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MBE Advance Access originally published online on August 11, 2004
Molecular Biology and Evolution 2004 21(12):2202-2209; doi:10.1093/molbev/msh230
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Molecular Biology and Evolution vol. 21 no. 12 © Society for Molecular Biology and Evolution 2004; all rights reserved.

Research Article

Nonneutral Evolution of the Transcribed Pseudogene Makorin1-p1 in Mice

Ondrej Podlaha and Jianzhi Zhang

Department of Ecology and Evolutionary biology, University of Michigan, Ann Arbor

E-mail: jianzhi{at}umich.edu.

Pseudogenes are nonfunctional relics of formerly functional genes and are thought to evolve neutrally. In some pseudogenes, however, the molecular evolutionary patterns are atypical of neutrally evolving sequences, exhibiting sequence conservation, codon-usage bias, and other features associated with functional genes. Makorin1-p1 is a transcribed pseudogene first identified in the mouse Mus musculus. The transcript of Makorin1-p1 can regulate the stability of the transcript of its paralogous functional gene Makorin1. Specifically, the half-life of Makorin1 mRNA increases significantly in the presence of Makorin1-p1 transcript, and targeted deletion of Makorin1-p1 is lethal in mice. Here, we show that Makorin1-p1 originated after the separation of Mus and Rattus but before the divergence of M. musculus and M. pahari. The transcribed region of Makorin1-p1 exhibits rates of point and indel substitutions that are two to four times lower than those in the untranscribed region, suggesting that the transcribed region is under functional constraint and is not evolving neutrally. Although the transcript of Makorin1-p1 likely functions by its sequence similarity to Makorin1, we find no evidence of gene conversion between them, indicating that functional conservation alone is sufficient to maintain their coordinated evolution. A duplication-degeneration model is proposed to explain how Makorin1-p1 was co-opted into the regulatory system of Makorin1. There are over 10,000 pseudogenes in a typical mammalian genome, and it is plausible that many functional but untranslatable pseudogenes exist. Our results illustrate the potential of using evolutionary analysis to identify such pseudogenes from genome sequences.

Key Words: substitution rate • neutrality • pseudogene • Makorin • rodents • mice


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