Journal of Proteomics & Bioinformatics
Open Access

Abstract

Comparative In silico Analysis of Partial Coat Protein Gene Sequence of Zucchini Yellow Mosaic Virus Infecting Summer Squash (Cucurbita pepo L.) Isolated From India

Sharma Neha, Bhardwaj Satya Vrat, Jarial Kumud, Thakur P D, Kaur Rajinder and Handa Anil

Zucchini yellow mosaic virus (ZYMV; Family: Potyviridae, Genus: Potyvirus) is a serious virus infecting summer squash causing severe damage to both crop and ornamental cucurbit crop production. In the present study, molecular characterization of ZYMV (at genomic and proteomic level) infecting summer squash was carried out and cDNA of approximately 700bp was amplified. The PCR amplified product was further sequenced and analyzed. The sequence of partial coat protein of 154 nucleotides of Indian isolate of zucchini yellow mosaic virus (ZYMV) was determined and translated to proteins. Later, the sequence was submitted to NCBI and has got accession no. GU144796 with protein id ACZ36948. In BLASTN analysis, nucleotide test sequence showed 91% homology with D13914 (sequence from USA), whereas, protein test sequence was 75.9% homologous in BLASTP analysis with a number of protein sequences present in the database. The alignment score of test sequence with 67 other isolates of ZYMV retrieved from NCBI database was highest for USA among varied countries and lowest for China in case of nucleotides and Korea in case of proteins. Phylogenetic analysis revealed similarity of the test virus sequence with a USA ZYMV CP (D13914) and similarity of the partial polyprotein sequence with that of Japan (BAE75935). Conserved domain of the test virus was found to show homology with the potyvirus coat protein domain alignment collection (pfam00767). Computational restriction digestion revealed that 22 different restriction enzymes restrict present isolate of ZYMV. Secondary structures for polyprotein of the test virus was predicted which inferred dominance of alpha (a) helix in the protein sequence.