PJB-2019-247
Bioinformatics prediction and annotation of apple microRNAs and their targets
Iftekhar Ahmed Baloch, Muhammad Younas Khan Barozai Abdul Hameed Baloch, Tahira Bibi and Muhammad Din
Abstract
MicroRNAs are non-protein coding regulatory RNAs. These endogenously expressed RNAs range from 18-26 nucleotides in length. Their important functions have been widely reported in animals and plants during organogenesis, growth, transgene inactivation, cell signaling processes, disease development and defense against the attacking viruses and bacteria. These small molecules are evolutionarily conserved from species to species in the same kingdom and their conserved nature becomes an important logical tool for the hunt of new conserved miRNAs in other species by homology search. Apple (Malus domestica L.) is cultivated worldwide. It is the fourth major fruit of Pakistan and several cultivars of apple are grown in Pakistan. Bioinformatic analysis of 325,020 apple ESTs resulted in identification of sixty nine (69) new conserved miRNAs after filtration and completion of the process. The 69 potential apple miRNAs belong to 63 miRNA families (i-e. miR158, 161, 163, 165, 172, 400, 403, 472, 838, 850, 859, 866, 1120, 1170, 1310, 1313, 1426, 1427, 1428, 1438, 1509, 1510, 1512, 1513, 1514, 1518, 1533, 1847, 1861, 1863, 1873, 3629, 3630, 3633, 3635, 3694, 3699, 3706, 3707, 3711, 3954, 4354, 4407, 4412, 4413, 5138, 5142, 6260, 6261, 6271, 6275, 6280, 6290, 6295, 7516, 7520, 7521, 7526, 7528, 7532, 7536, 9672, 9776). One of the identified pre-miRNAs, i.e. mdm-mir-6271 showed 95% query coverage and 85% identity with the peach pre-miRNA. To our knowledge this is the first ever report of a plant precursor microRNA conservation and this interesting finding would open new vistas for miRNA research community. The mdm-mir 3630 pre-miRNA cluster was observed with two mature miRNA sequences. Four of the apple miRNAs (mdm-mir172, mdm-mir403, mdm-mir3635, mdm-miR6271) were found to be transcribed in sense/antisense orientation. Moreover, twelve of the newly predicted miRNAs were randomly selected for experimental validation through RT-PCR. Experimental validation of computationally predicted miRNAs endorses the powerfulness of bioinformatics prediction of miRNAs. The 69 new conserved apple miRNAs targeted a total of 84 mRNAs. These miRNA target are various proteins involved in numerous biological processes i.e. cell signaling, development, stress management and playing role as transcription factors. The results of this research would contribute in understanding the miRNA mediated life processes in apple
To Cite this article:
Baloch, I.A., M.Y.K. Barozai, A.H. Baloch, T. Bibi and M. Din. 2019. Bioinformatics prediction and annotation of apple microRNAs and their targets. Pak. J. Bot., 51(3): DOI: http://dx.doi.org/10.30848/PJB2019-3(32)
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