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Pervasive indels and their evolutionary dynamics after the fish-specific genome duplication.
Baocheng Guo1, Ming Zou, Andreas Wagner
1Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
Molecular Biology and Evolution
|April 12, 2012
Summary
Insertions and deletions (indels) drive evolution in duplicate genes. These genetic variations accumulate rapidly after gene duplication, leading to significant protein structural changes and divergence.
Area of Science:
- Evolutionary Biology
- Genomics
- Molecular Biology
Background:
- Insertions and deletions (indels) are key drivers of genetic variation.
- The impact of indels on duplicate gene divergence remains largely unknown.
- Gene duplication events, like the fish-specific genome duplication (FSGD), create opportunities for evolutionary innovation.
Purpose of the Study:
- To investigate the role of indels in the divergence of duplicate genes.
- To quantify indel accumulation patterns after gene duplication.
- To understand how indels influence protein structure and sequence evolution in duplicate genes.
Main Methods:
- Analysis of thousands of duplicate genes across five fish species with sequenced genomes.
- Comparative genomics to identify and quantify indel accumulation.
- Examination of indel distribution in protein secondary structures and solvent accessibility.
Main Results:
- Duplicate genes exhibit at least 25% more indels than single-copy genes.
- Indels accumulated most rapidly in the first 40 million years post-FSGD.
- A consistent 30-80% excess of deletions over insertions was observed.
- Indel density correlates with DNA sequence divergence and explains tertiary structure divergence.
Conclusions:
- Indels play a significant role in the early evolution of duplicate genes.
- Relaxed selection likely permits indel accumulation in both gene copies.
- Indels are major contributors to evolutionary change and protein structural divergence in duplicate genes.
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