Endogenous rice ( Oryza Sativa ) miRNAs and their potential targets against Rice Tungro Virus using various string matching algorithms

Abstract

Rice is the major growing crop in South and Southeast Asia and half of the world population takes rice as staple food. But rice production hampered because of rice tungro disease caused by two viruses. MicroRNA(miRNA) act major role in plant resistance against viruses. miRNAs are short around 22 nucleotides RNA molecules found in eukaryotic cells that regulate gene expression by translational inhibition or cleavage of complementary mRNAs. The present work emphasizes on different string matching algorithms such as Boyer-Moore, Knuth-Morris, Rabin-Karp to elucidate the potentiality of rice miRNAs target against rice plant infecting tungro viruses of both Rice Tungro Spherical Virus (RTSV) and Rice Tungro Baciliform Virus (RTBV). 581 number of miRNA sequence from miRBase has been collected and target rice tungro viruses genes like coat proteins CP1,CP2,CP3, poly-protein of RTSV and ORF1, ORF2, ORF3, P12, P24, P46 and P194 of RTBV considered for simulation. The potential endogenous rice miRNAs targeted found by three different algorithms in our approach also compared with the web based sever psRNATarget. The novel target site findings of rice miRNAs and tungro virus will be helpful to manipulate in new biotechnological approaches for enhance rice production.