MBE Advance Access published online on October 1, 2003
Molecular Biology and Evolution, doi:10.1093/molbev/msg243
Molecular Biology and Evolution © Society for Molecular Biology and Evolution 2003; all rights reserved
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1 Laboratory of Biometrics and Bioinformatics, Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan; Institute for Bioinformatics Research and Development (BIRD), Japan Science and Technology Corporation (JST), Japan
* To whom correspondence should be addressed. E-mail: zzhang{at}lbm.ab.a.u-tokyo.ac.jp.
In some Drosophila species, there are two types of greatly diverged amylase (Amy) genes (Amy clusters 1 and 2), each encoding active amylase isozymes. Cluster 1 is located at the middle of its chromosomal arm, and the region has a normal local recombination rate. However, cluster 2 is near the centromere, and this region is known to have a reduced recombination rate. Although nonsynonymous substitutions follow a molecular clock, synonymous substitutions were accelerated in cluster 2 after gene duplications. This resulted in a higher GC content at the third codon position (GC3) and codon usage bias in cluster 1, and lower GC3 content and codon usage bias in the cluster 2. However, no systematic difference in GC content was observed in the first and second codon positions or the 3'-flanking regions. Therefore, differences in local recombination rate rather than mutation bias might explain the divergence at synonymous sites between the two Amy clusters within species (Hill-Robertson effect). Alternatively, the different patterns and levels of expression between the two clusters may imply that the reduced expression level in cluster 2 caused by chromatin potentiation decreased the codon bias. Both of these hypotheses imply the importance of the genomic background as a driving force of divergence between non-tandemly duplicated genes. Key Words:
amylase, duplicated genes, genomic background, evolutionary fate, Drosophila
© 2003 Society for Molecular Biology and Evolution
Original Articles
Genomic Background Drives the Divergence of Duplicated Amylase Genes at Synonymous Sites in Drosophila
2 Laboratory of Biometrics and Bioinformatics, Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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