Identification of microRNA elements from genomic data of European hazelnut (Corylus avellana L.) and its close relatives

Abstract

Plant microRNAs (miRNAs) are small and non-coding endogenous RNAs which have numerous regulatory roles in cells. These critical players regulate pathways either by inducing translational repression or messenger RNA (mRNA) decay. Newly developed bioinformatics tools and computational methods have been increased to identify miRNAs with their targets inside the genome. In this study, we predicted and identified 57 putative miRNAs through Corylus avellana (C. avellana) genomic data in silico. We also predicted some other putative miRNAs from Arabidopsis thaliana (A. thaliana), Ricinus communis (R. communis), Populus trichocarpa (P. trichocarpa) and Vitis vinifera (V. vinifera) to compare with the C. avellana organism since previous studies have indicated high similarities between these genomes and proteome atlases. The miRBase 21 was used as a reference dataset and the putative miRNAs were identified for the genome of each organism. We used homology conserved method to identify putative miRNAs. Based on our findings, C. avellana miRNA content was found to be highly similar to V. vinifera, R. communis and P. trichocarpa. Also, we found the targets of these hazelnut putative miRNAs and their possible functions inside the cell. One of our major discoveries is that miR171 families are highly represented (the copy number of miRNA) in the hazelnut genome to provide clues for microRNA domestication. The miR396, miR482, and miR2118 families were found as in silico expressed putative miRNAs by using computational methods. All these findings may help us better understanding the miRNA repertoire of the hazelnut organism and provide valuable insight about the regulatory roles of predicted putative miRNAs which are shared with other organisms (A. thaliana, R. communis, P. trichocarpa, V. vinifera) for further studies.

Identification of vital candidate microRNA/mRNA pairs regulating ovule development using high-throughput sequencing in hazel

“…All of these miRNAs could be assigned to 165 families. We identified 40, 37 and 38 members in the miR171, miR396 and miR482 families, respectively, suggesting that our results are consistent with the in silico miRNA prediction of the European hazel genome [23]. Clearly, the in silico Fig.…”

“…By mining genomic data in silico, 57 putative miRNAs were predicted and identified in C. avellana 'Jefferson' (OSU 703.007) [22][23][24]. In the European hazel genome, miR171, miR396, miR482, and miR2118 families were found as in silico expressed putative miRNAs [23].…”

A chromosome‐scale genome assembly of European hazel (Corylus avellana L.) reveals targets for crop improvement

“…MicroRNAs are ubiquitous post-transcriptional regulators in plants and a previous study identified putative miRNA genes in the draft C. avellana cv. Jefferson genome (Avsar and Aliabadi, 2017). In the Tombul genome, 153 putative conserved miRNA genes were annotated, including members of 52 different miRNA families (Table S11).…”

<p>Preface</p>

“…In short-term solutions, agricultural residues produced on a provincial scale can play a significant role, as they entail fairly low costs and great accessibility. For instance, Turkey is one of the major hazelnut producers, and hazelnut is the most important tree nut crop for the country's economy; hence, the Turkish hazelnut cultivar's genome has recently been sequenced to unravel the critical properties for crop improvement (Avşar and Esmaeili Aliabadi 2017;Lucas et al 2021). Most hazelnut production in Turkey occurs in Ordu, Samsun, and Giresun near the Black Sea Coast.…”