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OJBTM
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.
ABSTRACT
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.
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