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Origin and evolution of new exons in rodents
Wen Wang1, Hongkun Zheng, Shuang Yang
1CAS-Max Planck Junior Research Group, Key Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China. wwang@mail.kiz.ac.cn
Genome Research
|August 20, 2005
Summary
New gene evolution is key to life's diversity. Researchers found that new exons, the building blocks of genes, originate rapidly, often from non-coding DNA, and are shaped by positive selection.
Area of Science:
- Evolutionary Biology
- Genomics
- Molecular Biology
Background:
- New gene origination is a fundamental process in evolution, driving biodiversity.
- Exon shuffling is a known mechanism for new gene formation, but exon origin and evolution remain unclear.
Purpose of the Study:
- To investigate the origin, evolution, and rate of new exons in mammals.
- To understand the evolutionary forces driving the rapid divergence of new exons.
Main Methods:
- Comparative genomics analysis of expressed sequences from human, mouse, and rat.
- Utilized pig expressed sequence tags (ESTs) as an outgroup for phylogenetic analysis.
- Quantified new exon origination rates and evolutionary rates (Ka/Ks ratios).
Main Results:
- Identified 2695 newly evolved exons in mouse and rat compared to human.
- Calculated a new exon origination rate of approximately 2.71 x 10^-3 per gene per million years.
- Observed accelerated rates of nonsynonymous substitutions and indels in new exons, with higher Ka/Ks ratios, suggesting positive selection.
- Found that most new exons are unique, likely originating from intronic sequences ('exonization'), and often function as alternative exons expressed at low levels.
Conclusions:
- New exons originate at a significant rate and evolve rapidly, driven by positive selection.
- Exonization of intronic sequences is a major source of novel exons.
- These newly evolved exons contribute to genomic novelty and potentially adaptive evolution.