Identification of miRNAs and Their Targets Involved in Flower and Fruit Development across Domesticated and Wild Capsicum Species
| Autor: | Menuka Bhandari, Padma Nimmakayala, Umesh K. Reddy, Carlos Lopez-Ortiz, Purushothaman Natarajan, Yadira Peña-Garcia, John R. Stommel, Venkata Lakshmi Abburi |
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| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
0106 biological sciences
0301 basic medicine Amino Acid Transport Systems 01 natural sciences Fructokinase Domestication Gene Expression Regulation Plant Biology (General) Spectroscopy Plant Proteins chemistry.chemical_classification Genetics Gene Expression Regulation Developmental High-Throughput Nucleotide Sequencing food and beverages Ripening General Medicine Computer Science Applications Amino acid flower Chemistry RNA Plant Capsicum species Capsicum Metabolic Networks and Pathways Glycoside Hydrolases QH301-705.5 Flowers Carbohydrate metabolism Biology Catalysis Article Inorganic Chemistry Fructokinases 03 medical and health sciences microRNA Humans Physical and Theoretical Chemistry KEGG Molecular Biology Gene Transcription factor QD1-999 miRNA Gene Expression Profiling Organic Chemistry Molecular Sequence Annotation MicroRNAs 030104 developmental biology Gene Ontology chemistry Fruit fruit development 010606 plant biology & botany Transcription Factors |
| Zdroj: | International Journal of Molecular Sciences, Vol 22, Iss 4866, p 4866 (2021) International Journal of Molecular Sciences Volume 22 Issue 9 |
| ISSN: | 1661-6596 1422-0067 |
| Popis: | MicroRNAs (miRNAs) are regulators of the post-transcription stage of gene activity documented to play central roles in flower and fruit development in model plant species. However, little is known about their roles and differences in domesticated and wild Capsicum species. In this study, we used high-throughput sequencing to analyze the miRNA content at three developmental stages (flower, small fruit, and middle fruit) from two cultivated (C. baccatum and C. annuum) and two wild (C. chacoense and C. eximium) pepper species. This analysis revealed 22 known and 27 novel miRNAs differentially expressed across species and tissues. A number of stage- and species-specific miRNAs were identified, and Gene Ontology terms were assigned to 138 genes targeted by the miRNAs. Most Gene Ontology terms were for the categories “genetic information processing”, “signaling and cellular processes”, “amino acid metabolism”, and “carbohydrate metabolism”. Enriched KEGG analysis revealed the pathways amino acids, sugar and nucleotide metabolism, starch and sucrose metabolism, and fructose-mannose metabolism among the principal ones regulated by miRNAs during pepper fruit ripening. We predicted miRNA–target gene interactions regulating flowering time and fruit development, including miR156/157 with SPL genes, miR159 with GaMYB proteins, miR160 with ARF genes, miR172 with AP2-like transcription factors, and miR408 with CLAVATA1 gene across the different Capsicum species. In addition, novel miRNAs play an important role in regulating interactions potentially controlling plant pathogen defense and fruit quality via fructokinase, alpha-L-arabinofuranosidase, and aromatic and neutral amino acid transporter. Overall, the small RNA-sequencing results from this study represent valuable information that provides a solid foundation for uncovering the miRNA-mediated mechanisms of flower and fruit development between domesticated and wild Capsicum species. |
| Databáze: | OpenAIRE |
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