Identification of Gossypium hirsutum miRNA targets in the genome of Cotton leaf curl Multan virus and betasatellite

Cotton leaf curl Multan virus (CLCuMV.) in association with betasatellite causes devastating cotton leaf curl disease in cotton plants. Bioinformatics approaches were applied to search cotton (Gossypium hirsutum) miRNA targets in the genomes of CLCuMV (DNA-A) and betasatellite (DNA beta). A total of 18 nucleotide sequences representing full-length genome (DNA-A) of CLCuMV and 58 nucleotide sequences of full-length DNA beta were screened against a set of 60 mature miRNAs of G. hirsutum. Efficacy of cotton miRNAs against putative viral mRNA targets having an antiviral activity was analyzed on the basis of complementarity of miRNA-mRNA target pairings, leading to either translational inhibition or endonucleolytic mRNA cleavage, or both. This study revealed 34 putative miRNA targets in DNA-A encoded proteins loci and 2 putative miRNA targets in beta C1 gene of DNA beta above threshold values. miRNAs, viz., miR168, miR169, naiR390, miR395, miR399, miR414, miR779, miR2948, miR2950 and miR3476, were found to be the most potential and could target DNA-A with perfect or nearly perfect complementarity at multiple loci. Similarly, beta C1 was targeted by 2 miRNAs, viz., miR398 and miR2950. Among them, miR168, miR169, miR398, miR399, miR779, miR2948 and miR2950 strongly cleaved the mRNA target sites, while miR390, miR414, and miR3476 were probably translational inhibitors. Though miRNA targets were available in different genes of DNA-A, majority of them were found in AC1 gene of DNA-A and satellite conserved region in DNA beta. AC1 gene was significantly targeted by 14 miRNAs and beta C1 by 2 miRNAs. Interestingly, miR2950 was capable of targeting mRNAs representing both DNA-A and DNA beta. Artificially designed miR168, miR169, miR390, miR395, miR398, miR399, miR414, miR779, miR2948, miR2950 and miR3476 targeting DNA-A of CLCuV and beta C1 gene of DNA beta may have the potential to confer effective resistance against CLCuD infection in transformed cotton.