GENOME ANNOTATION AND PHYLOGENETIC ANALYSIS OF 27 SALMONELLA STRAINS BASED ON BIOINFORMATIC ANALYSIS OF RESPECTIVE GENOMES AND THREE GENES
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Salmonella is the most common food-borne bacterial infectious pathogen worldwide. Different serovars of Salmonella are capable of infecting different kinds of hosts, such as humans, mice, pigs, chickens, and can also lead to different syndromes, such as enterica fever, enterocolitis and diarrhea, bacteremia and chronic asymptomatic carriage. Although Salmonella strains are quite diverse, strains within the same serovar usually infect the same host and cause similar symptoms. Thus, it is important, especially in food-borne disease outbreaks, to know which type of Salmonella is present. The current method of typing Salmonella is based on the Kaufmann-White scheme and MLEE, which are laborious and expensive. Although the reliability of this method has not been previously verified, the evolutionary relationship reflected by phylogenetic trees can be a possible alternative to the way of typing the Salmonella strains; this method would be less labor intensive and more economical. MLST is considered as a “gold standard” of typing for many species includes Salmonella. And genome sequence, which certainly reflects the evolutionary relationship of strains, is the most ideal data to construct a more reliable phylogenetic tree; however, genome sequencing is also a laborious and expensive process. Thus, conserved and ubiquitous gene data, which can be accessed with little effort, are generally used to minimize cost. Using16s rRNA is the most widely used method. In this study, 27 Salmonella genome sequences are annotated with RAST, and phylogenetic trees are constructed using three software, (phylip3.69, MEGA5.1, and CVTree). And MLST is also used to construct phylogenetic tree in this study, and the result is used to be compared with genome phylogenetic tree to find a more reliable reference tree. Although Neighbor-Joining method is the only algorithms x available in CVTree, phylip3.69 and MEGA5.1 are capable to use three separate algorithms(Maximum Parsimony, Maximum Likelihood, and Neighbor-Joining, respectively). Finally, these trees are compared in an effort to find a good alternative to replace the reference phylogenetic tree. In this study, it was determined that the groEL gene would be the best replacement.