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MBE Advance Access originally published online on April 13, 2007
Molecular Biology and Evolution 2007 24(7):1443-1446; doi:10.1093/molbev/msm072
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© 2007 The Authors.
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Letters

Opposite Evolutionary Effects between Different Alternative Splicing Patterns

Feng-Chi Chen*, Shu-Miaw Chaw{dagger}, Yun-Huei Tzeng{ddagger}, Sheng-Shun Wang{ddagger} and Trees-Juen Chuang{ddagger}

* Division of Biostatistics and Bioinformatics, National Health Research Institutes, Miaoli County, Taiwan
{dagger} Research Center for Biodiversity, Academia Sinica, Taipei, Taiwan
{ddagger} Genomics Research Center, Academia Sinica, Taipei, Taiwan

E-mail: trees{at}gate.sinica.edu.tw.

Accepted for publication April 10, 2007.

Alternative splicing (AS) has been recognized as a mechanism of relaxing selection pressure on protein subsequences. Here, we show that AS may also yield contrary evolutionary effects. We compare the evolutionary rates of 2 types of alternatively spliced exons (ASEs)—simple and complex. The former does not change the boundaries of its flanking exons, whereas the latter does. By analyzing over 26,000 human–mouse orthologous exons, we demonstrate that complex ASEs have lower Ka and Ka/Ks ratio and higher Ks than constitutively spliced exons (CSEs), whereas simple ASEs have evolutionary rates to the opposite of CSEs. Our results indicate that complex ASEs are subject to stronger selection pressure than CSEs at the protein level, but the trend is reversed at the RNA level. Therefore, the previous view that ASEs accelerate evolution of protein subsequences needs to be modified.

Key Words: simple alternatively spliced exons • complex alternatively spliced exons • constitutively spliced exons • selective constraint • lineage specificity • comparative genomics

Sudhir Kumar, Associate Editor


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