Identification and annotation of newly conserved microRNAs and their targets in wheat (Triticum aestivum L.)

Abstract

MicroRNAs (miRNAs) are small, non-coding and regulatory RNAs produce by cell endogenously. They are 18–26 nucleotides in length and play important roles at the post-transcriptional stage of gene regulation. Evolutionarily, miRNAs are conserved and their conservation plays an important role in the prediction of new miRNAs in different plants. Wheat (Triticum aestivum L.) is an important diet and consumed as second major crop in the world. This significant cereal crop was focused here through comparative genomics-based approach to identify new conserved miRNAs and their targeted genes. This resulted into a total of 212 new conserved precursor miRNAs (pre-miRNAs) belonging to 185 miRNA families. These newly profiled wheat’s miRNAs are also annotated for stem-loop secondary structures, length distribution, organ of expression, sense/antisense orientation and characterization from their expressed sequence tags (ESTs). Moreover, fifteen miRNAs along with housekeeping gene were randomly selected and subjected to RT-PCR expressional validation. A total of 32927 targets are also predicted and annotated for these newly profiled wheat miRNAs. These targets are found to involve in 50 gene ontology (GO) enrichment terms and significant processes. Some of the significant targets are RNA-dependent DNA replication (GO:0006278), RNA binding (GO:0003723), nucleic acid binding (GO:0003676), DNA-directed RNA polymerase activity (GO:0003899), magnesium ion transmembrane transporter activity (GO:0015095), antiporter activity (GO:0015297), solute:hydrogen antiporter activity (GO:0015299), protein kinase activity (GO:0004672), ATP binding (GO:0005524), regulation of Rab GTPase activity (GO:0032313) Rab GTPase activator activity (GO:0005097), regulation of signal transduction (GO:0009966) and phosphoprotein phosphatase inhibitor activity (GO:0004864). These findings will be helpful to manage this economically important grain plant for desirable traits through miRNAs regulation.

Profiling of 21 novel microRNA clusters and their targets in an important grain: wheat (Triticum aestivum L.)

“…3, the red highlighted box shows the conserved regions of matures related to other plants like; Oryza sativa, B. distachyon and Zea mays. Similar outcomes have been noted by various specialists previously (Din et al, 2018;Achakzai et al, 2018).…”

Analysis of miRNAs in Two Wheat Cultivars Infected With Puccinia striiformis f. sp. tritici

“…Of 163 miRNAs identified, 10 were variants (≤2 mismatches) of miRNAs from other monocots-Aegilops tauschii, Brachypodium distachyon, Hordeum vulgare, Festuca arundinacea, Oryza sativa, and Zea mays, while 7 matched miRNAs from dicot species-Citrus sinensis, Populus trichocarpa, Theobroma cacao, and Medicago truncatula (Supplementary Table 7). We found tae-miR43, tae-miR122, and taemiR-155 to be variants of taemiR818a, taemiR6220, and taemiR3633, respectively (Achakzai et al, 2018). The lack of homology with known miRNAs suggests that the majority of novel miRNAs identified are not conserved across diverse plant families.…”

“…Recent advances in next-generation sequencing and availability of plant genomes have accelerated discovery of miRNAs and the processes under their regulation. With the availability of the wheat genome sequence, several groups have discovered wheat miRNAs that are conserved across plant species (Yao et al, 2007;Wei et al, 2009;Su et al, 2014;Achakzai et al, 2018) miRNAs involved in development (Li et al, 2013;Meng et al, 2013;Han et al, 2014;Li et al, 2015) and abiotic (Qiu et al, 2016) or biotic stress responses (Xin et al, 2010;Inal et al, 2014;Feng et al, 2015a;Feng et al, 2015b;Kumar et al, 2017). However, owing to the complexity of the wheat genome and the spatial/temporal nature of miRNA expression, a large number of miRNAs still remain to be discovered (Budak and Akpinar, 2015).…”

The identification of eighteen precursor miRNA clusters and their targets in barley (Hordeum vulgare L.)

“…MiRNA* sequences both mature and precursor sequences were subjected to Basic Local Alignment Search Tool (BLAST) against barley ESTs using BLASTn program http://blast.ncbi.nlm.nih.gov/Blast.cgi according to reported procedures (Altschul et al, 1990;Achakzai et al, 2018) following 0-4 mismatches with miRNAs*.…”