequencing

Abstract

Peach (Prunus persica L.) is one of the most important worldwide fresh fruits. Since fruit growth largely depends on adequate water supply, drought stress is considered as the most important abiotic stress limiting fleshy fruit production and quality in peach. Plant responses to drought stress are regulated both at transcriptional and post-transcriptional level. As post-transcriptional gene regulators, miRNAs (miRNAs) are small (19–25 nucleotides in length), endogenous, non-coding RNAs. Recent studies indicate that miRNAs are involved in plant responses to drought. Therefore, Illumina deep sequencing technology was used for genome-wide identification of miRNAs and their expression profile in response to drought in peach. In this study, four sRNA libraries were constructed from leaf control (LC), leaf stress (LS), root control (RC) and root stress (RS) samples. We identified a total of 531, 471, 535 and 487 known mature miRNAs in LC, LS, RC and RS libraries, respectively. The expression level of 262 (104 up-regulated, 158 down-regulated) of the 453 miRNAs changed significantly in leaf tissue, whereas 368 (221 up-regulated, 147 down-regulated) of the 465 miRNAs had expression levels that changed significantly in root tissue upon drought stress. Additionally, a total of 197, 221, 238 and 265 novel miRNA precursor candidates were identified from LC, LS, RC and RS libraries, respectively. Target transcripts (137 for LC, 133 for LS, 148 for RC and 153 for RS) generated significant Gene Ontology (GO) terms related to DNA binding and catalytic activites. Genome-wide miRNA expression analysis of peach by deep sequencing approach helped to expand our understanding of miRNA function in response to drought stress in peach and Rosaceae. A set of differentially expressed miRNAs could pave the way for developing new strategies to alleviate the adverse effects of drought stress on plant growth and development.

Identification of Drought-Responsive microRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing

“…However, only 58 -73% of the reads sequenced in alfalfa roots matched to the M. truncatula. This similar results can be found in several previous studies, such as the studies on peach [44]and even on M. truncatula [22]. The known miRNAs comprised a range of the mapped reads (5.1-12.9 %), with DL and DR having the higher amount (10.1-12.5 %) while WL and WR have the lower amount (5.9-9.0 %).…”

“…For profiling the expression of the novel miRNAs, an enhanced sequencing depth might need to be performed. Moreover, the expression level of the predicted miRNA candidates is relatively lower than conserved miRNAs, and this result is agreed with the former reports [22,44,46,47]. One possible explanation for this result is that the conserved miRNAs regulate the target genes which might be involved in lots of important metabolic processes in viridiplantae, meanwhile the expression of nonconserved miRNAs might be environmentally inducible or tissue specific, thus the expression level of conserved miRNAs may be higher than non-conserved miRNAs [46,47].…”

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

“…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). miR160 showed downregulation in I. campanulata and upregulation in J. pentantha under drought.…”

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

“…Similarly, miR535 was the most abundant miRNA in drought-exposed peach (Eldem et al, 2012). It has been suggested that stress-regulated miRNAs might be regulated by stress-related transcription factors.…”