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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.
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.