The Bioinformatics Method For Comparative Genomics & Complete Genome Sequence Of Methylacidiphilum Inferorum V4, Escherichia Coli O55:H7 CB9615 And K-12 BW2952 And Its Derivatives

There have been about twenty years since the emergency of the genomics. More and more genomes were sequenced after the application of new generation sequencing method in 2004. How to deal with these massive genomic data becomes the most important problem in the post-genomic researches.Both of the two new bioinformatic methods in this work can greatly improve the comparative genomic analysis. Using these methods, together with other functional and comparative genomics methods, we analyzed 8 bacterial genomes and deduced the evolution and charatistic of them.Due to these methods and researches, we improved our knowledges, especially on the genetic nature of micro-organisms.â… Due to the development of high-throughput sequencing and the explosion of completed genomes, comparative genomics becomes more and more important at the post-genomic Era. Comparative genomics compares the genomes from different organisms to re-construct their phylogenic relationships and differences in genotypes, as well as the potential changes in phenotypes. The detection of orthologs is the basis of comparative genomics and other further researches. However, all the present methods for the detection of orthologs are based on the given annotations, which are full of errors.Using the Escherichia coli and archaea, we designed a new ortholog detect method that compares genes against genomes directly. We apply tblastn to predict putative homologs, use Inparanoid to generate ortholog pairs, and finally cluster the pairs and generate the ortholog groups using MCL method.This method does not need original annotation and can find much larger core-genomes in both E. coli and archaea. The phylogenic relationships of both of the species were re-build and gene contraction was found in E. coli.â…¡A key problem in comparative genomics is to rebuild the phylogenic relationships. The basis of the phylogenetic analysis is the base changes in the DNA or amino acid sequences. Mutation is one of the important power to cause base changes and lead to a tree-like structure in the evolution of an organism. However, recombination can bring in foreign fragments that carry many base changes in a very short time. These two types of base changes can not be easily identified and will interrupt our phylogenetic analysis.The Poisson model was imported to describe the random mutations in this part. Then the recombinations and mutations can be identified using statistic method. The MaxFisher method was adopted to verify the bounders and differ the genome to be alternative recombinant or mutational blocks.We can rebuild the tree phylogenetic relationships using the mutations. We found the recombinations affect not only the branch length, but also the topology of the tree.â…¢Methylacidiphilum inferorum V4 can oxidation methane in the extremely acidophilic environment of the geothermal area, from which tons of methane was emitted per year. Previous researches have failed to detect any methanotroph in the extremely acidophilic geothermal area and all known methanotrophs have a lower limit of pH 4.0.We isolated and sequenced the genome of Methylacidiphilum inferorum V4, which can ultilize methane at a low pH of 2.0-2.5, and found a new pathway involved in methanotrophy. We also analyzed the central metabolic pathway and some other important pathways, and found that the genome of V4 was constructed by many LGT events. IVThere have been no genome studies of closely related clones which aimed at exposing the details of evolutionary change in evolution. E. coli O157:H7 is important EHEC that cause epidemics over the world. It is most related to 055:H7, which belongs to another pathogenic type of E. coli. The differences of the characteristic in these two lineages are caused by genetics differences in their genomes.We sequenced an 055:H7 strain and compared it to 2 completed O157:H7 genomes based on proteomics and bioinformatics results. We were able to allocate most of the genetic changes, including indels, mutations and recombinations, to different lineages. We estimated their divergence time based on the synonymous mutations. We also explored the recombination rate in 3 closely related ExPEC strains.The major difference between O55:H7 and 0157:117 is the recombinational event that shifts the O-antigen. Other than that, a unique T2SS is present in the chromosome of O55:H7. There are more T3SS effectors in O157:H7 than in O55:H7. The prophages in their chromosomes are greatly changed, as well. They were thought to be diverged within 400 years if we calculated based on the mutation rate from our previous researches on Vibrio cholerae. And the divergence time is 14k to 70k years if we using traditional mutation rate.VThe E. coli K-12 strain MC4100 is one of the mostly used type strains in the labs. The K-12 strains are kept on plates and many record or unknown genetic changes occur until the 1980s, from when the lyophilization was used to store the bacterium. These genetic changes cause the differences of the genotypes and phenotypes, especially the global regulations, in different K-12 strains.We sequenced the genome of K-12 strain MC4100 and compared it to other 3 completed K-12 genomes.194 SNPs and many indels events were found between those genomes.Many phenotype differences can be related to these SNPs and indels. However, the effect of most of these changes kept unknown. Most of these changes occur randomly and spontaneously rather than manual operations. We must consider the genetic differences before our explanation of the experiments using these K-12 strains.â…¥The theoretical basis of the evolutionary divergence has been discussed in the past century. Traditionally we believed the divergence is due to the complicated adaptation pressure in the environment. However, recent researches proved that the organisms trend to diverged events in a simple constant environment.The genome sequencing and proteomic researches were applied on 5 phenotypical different derivatives of the E. coli MC4100 that were cultured in Pi-limited chemostat environment for 37 days. We found the E. coli mutated different regulatory genes that related to rpoS to fit the environment. This study indicates the E. coli can increase their fitness to environment by changing different regulatory genes.