Comparative Genomics

Volume 396 of the series Methods In Molecular Biology™ pp 135-152

Analyzing Patterns of Microbial Evolution Using the Mauve Genome Alignment System

  • Aaron E DarlingAffiliated withDepartment of Computer Scienc, University of Wisconsin-Madison
  • , Todd J TreangenAffiliated withDepartment of Software, Technical University of Catalonia-Barcelona
  • , Xavier MesseguerAffiliated withDepartment of Software, Technical University of Catalonia-Barcelona, Barcelona Supercomputing Center (BSC)
  • , Nicole T PernaAffiliated withDepartment of Animal Health and Biomedical Sciences Genome Center, University of Wisconsin-Madison

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During the course of evolution, genomes can undergo large-scale mutation events such as rearrangement and lateral transfer. Such mutations can result in significant variations in gene order and gene content among otherwise closely related organisms. The Mauve genome alignment system can successfully identify such rearrangement and lateral transfer events in comparisons of multiple microbial genomes even under high levels of recombination. This chapter outlines the main features of Mauve and provides examples that describe how to use Mauve to conduct a rigorous multiple genome comparison and study evolutionary patterns.

Key Words

Microbial evolution sequence alignment comparative genomics genome alignment genome rearrangement lateral transfer Yersinia pestis