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Updated: Jul 16, 2026
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Methodology for the Study of Horizontal Gene Transfer in Staphylococcus aureus
Published on: March 10, 2017
Global extent of horizontal gene transfer
1Physical Biosciences Division, Lawrence Berkeley National Laboratory and Department of Chemistry, University of California, Berkeley, CA 94720, USA.
Summary
Horizontal gene transfer (HGT) is not rampant across all species but significantly impacts Archaea and Bacteria at the domain level. HGT has minimal effect on organismal phylogeny construction.
Area of Science:
- Genomics
- Evolutionary Biology
- Bioinformatics
Background:
- Horizontal gene transfer (HGT) is recognized for its role in species evolution and genome innovation.
- Previous research provided evidence for HGT in specific genes but lacked a global estimate.
- The overall extent of HGT across diverse organisms remains largely unquantified.
Purpose of the Study:
- To develop a method for identifying HGT events within protein families.
- To estimate the global prevalence of HGT across all Pfam protein domain families.
- To assess the impact of HGT on genome evolution and organismal phylogeny.
Main Methods:
- Developed a novel method to detect HGT events within protein families.
- Applied the method to approximately 8,000 curated protein domain families in the Pfam database.
- Analyzed HGT prevalence across three distinct taxonomic ranges.
Main Results:
- HGT is not a widespread phenomenon between distantly related organisms, affecting only 1.1-9.7% of surveyed Pfam families.
- Over 50% of Archaea and 30-50% of Bacteria possess protein domains acquired via HGT, compared to less than 10% in Eukarya.
- No significant preference for HGT was observed across protein families with specific cellular or molecular functions.
Conclusions:
- While not rampant globally, HGT significantly contributes to domain acquisition in Archaea and Bacteria.
- HGT has a negligible impact on phylogenetic analyses that utilize whole genomes, numerous common genes, or SSU rRNAs.
- The study provides a quantitative framework for understanding the global extent and impact of HGT in molecular evolution.
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