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OJBTM

Online Journal of Bioinformatics

Volume 20(3):194-209, 2019.


In silico identification and characterization of novel DOF genes from Sorghum by comparative genomics.

 

Hariom Kushwaha1, Vinay Kumar Singh2, Smita Rastogi1 and Dinesh Yadav3

 

1Department of Biotechnology, Integral University, Lucknow (Uttar Pradesh), 2School of Biotechnology, BHU, Varanasi (Uttar Pradesh), 3Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur (Uttar Pradesh), INDIA

 

ABSTRACT

 

Kushwaha H, Singh VK, Rastogi S, Yadav D, In silico identification and characterization of novel DOF genes from Sorghum by comparative genomics, Onl J Bioinform., 20(3):194-209, 2019. Two full length DOF genes SbDOF1 and SbDOF2 accession numbers FJ854505 and FJ854506 were identified In Silico annotated from BAC clones AY661659 and AC169375 of Sorghum bicolor. The sequences were further characterized in silico by homology search, multiple sequence alignment, phylogenetic tree construction and protein functional analysis to DOF proteins. The in silico Cis-regulatory element analysis of putative promoters of SbDOF1 and SbDOF2 genes clearly indicated its role in regulation of seed storage protein and defense related genes. The Cis-regulatory elements present in promoter of SbDOF1 were GCN4_motif, RYelement, Skn-1_motifs commonly observed with seed storage protein promoters whereas SbDOF2 motifs CGTCA, GC and TGACG are more associated with immunity. Motif scan analysis of corresponding proteins revealed glycine and proline rich region in SbDOF1 and SbDOF2 respectively. Secondary structure prediction of these proteins confirmed conserved DOF domain region with turns, sheets, coil and helix. We predicted 29 DOF genes including EU760632, FJ854505 and FJ854506 In silico from available complete genome sequence of sorghum by comparative genomics.

 

Key Words: DOF genes, Sorghum, genomics.