MBE Advance Access originally published online on April 6, 2006
Molecular Biology and Evolution 2006 23(6):1269-1285; doi:10.1093/molbev/msk013
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Research Article |
Evolution of Paralogous Genes: Reconstruction of Genome Rearrangements Through Comparison of Multiple Genomes Within Staphylococcus aureus
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* Department of Medical Genome Sciences, Graduate School of Frontier Science, University of Tokyo, Tokyo, Japan; Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan; Division of Molecular Biology, Institute of Medical Science, University of Tokyo, Tokyo, Japan; Division of Pathology, Immunology and Microbiology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan; and || Laboratory of Genome Informatics, Natural Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
E-mail: ikobaya{at}ims.u-tokyo.ac.jp.
Analysis of evolution of paralogous genes in a genome is central to our understanding of genome evolution. Comparison of closely related bacterial genomes, which has provided clues as to how genome sequences evolve under natural conditions, would help in such an analysis. With species Staphylococcus aureus, whole-genome sequences have been decoded for seven strains. We compared their DNA sequences to detect large genome polymorphisms and to deduce mechanisms of genome rearrangements that have formed each of them. We first compared strains N315 and Mu50, which make one of the most closely related strain pairs, at the single-nucleotide resolution to catalogue all the middle-sized (more than 10 bp) to large genome polymorphisms such as indels and substitutions. These polymorphisms include two paralogous gene sets, one in a tandem paralogue gene cluster for toxins in a genomic island and the other in a ribosomal RNA operon. We also focused on two other tandem paralogue gene clusters and type I restriction-modification (RM) genes on the genomic islands. Then we reconstructed rearrangement events responsible for these polymorphisms, in the paralogous genes and the others, with reference to the other five genomes. For the tandem paralogue gene clusters, we were able to infer sequences for homologous recombination generating the change in the repeat number. These sequences were conserved among the repeated paralogous units likely because of their functional importance. The sequence specificity (S) subunit of type I RM systems showed recombination, likely at the homology of a conserved region, between the two variable regions for sequence specificity. We also noticed novel alleles in the ribosomal RNA operons and suggested a role for illegitimate recombination in their formation. These results revealed importance of recombination involving long conserved sequence in the evolution of paralogous genes in the genome.
Key Words: genome comparison • genome rearrangements • deletion • recombination • restriction-modification
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