Ashraf, M.A.; Brown, J.K.; Iqbal, M.S.; Yu, N. Genome-Wide Identification of Cotton MicroRNAs Predicted for Targeting Cotton Leaf Curl Kokhran Virus-Lucknow. Microbiol. Res.2024, 15, 1-19.
Ashraf, M.A.; Brown, J.K.; Iqbal, M.S.; Yu, N. Genome-Wide Identification of Cotton MicroRNAs Predicted for Targeting Cotton Leaf Curl Kokhran Virus-Lucknow. Microbiol. Res. 2024, 15, 1-19.
Ashraf, M.A.; Brown, J.K.; Iqbal, M.S.; Yu, N. Genome-Wide Identification of Cotton MicroRNAs Predicted for Targeting Cotton Leaf Curl Kokhran Virus-Lucknow. Microbiol. Res.2024, 15, 1-19.
Ashraf, M.A.; Brown, J.K.; Iqbal, M.S.; Yu, N. Genome-Wide Identification of Cotton MicroRNAs Predicted for Targeting Cotton Leaf Curl Kokhran Virus-Lucknow. Microbiol. Res. 2024, 15, 1-19.
Abstract
Cotton leaf curl Kokhran virus (CLCuKoV) (genus, Begomovirus; family, Geminiviridae) is highly infectious, widespread and the most dangerous pathogen of cotton (Gossypium hirsutum L.) that is responsible to a serious disorder, cotton leaf curl disease (CLCuD). Begomoviruses are spread very efficiently by the whitefly Bemisia tabaci cryptic species, causing economic losses to cotton crop, all over the world. The ‘Lucknow’ strain of CLCuKoV has emerged as a divergent isolate that could cause CLCuD. The monopartite ssDNA genome of CLCuKoV-Lu (2.7 Kb) contains six open reading frames (ORFs) that was shown to encode four major proteins. RNA interference (RNAi)-based antiviral innate immunity is a sequence-specific biological phenomenon and a powerful tool to control plant viruses. The present study aims to determine cotton locus-derived microRNAs (ghr-miRNAs) that are identified for targeting the CLCuKoV-Lu ss-DNA-encoded mRNAs using a predictive approach that involves four computational algorithms, miRanda, RNA22, psRNATarget and RNAhybrid. Mature ghr-miRNA sequences (n=80) from allotetraploid upland cotton (2n = 4x = 52) were selected from the miRBase and were tested for alignment with the CLCuKoV-Lu genome. Among the 80 cotton locus-derived ghr-miRNAs evaluated, only one consensus cotton locus-derived ghr-miRNA (ghr-miR2950) was concluded to have effective ghr-miRNA target site at common nucleotide position 82 in the CLCuKoV-Lu genome respectively, using a stringent criterion, identified by all the algorithms used. The miRNA targeting is reliant on base pairing of miRNA-mRNA target pairings. Conservation of the hybridization binding site of the predicted ghr-miR2950 was validated using multiple sequence alignment within all the strains of CLCuKoV. We constructed a regulatory interaction network of miRNA–mRNA to identify novel targets. The efficacy of the predicted miRNAs against CLCuKoV-Lu was evaluated by RNAi-mediated targeted mRNA cleavage. The current investigated miRNA targets provide evidence for the development of CLCuD-resistant cotton plants.
Biology and Life Sciences, Biology and Biotechnology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
