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Open AccessArticle

Identification of miRNAs and Their Targets Involved in Flower and Fruit Development across Domesticated and Wild Capsicum Species

1
Department of Biology, Gus R. Douglass Institute, West Virginia State University, West Virginia, WV 25112, USA
2
Genetic Improvement of Fruits and Vegetables Laboratory, USDA, ARS, Beltsville, MD 20705, USA
*
Author to whom correspondence should be addressed.
Academic Editor: María Serrano
Int. J. Mol. Sci. 2021, 22(9), 4866; https://doi.org/10.3390/ijms22094866
Received: 1 April 2021 / Revised: 29 April 2021 / Accepted: 2 May 2021 / Published: 4 May 2021
(This article belongs to the Section Molecular Plant Sciences)
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. View Full-Text
Keywords: miRNA; flower; fruit development; Capsicum species miRNA; flower; fruit development; Capsicum species
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MDPI and ACS Style

Lopez-Ortiz, C.; Peña-Garcia, Y.; Bhandari, M.; Abburi, V.L.; Natarajan, P.; Stommel, J.; Nimmakayala, P.; Reddy, U.K. Identification of miRNAs and Their Targets Involved in Flower and Fruit Development across Domesticated and Wild Capsicum Species. Int. J. Mol. Sci. 2021, 22, 4866. https://doi.org/10.3390/ijms22094866

AMA Style

Lopez-Ortiz C, Peña-Garcia Y, Bhandari M, Abburi VL, Natarajan P, Stommel J, Nimmakayala P, Reddy UK. Identification of miRNAs and Their Targets Involved in Flower and Fruit Development across Domesticated and Wild Capsicum Species. International Journal of Molecular Sciences. 2021; 22(9):4866. https://doi.org/10.3390/ijms22094866

Chicago/Turabian Style

Lopez-Ortiz, Carlos; Peña-Garcia, Yadira; Bhandari, Menuka; Abburi, Venkata L.; Natarajan, Purushothaman; Stommel, John; Nimmakayala, Padma; Reddy, Umesh K. 2021. "Identification of miRNAs and Their Targets Involved in Flower and Fruit Development across Domesticated and Wild Capsicum Species" Int. J. Mol. Sci. 22, no. 9: 4866. https://doi.org/10.3390/ijms22094866

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