Genome-wide detection of selection and other evolutionary forces
Research output: Chapter in Book/Report/Conference proceeding › Book chapter › Research › peer-review
As is well known, pathogenic microbes evolve rapidly to escape from the host immune system and antibiotics. Genetic variations among microbial populations occur frequently during the long-term pathogen–host evolutionary arms race, and individual mutation beneficial for the fitness can be fixed preferentially. Many recent comparative genomics studies have pointed out the importance of selective forces in the molecular evolution of bacterial pathogens. The public availability of large-scale next-generation sequencing data and many state-of-the-art statistical methods of molecular evolution enable us to scan genome-wide alignments for evidence of positive Darwinian selection, recombination, and other evolutionary forces operating on the coding regions. In this chapter, we describe an integrative analysis pipeline and its application to tracking featured evolutionary trajectories on the genome of an animal pathogen. The evolutionary analysis of the protein-coding part of the genomes will provide a wide spectrum oof genetic variations that play potential roles in adaptive evolution of bacteria.
Original language | English |
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Title of host publication | Bacterial pangenomics : methods and protocols |
Editors | Alessio Mengoni, Marco Galardini, Marco Fondi |
Number of pages | 17 |
Publisher | Springer |
Publication date | 2015 |
Pages | 271-287 |
ISBN (Print) | 978-1-4939-1719-8 |
ISBN (Electronic) | 978-1-4939-1720-4 |
DOIs | |
Publication status | Published - 2015 |
Series | Methods in Molecular Biology |
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ISSN | 1064-3745 |
- Adaptive evolution, Bacteria, Intragenic homologous recombination, Positive selection, Sequence alignment
Research areas
ID: 153604954