In silico Analysis of ama-1 Gene of the Southern Root-Knot Nematode, Meloidogyne incognita

Abstract

House-keeping genes play crucial role in nematode metabolism and development. The model nematode, Caenorhabditis elegans has been explored by molecular biologist for more or less all the genes but, role of most of the genes, their genomics and transcriptomic studies in PPNs are meagre. In the present study, a house-keeping gene (ama-1) from southern root-knot nematode, Meloidogyne incognita was characterized using bioinformatic tools. A partial segment of 701bp was analysed on M. incognita INRA genome resource to obtain 5460 bp long full CDS specifying the open reading frame. The domain prediction analysis revealed that ama-1 gene encodes RNA polymerases which catalyses the DNA dependent polymerisation of RNA and helps in DNA binding and DNA-directed 5’-3’ RNA polymerase activity. A phylogenetic tree based on the amino acid sequences showed evolutionary relationship of Minc17041 gene with house-keeping genes of other nematodes. The 3D models and Ramachandran plot for Minc17041gene was predicted with the best confidence score at -1.64.