Small RNA deep sequencing reveals the important role of microRNAs in the halophyte Halostachys caspica

Abstract

SummaryMicroRNAs (miRNAs), an extensive class of small regulatory RNAs, play versatile roles in plant growth and development as well as stress responses. However, the regulatory mechanism is unclear on miRNA-mediated response to abiotic stress in plants. Halostachys caspica is a halophytic plant species and a great model for investigating plant response to salinity stress. However, no research has been performed on miRNAs in H. caspica. In this study, we employed deep sequencing to identify both conserved and novel miRNAs from salinity-exposed H. caspica and its untreated control. Among the 13-19 million sequences generated from both treatments, a total of 170 conserved miRNAs, belonging to 151 miRNA families, were identified; among these miRNAs, 31 were significantly up-regulated and 48 were significantly down-regulated by salinity stress. We also identified 102 novel miRNAs from H. caspica; among them, 12 miRNAs were significantly up-regulated and 13 were significantly down-regulated by salinity. qRT-PCR expression analysis validated the deep sequencing results and also demonstrated that miRNAs and their targeted genes were responsive to high salt stress and existed a negative expression correlation between miRNAs and their targets. miRNA-target prediction, GO and KEGG analysis showed that miRNAs were involved in salt stress-related biological pathway, including calcium signalling pathway, MAPK signalling pathway, plant hormone signal transduction and flavonoid biosynthesis, etc. This suggests that miRNAs play an important role in plant salt stress tolerance in H. caspica. This result could be used to improve salt tolerance in crops and woods.

Genome-Wide Identification and Characterization of Salinity Stress-Responsive miRNAs in Wild Emmer Wheat (Triticum turgidum ssp. dicoccoides)

“…The GO terms of the putative targets were involved in nucleic acid binding (transcription factors) and catalytic activities regulating the development and response to abiotic stresses (Figure 2, Table S6), thereby providing useful information regarding their regulatory roles in plant physiological processes like defense and signaling. Through the KEGG analysis (Table S7), some targets of salinity response miRNAs in wild emmer were mapped to salt stress-related pathways, such as plant hormone signal transduction, flavonoid biosynthesis, ubiquitin-mediated proteolysis, apoptosis, ABC transporter, peroxisome and DNA repair [41]. …”

Contemporary Understanding of miRNA-Based Regulation of Secondary Metabolites Biosynthesis in Plants

“…Overexpression of miR8154 and miR5298b in sub-cultured Taxus cell lines revealed their crucial role in the regulation of taxol, phenylpropanoid, and flavonoid biosynthesis pathways (Zhang et al, 2015). Similarly, several other miRNAs of phenylpropanoid pathway, such as miR395p-3p/ targeting bHLH mRNA in D. kaki (Luo et al, 2015), miR396b and miR828a targeting mRNAs coding for Kaempferol 3-O-beta-D-galactosyltransferase and anthocyanin regulatory C1 protein respectively in R. serpentina (Prakash et al, 2016), miR858a targeting R2R3-MYB mRNA in A. thaliana (Sharma et al, 2016), miR6194 targeting Flavanone 3b-hydroxylase mRNA (F3H) in H. caspica (Yang et al, 2015), miR1061-3p and miR1318 in pear fruit (Wu et al, 2014) etc., (Table 1) have been reported.…”

Genome‐wide identification and characterization of Eutrema salsugineummicroRNAs for salt tolerance

“…In addition, seu‐miR160a, seu‐miR164a‐5p, seu‐miR164b, seu‐miR164d, seu‐miR167e, seu‐miR172d, seu‐miR319a‐3p and seu‐miR396i were suppressed in salt‐treated euhalophyte Salicornia europaea shoots or roots, as determined using high‐throughput sequencing technology; whereas seu‐miR171b, seu‐miR396b and seu‐miR396c were upregulated (Feng et al ). Finally, hcmiR171b‐3p, hcmiR160a‐3p and hcmiR172e‐3p were downregulated by salinity stress, and hcmiR160 was upregulated in halophyte Halostachys caspica (Yang et al ). Moreover, in our study, many miRNAs have a similar expression profile under salt stress in some species, but were regulated differently in other species.…”