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Online Journal of Bioinformatics ©
Volume 13 (1):80-92, 2012
Insights to sequences of PCR amplified pectin lyase genes from different fungal strains
Amit Kumar Dubey1 (M.Sc.), Sangeeta Yadav1(Ph.D.), Gautam Anand1(M.Sc.), Naveen C Bisht2(M.Sc.) and Dinesh Yadav*1(Ph.D.)
1Department of Biotechnology, D.D.U Gorakhpur University, Gorakhpur (U.P.) 2National Institute of Plant Genome Research, JNU Campus, New Delhi,India.
Dubey AK, Yadav S, Anand G, Bisht NC, Yadav D., Insights to sequences of PCR amplified pectin lyase genes from different fungal strains, Online J Bioinform, 13 (1):80-92, 2012. Pectin lyase genes from fungal strains viz., Aspergillus niger MTCC404, Aspergillus versicolor MTCC3071, Aspergillus foetidus MTCC151, Aspergillus terricola MTCC7588, Aspergillus aculeatus MTCC7590, Aspergillus ficcum MTCC7591, Aspergillus flavus MTCC7589 and Penicillium citrinum MTCC8897 were PCR amplified , gel eluted and sequenced. A total of 18 pectin lyase gene sequences with assigned GenBank accession numbers JF447757-JF447774 ranging from 396 to 940 bp were subjected to in silico characterization for homology search, multiple sequence alignment, phylogenetic tree construction and motif analysis. BLAST analysis revealed its identity to pectin lyase gene family and multiple sequence alignment showed highly conserved three nucleotides namely G, G and C at 259, 434 and 451 positions respectively. The phylogenetic tree by NJ method revealed two major clusters with pectin lyase genes amplified by same set of primers being grouped together irrespective of the source organisms. The three frequently observed motifs among these sequences revealed its identity to Pec_Lyase_C superfamily, a typical feature of pectin lyase and pectate lyases.
Key words: Pectin lyase, PCR amplification, Multiple Sequence Alignment, Motif, BLAST, Fungal strains.