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

Abstract

Eutrema salsugineum, a close relative of Arabidopsis thaliana, is a valuable halophytic model plant that has extreme tolerance to salinity. As posttranscriptional gene regulators, microRNAs (miRNAs) control gene expression and a variety of biological processes, including plant-stress responses. To identify salt-stress responsive miRNAs in E. salsugineum and reveal their possible roles in the adaptive response to salt stress, we chose the Solexa sequencing platform to screen the miRNAs in 4-week-old E. salsugineum seedlings under salt treatment. A total of 82 conserved miRNAs belonging to 27 miRNA families and 17 novel miRNAs were identified and 11 conserved miRNA families and 4 novel miRNAs showed a significant response to salt stress. To investigate the possible biological roles of miRNAs, 1060 potential targets were predicted. Moreover, 35 gene ontology (GO) categories and 1 pathway, including a few terms that were directly and indirectly related to salt stress, were significantly enriched in the salt-stress-responsive miRNAs targets. The relative expression analysis of six target genes was analyzed using quantitative real-time polymerase chain reaction (PCR) and showed a negative correlation with their corresponding miRNAs. Many stress regulatory and phytohormone regulatory cis-regulatory elements were widely present in the promoter region of the salt-responsive miRNA precursors. This study describes the large-scale characterization of E. salsugineum miRNAs and provides a useful resource for further understanding of miRNA functions in the regulation of the E. salsugineum salt-stress response.

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

“…For the confirmation of hairpin structures, all the precursors of these miRNAs possessed the typical stem-loop structures (Figure S1 and Figure S3). Previous studies reported that base composition can affect the physiochemical properties and the secondary structures of miRNAs [37]. Analysis of the nucleotide bias in the total miRNAs of wild emmer wheat showed the first and 24th nucleotide position preferred U (Figure S2A).…”

“…For wild emmer wheat, although it was considered as a vital genetic resource for salinity tolerant improvement, no systematic identification of miRNAs by sequencing has been reported till now. High-throughput sequencing is an effective method for miRNA discovery and miRNA expression profiling analysis and has been widely applied to miRNA research [37]. The technology is able to capture extensive collections of genome-wide or transcriptome-wide miRNAs [9].…”

Halophytism: What Have We Learnt From Arabidopsis thaliana Relative Model Systems?

“…Moreover, a large proportion of the conserved noncoding sequences are adjacent to coding regions, yet their functional significance is unknown. In contrast, there is increasing evidence for the functional and evolutionary significance of noncoding RNA families in the E. salsugineum and S. parvula genomes, but this evidence remains in the realm of in silico predictions (Zhang et al, 2013;Rathore et al, 2016;Wu et al, 2016). (3) While there can be many novel or modified functions in the orthologous genes found in the extremophytes that are not yet described in Arabidopsis, there also is a significant fraction of lineage-specific genes with unknown functions in the extremophyte genomes (Dassanayake et al, 2011a;Wu et al, 2012;Yang et al, 2013).…”

“…Since that pioneering meeting, over 125 articles have been published on E. salsugineum and the related (and even more salt-tolerant [Orsini et al, 2010]) Schrenkiella parvula (formally Thellungiella parvula and Eutrema parvulum). Furthermore, various genetic resources have been generated, including chromosome-level genome assemblies, natural accession collections, full-length cDNA and EST collections, transformation protocols, a plant transformation-competent large-insert DNA library, Arabidopsis lines expressing an E. salsugineum cDNA library, nuclear and organelle genome sequences, microRNA sequences, cDNA microarrays, RNA sequencing data sets (Wang et al, 2004(Wang et al, , 2018a(Wang et al, , 2018bWong et al, 2005;Du et al, 2008;Taji et al, 2008;Zhang et al, 2008Zhang et al, , 2013Amtmann, 2009;Dassanayake et al, 2011a;Oh et al, 2012;Wu et al, 2012;Bartels and Dinakar, 2013;Champigny et al, 2013;Lee et al, 2013;Yang et al, 2013;Batelli et al, 2014;Fukami-Kobayashi et al, 2014;Guo et al, 2016;He et al, 2016;Yin et al, 2018), and dedicated Web resources (http:// extremeplants.org/). Given their increasing importance as model systems (Box 1), E. salsugineum and S. parvula were ranked by the journal Cell as one of the next top models (Zhu et al, 2015).…”

Identification and Functional Characterization of Plant MiRNA Under Salt Stress Shed Light on Salinity Resistance Improvement Through MiRNA Manipulation in Crops

“…Zhang et al (2013) identified 246 miRNAs candidates in E. salsugineum. In addition, 26 conserved miRNAs and 4 novel miRNAs were found to display a significant response to salt stress in E. salsugineum (Zhang et al, 2013;Wu et al, 2016). Recently, 88 conserved miRNAs and 13 novel miRNAs were identified from Reaumuria soongorica seeds treated with various NaCl concentrations, providing a useful reference for salt resistance improvement of seed germination .…”