biologia plantarum

Biologia plantarum 68:1-11, 2024 | DOI: 10.32615/bp.2023.038

Comparative analysis of bioinformatic tools to predict and quantify active circular RNAs during grape cluster development

S. Ranjbar¹, A. Emamjomeh^{1, 2, *}, M. Ebrahimi^{3, 4}, A. Ghorbani⁵, E. Ebrahimie^{4, 6, 7}, Y. Shiri^{8, 9}

¹ Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, 9861335856, Iran

² Laboratory of Computational Biotechnology and Bioinformatics (CBB), Department of Bioinformatics, Faculty of Basic Sciences, University of Zabol, Zabol, 9861335856, Iran

³ Department of Biology, School of Basic Science, University of Qom, Qom, 3716146611, Iran

⁴ School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA 5371, Australia

⁵ Nuclear Agriculture Research School, Nuclear Science and Technology Research Institute (NSTRI), Karaj, 1439951113, Iran

⁶ Genomics Research Platform, School of Agriculture, Biomedicine and Environment, La Trobe University, Melbourne, 3083, Australia

⁷ School of BioSciences, University of Melbourne, Melbourne, 3052, Australia

⁸ Agronomy and Plant Breeding Department, Agriculture Research Center, Zabol Research Institute, Zabol, 9861673831, Iran

⁹ Department of Horticulture, Faculty of Agriculture and Natural Resources, Mohaghegh Ardabili University, Ardabil, 5619911367, Iran

Circular RNAs (circRNAs) are relatively new members of the RNA world and can contribute to crucial biological functions. CircRNAs have tissue-specific expression profiles depending on cell type and developmental stage. In Sistan region cultivated grapes are seedless but have small berries. The compact clusters are another notable characteristic of these grape cultivars, which negatively impacts their marketability. In this study, we aimed to identify the circRNAs that are active in cluster formation and investigated the effects of gibberellin treatment on their expression. Eight detection tools were used to predict the expressed circRNAs. Reliable circRNAs were used to identify potential functions of differentially expressed circRNAs by gene ontology (GO) analysis and prediction of target microRNAs (miRNAs). Of the 28 157 circRNAs detected, 3 715 were reliable. 900 differently expressed circRNAs were identified in the three developmental stages of the cluster under gibberellin treatment. Among the 503 target miRNAs found, 12 miRNAs were selected based on the number and expression of their circRNA sponges. Of the 29 circRNAs in the circRNAs-miRNAs-mRNAs interaction network, 12 circRNAs are highly conserved. Our results suggest that circRNAs in grape may play a key role in developmental and environmental adaptation in perennial plants.

Keywords: circular RNAs, gene ontology, gibberellin, micro RNAs.

Received: June 21, 2023; Revised: November 9, 2023; Accepted: November 22, 2023; Published online: January 12, 2024  Show citation