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Related Experiment Videos

Bootstrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses.

Olga Zhaxybayeva1, J Peter Gogarten

  • 1Department of Molecular and Cell Biology, University of Connecticut, 75 North Eagleville Road Storrs, CT 06269-3044, USA. olga@carrot.mcb.uconn.edu

BMC Genomics
|March 29, 2002
PubMed
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Horizontal gene transfer (HGT) creates mosaic microbial genomes. New tools map gene evolution, revealing that prokaryotic genomes have diverse evolutionary histories, not a single tree-like pattern.

Area of Science:

  • Genomics
  • Microbial Evolution
  • Bioinformatics

Background:

  • Horizontal gene transfer (HGT) significantly shapes microbial genomes.
  • HGT impacts not only accessory genes but also core genes, including those for information processing and ribosomal RNA.
  • Understanding the mosaic nature of microbial genomes is crucial for evolutionary studies.

Purpose of the Study:

  • To develop and assess tools for analyzing the mosaic structure of microbial genomes.
  • To provide graphic illustrations of genome evolution.
  • To compare different phylogenetic mapping techniques for analyzing gene transfer.

Main Methods:

  • Adapted Maximum Likelihood (ML) mapping for analyzing quartets of orthologous genes across multiple genomes.
  • Automated the assembly and analysis of orthologous gene quartets.

Related Experiment Videos

  • Compared ML mapping with Bayesian probability and Bootstrap mapping techniques.

    • Main Results:

    • ML mapping, Bayesian, and Bootstrap approaches yielded qualitatively equivalent results in phylogenetic analysis.
    • Mitochondrial genomes, assumed to be single linkage groups, were used to test the tools.
    • Analysis revealed complex evolutionary histories within prokaryotic genomes.

    Conclusions:

    • Prokaryotic genomes are mosaics with different evolutionary trajectories for various gene sets.
    • Phylogenetic relationships cannot be solely inferred from a core set of rarely transferred genes.
    • Probability mapping is an effective tool for exploring the mosaic nature of genomes and understanding horizontal gene transfer.