Computational analysis of common bean (Phaseolus vulgaris L., genotype BAT93) lycopene -cyclase and -carotene hydroxylase genes cDNA



Subhash Janardhan Bhore1, 2*, Kassim Amelia1, 2, Edina Wang2, Sindhuja Priyadharsini2 & Farida Habib Shah1, 3



1Molecular Biology Division, Melaka Institute of Biotechnology, Lot 7, Melaka International Trade Centre City, 75450 Ayer Keroh, Melaka, Malaysia; 2Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong-Semeling Road, Bedong, 08100, Kedah, Malaysia; 3Novel Plants Sdn. Bhd., 27C Jln Petaling Utama 12, 7.5 miles Old Klang Road, 46000 Petaling Jaya, Malaysia.


Email; *Corresponding author


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Received December 09, 2012; Accepted December 21, 2012; Published February 21, 2013



The identification of genes and understanding of genes expression and regulation in common bean (Phaseolus vulgaris L.) is necessary in order to strategize its improvement using genetic engineering techniques. Generation of expressed sequence tags (ESTs) is useful in rapid isolation, identification and characterization of the genes. To study the gene expression in P. vulgaris pods tissue, ESTs generation work was initiated. Early stage and late stage bean-pod-tissues cDNA libraries were constructed using CloneMiner cDNA library construction kit. In total, 5972 EST clones were isolated using random method of gene isolation. While processing ESTs, we found lycopene -cyclase (PvLCY-) and -carotene hydroxylase (PvCHY-) genes cDNA. In carotenoid biosynthesis pathway, PvLCY- catalyzes the production of carotene; and PvCHY- is known to function as a catalyst in the production of lutein and zeaxanthin. To understand more about PvLCY- and PvCHY-, both strands of both cDNA clones were sequenced using M13 forward and reverse primers. Nucleotide and deduced protein sequences were analyzed and annotated using online bioinformatics tools. Results showed that PvLCY- and PvCHY- cDNAs are 1639 and 1107 bp in length, respectively. Analysis results showed that PvLCY- and PvCHY- genes cDNA contains an open reading frame (ORF) that encodes for 502 and 305 amino acid residues, respectively. The deduced protein sequence analysis results also showed the presence of conserved domains needed for PvLCY- and PvCHY- functions. The phylogenetic analysis of both PvLCY- and PvCHY- proteins showed its closeness with the LCY- and CHY- proteins from Glycine max, respectively. The nucleotide sequence of PvLCY- and PvCHY- genes cDNA and its annotation is reported in this paper.



Expressed sequence tags, Genetic engineering, Health, Human population, Malaysia, Natural products, Nutrition, Phaseomics, Proteins, Vegetables.



Bhore et al.   Bioinformation 9(4): 197-206 (2013)


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P Kangueane






Biomedical Informatics



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