Identification of miRNAs and their targets involved in flower and fruit development across domesticated and wild capsicum species

Authors: LOPEZ-ORTIZ, CARLOS - West Virginia State University; PENA-GARCIA, YADIRA - West Virginia State University; BHANDARI, MENUKA - West Virginia State University; ABBURI, VENKATA LAKSHMI - West Virginia State University; Stommel, John; NIMMAKAYALA, PADMA - West Virginia State University; REDDY, UMESH - West Virginia State University

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/2/2021
Publication Date: 5/4/2021
Citation: Lopez-Ortiz, C., Pena-Garcia, Y., Bhandari, M., Abburi, V., Stommel, J.R., Nimmakayala, P., Reddy, U.K. 2021. Identification of miRNAs and their targets involved in flower and fruit development across domesticated and wild capsicum species. International Journal of Molecular Sciences. U.K. 2021. https://doi.org/10.3390/ijms22094866.
DOI: https://doi.org/10.3390/ijms22094866

Interpretive Summary: Flower and fruit development are complex biological processes that are controlled by the expression of numerous genes. Whereas some of the genes that influence flower and fruit development have been described, additional knowledge is required to characterize these complex processes. MicroRNAs (miRNAs) are small RNAs involved in gene expression and play an important role in several essential plant biological processes, including flower and fruit developmental. In this study, we used high-throughput sequencing to identify pepper miRNAs at three different developmental stages (flowering, small fruit, and mid-size fruit) in four species of pepper. Stage- and species-specific miRNAs were identified that corresponded to genetic information processing, signaling and cellular processes, amino acid metabolism, and carbohydrate metabolism. In addition, we predicted miRNA–gene interactions regulating flowering time and fruit ripening. The identification of conserved and novel miRNAs across different species of pepper provides valuable insights into the evolution of microRNAs with respect to pepper domestication events related to fruit development. These results are valuable for characterization of key pepper flower and fruit developmental processes and will be of further value in identification of key regulatory and biosynthetic genes for pepper improvement.

Technical Abstract: 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 in flower and fruit samples at two developmental stages 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 sugar 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 flower time and fruit ripening, including miR156/157 with SPL genes, miR159 with GaMYB proteins, miR160 with ARF genes, and miR172 with AP2-like transcription factors 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.