In silico Analysis of MicroRNAs in Spinacia oleracea Genome and Transcriptome

Avşar, Bihter; Aliabadi, Danial Esmaeili

doi:10.17706/ijbbb.2017.7.2.84-92

Cited by 3 publications

(3 citation statements)

References 22 publications

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“…We identified the putative miRNA families from C. avellana, V. vinifera, A. thaliana, R. communis, and P. trichocarpa by using homology-based conservation approach (Avsar and Aliabadi, 2015;Avsar and Aliabadi, 2017). After using UNAFold, an implementation of the Zuker folding algorithm, we predicted putative miRNA families in organisms from their pre-miRNA stem-loop structures (see Fig 1; Data S1,S2,S3,S4, and S5).…”

Section: Resultsmentioning

confidence: 99%

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

Avşar¹,

Esmaeilialiabadi²

2017

Plant Omics

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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.

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Section: Resultsmentioning

confidence: 99%

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

Avşar¹,

Esmaeilialiabadi²

2017

Plant Omics

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“…Our script is a stand-alone user-friendly package that rapidly omits false-positive miRNA candidates, and generates report in both tabular and visual formats. Our previous studies have been subjected to miRCurator as case studies for the curation of miRNAs from the kiwifruit genome [11], hazelnut genome [12,13], spinach transcriptome [14], fabaceae family members [15], and medicinal plant transcriptome [16,17].…”

Section: Introductionmentioning

confidence: 99%

miRCurator: A rapid curation and analysis tool for plant microRNA studies

Avşar

Aliabadi

2023

Preprint

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Plant microRNAs (miRNAs) are tiny, non-coding RNAs that regulate the biological pathways either by inducing translational repression or messenger RNA decay. The advent of sequencing technologies increases the number of biological tools and computational methods to identify miRNAs with their targets inside the genome and transcriptome. In this study, we present a rapid curation software tool, the so-called miRCurator, which filters out unwanted microRNA candidates based on three significant criteria: (1) the pre-miRNA sequence should be deprived of multi-branched loops; (2) less than four mismatches on between mature miRNA and miRNA* strand are allowed; (3) no mismatches at DICER cut points are permitted on a mature miRNA strand. miRCurator is a stand-alone user-friendly package that does not rely on cutting-edge computing platforms. We have examined our tool on different organisms, which are shown as case studies, and it was able to successfully identify all the unwanted miRNA candidates. The developed tool helps to identify genuine miRNAs and provides reliable outcomes in an automated fashion by eliminating false-positive predictions.

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“…To verify whether miRNA can serve as sex determining gene in spinach, miRNAs resource should be firstly harvested. In 2017, spinach miRNAs were analyzed via in silico prediction in vegetative tissues of spinach [47]. Flower development-related genes are crucial for sex determination and differentiation, so we performed small RNA sequencing using 18 spinach flower samples at three early female and male flower development stages to identify some candidate miRNAs for spinach sex determination or differentiation.…”

Section: Introductionmentioning

confidence: 99%

Identification of Sex Differentiation-Related microRNAs in Spinach Female and Male Flower

Wang

et al. 2022

IJMS

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Sex determination and differentiation is an important biological process for unisexual flower development. Spinach is a model plant to study the mechanism of sex determination and differentiation of dioecious plant. Till now, little is known about spinach sex determination and differentiation mechanism. MicroRNAs are key factors in flower development. Herein, small RNA sequencing was performed to explore the roles of microRNAs in spinach sex determination and differentiation. As a result, 92 known and 3402 novel microRNAs were identified in 18 spinach female and male flower samples. 74 differentially expressed microRNAs were identified between female and male flowers, including 20 female-biased and 48 male-biased expression microRNAs. Target prediction identified 22 sex-biased microRNA-target pairs, which may be involved in spinach sex determination or differentiation. Among the differentially expressed microRNAs between FNS and M03, 55 microRNAs were found to reside in sex chromosome; one of them, sol-miR2550n, was functionally studied via genetic transformation. Silencing of sol-miR2550n resulted in abnormal anther while overexpression of sol-miR2550n induced early flowering, indicating sol-miR2550n was a male-promoting factor and validating the reliability of our small RNA sequencing data. Conclusively, this work can supply valuable information for exploring spinach sex determination and differentiation and provide a new insight in studying unisexual flower development.

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In silico Analysis of MicroRNAs in Spinacia oleracea Genome and Transcriptome

Cited by 3 publications

References 22 publications

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

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

miRCurator: A rapid curation and analysis tool for plant microRNA studies

Identification of Sex Differentiation-Related microRNAs in Spinach Female and Male Flower

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