Identification and Annotation of the 21 Novel Sugar Cane (Saccharum officinarum) MicroRNA Clusters and Their Significant Biological, Molecular and Cellular Targets
{"title":"Identification and Annotation of the 21 Novel Sugar Cane (Saccharum officinarum) MicroRNA Clusters and Their Significant Biological, Molecular and Cellular Targets","authors":"","doi":"10.1007/s12042-023-09352-y","DOIUrl":null,"url":null,"abstract":"<h3>Abstract</h3> <p>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.</p> <span> <h3>Graphical Abstract</h3> <p> <span> <span> <img alt=\"\" src=\"https://static-content.springer.com/image/MediaObjects/12042_2023_9352_Figa_HTML.png\"/> </span> </span></p> </span>","PeriodicalId":54356,"journal":{"name":"Tropical Plant Biology","volume":"28 1","pages":""},"PeriodicalIF":1.8000,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Tropical Plant Biology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1007/s12042-023-09352-y","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"PLANT SCIENCES","Score":null,"Total":0}
引用次数: 0
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.
期刊介绍：
Tropical Plant Biology covers the most rapidly advancing aspects of tropical plant biology including physiology, evolution, development, cellular and molecular biology, genetics, genomics, genomic ecology, and molecular breeding. It publishes articles of original research, but it also accepts review articles and publishes occasional special issues focused on a single tropical crop species or breakthrough. Information published in this journal guides effort to increase the productivity and quality of tropical plants and preserve the world’s plant diversity. The journal serves as the primary source of newly published information for researchers and professionals in all of the aforementioned areas of tropical science.
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