PCR Amplification, Sequencing, and In Silico Characterization of Pectin Lyase Genes from Aspergillus flavus NIICC8142

  • Amit Kumar Dubey
  • Sangeeta Yadav
  • Gautam Anand
  • Dinesh YadavEmail author


The genomic sequences of Aspergillus flavus NRRL 3357 revealed seven pectin lyase (pnl) genes, which were used to design gene-specific primers and these genes were amplified through polymerase chain reaction (PCR) from five strains of A. flavus, namely A. flavus MTCC 7589, A. flavus MTCC 10938, A. flavus MTCC 8836, A. flavus NIICC 8142 and A. flavus NIICC 8147. All the seven predicted pnl genes were amplified from the genomic DNA of A. flavus NIICC 8142, while six pnl genes were from A. flavus MTCC8837 and five pnl genes from the remaining strains, respectively. A total of five pnl gene sequences of A. flavus NIICC 8142 designated as Afpnl-1, Afpnl-2, Afpnl-3, Afpnl-4, and Afpnl-5 were submitted to GenBank and assigned accession numbers JQ735890 to JQ735894, respectively. These sequences were subjected to in silico characterization for homology search, multiple sequence alignment, phylogenetic tree construction, and motif analysis. The homology search revealed their identity to the predicted pectin lyase genes of A. flavus NRRL 3357, and multiple sequence alignment of these five genes showed various conserved residues. The phylogenetic tree revealed two distinct clusters and four subclusters with five pectin lyase genes of A. flavus occupying distinct position among the PCR-amplified pectin lyase genes from different fungi. The presence of unique pec_lyase C domain was observed among these sequences.


Pectin lyase Aspergillus flavus Multiple sequence alignment Motif Phylogenetic tree 



The authors wish to acknowledge the Head of the Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur for providing the infrastructural facilities. The financial support by the UGC, India in the form of UGC-Major Project (F. no. 37–133/2009-SR) to Dinesh Yadav and by the DST, India in the form of Fast Track Young Scientist Fellowship (FT/LS-125/2008) to Sangeeta Yadav is duly acknowledged.


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Copyright information

© Springer India 2014

Authors and Affiliations

  • Amit Kumar Dubey
    • 1
  • Sangeeta Yadav
    • 1
  • Gautam Anand
    • 1
  • Dinesh Yadav
    • 1
    Email author
  1. 1.Department of BiotechnologyD.D.U Gorakhpur UniversityGorakhpurIndia

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