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OJBTM
Online
Journal of Bioinformatics©
Established 1995
ISSN 1443-2250
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)
ABSTRACT
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.
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