Abstract
Twenty primers of 20 mer referred to universal rice primer (URP) were developed from a repetitive sequence of rice genome. URP-PCR protocol employed stringent PCR with high annealing temperature throughout the thermo-cycling reaction, giving high reproducibility. Under the PCR condition, each single URP primer produced characteristic fingerprints from diverse genomes of bacterial species. The universal application of URP-PCR was demonstrated by applying it to 24 strains from Pectobacterium carotovoum subsp. carotovorum, 41 Agrobacterium vitis strains, 3 Xanthomonas spp. 5 Pseudomonas spp, Rhizobium sp. plant pathogenic bacteria, human and animal pathogenic bacterial strains including 6 Escherichia coli, 4 Salmonella spp., 7 Mycobacterium spp and 3 Blucella abortus strains. In addition, thermophilic bacteria were randomly isolated form high temperature compost and their URP-PCR polymorphisms were characterized with genetic relatedness. PCR approach using URP primers will be useful for studying DNA diversity of diverse prokaryotic genomes, especially at inter- and intra species levels.
Highlights
The classic taxonomical methods of bacteria, relies on fatty acids, nutritional composition, and biochemical properties and so on (Garrity et al, 2002)
Various molecular typing methods such as extragenic palindromic (REP) sequence, 124-127 enterobacterial repetitive intergenic consensus (ERIC) sequence 154 bp and BOX that are derived from repetitive sequences located in bacterial genomes have widely been used for discrimination of various bacterial strains at inter species level (De Brujin, 1992, Hulton et al, 1991) Recently, in silico genomic fingerprints were devised to be produced by virtual hybridization of 191 fully sequenced bacterial genomes using a set of 15,264 13mer probes specially designed to produce universal whole genome fingerprints(JaimesDiaz et al, 2011)
PCR approach using universal rice primer (URP) primers offers a powerful tool for studying DNA diversity of prokaryotic genomes, with potential use in taxonomic and phylogenic analysis, as well as in genotypic screening of strains in species, especially at inter- and intra-species levels
Summary
The classic taxonomical methods of bacteria, relies on fatty acids, nutritional composition, and biochemical properties and so on (Garrity et al, 2002). PCR FINGERPRINTING OF DIVERSE GENOMES FROM BACTERIAL STRAINS USING UNIVERSAL RICE PRIMER (URP) Hee Wan Kang rDNA sequence region is widely used as a species-specific identification of bacterial species (Chang et al, 1997, Garrity et al, 2002 ). Since these rDNA regions are highly preserved areas, there is a limit to find polymorphism at level of inter-species such as subspecies, pathovar and race strains within species. Fingerprinting of a variety of organisms Bacterial strains and genomic DNA including animals, other plants, and extraction microorganisms, as well as rice and named as Fourty one Agrobacterium vitis universal rice primer (URP).
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