Abstract
MicroRNAs (miRNAs) are generated in a cell endogenously which have a nucleotide length of 18 to 26 and are also known as short non-protein coding RNAs. The majority of them are evolutionarily conserved in nature, suggesting a logical foundation for the anticipation of new miRNAs in association with their clusters in numerous plants. Considering this study, physical, bioinformatics and efficient methods are integrated to predict the fresh miRNA clusters along with their targets in sugar cane. In sugar cane, there were a total of 21 new miRNA clusters identified, which were linked to 15 miRNA families. These families are as 165a, 166b, 528a, 827, 2118, 2120b, 5168, 5564c, 5565g, 5568c, 6220, 6225, 6226, 6232a and 7540a. Multiple characteristics of such miRNA clusters, including web logo, phylogenetic tree and secondary structures have been developed. The minimal free energy (MFE) of the secondary structures has been attained and reported as well. In addition, mature miRNAs have been sought in stem section of the structure. Consequently, 115 miRNA targets were also found. These targets include substantial GO term which have important targets in the reproduction, DNA packaging, multicellular organismal process, gene expression, translation, transcription factors, protein binding, transporter activity, secretion, cell division, binding, growth & development and aging. Hence, the achieved results of novel sugar cane miRNA clusters target several types of significant genes which help in managing the environment for sugar cane for better crop production.
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Acknowledgements
The authors are thankful to the faculty members of Center for Applied Molecular Biology, University of Punjab, Lahore (CAMB) for encouragement and providing necessary facilities. The authors also acknowledge the Department of Botany, University of Balochistan for providing the necessary resources.
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Conceived and designed the data: Abdul Baqi, Samiullah & Muhammad Zafar Saleem. Arranged the tools: Abdul Baqi & Muhammad Zafar Saleem. Analyzed the data: Abdul Baqi & Muhammad Zafar Saleem. Contributed tools: Muhammad Zafar Saleem, Muhammad Ayub & Shazia Saeed. Wrote the paper: Abdul Baqi, Samiullah & Muhammad Zafar Saleem.
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Communicated by Rui Xia.
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Baqi, A., Samiullah, Saleem, M.Z. et al. Identification and Annotation of the 21 Novel Sugar Cane (Saccharum officinarum) MicroRNA Clusters and Their Significant Biological, Molecular and Cellular Targets. Tropical Plant Biol. 17, 65–81 (2024). https://doi.org/10.1007/s12042-023-09352-y
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DOI: https://doi.org/10.1007/s12042-023-09352-y