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Online Journal of Bioinformatics©
Volume 23 (1):19-29, 2022.
In silico cloning calmodulin genes in cereals and millets.
Manoj Nath PhD, Anshita Goel MSc, Anil Kumar PhD.
Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar (Uttarakhand)
Nath M, Goel A, Kumar A., In silico cloning calmodulin genes in cereals and millets, Onl J Bioinform., 23 (1):19-29, 2022. We describe molecular mechanisms for accumulation of calcium in cereals and millets by calmodulin gene (CaM). We cloned an In silico calcium sensor by PCR from cereals and millets with leusine coracana ESTs primers in dbEST database. PCR amplicons of 613bp were found in all cereals and millets except Setaria italica. Amplicons were gel eluted, cloned, sequenced, homology searched, multiple sequence aligned for phylogenetic tree and motif analysis. Homology search confirmed CaM genes except Triticum aestivum. By sequence alignment of CaM we found 110 conserved amino acid in cereals and millets except in Sorghum bicolor. The phylogenetic tree showed close evolutionary relationship between Eleusine coracana (PRM-1, PRM-701 and PRM-801) and Hordeum vulgare compared with other cereals and millets. Three EF-hands associated with a CaM gene were present in all cereals and millets except Sorghum bicolor, having only two EF-hand. The in silico 3D-structural analysis of cloned sequences showed similar pattern and reveals high degree of conservedness in CaM of cereals and millets in terms of structure and interaction with calcium ions, thus reflecting to further investigate the role of CaM isoforms, their expression patterns and downstream interaction with transport machinery involved in calcium accumulation.
Keywords: CaM, Cereals, Millets, Multiple sequence alignment, Motif, EF-hand.