MBE Advance Access published online on December 5, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl190
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© 2006 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.
Research Article |
Heterogeneity in Regional GC Content and Differential Usage of Codons and Amino Acids in GC-Poor and GC-Rich Regions of the Genome of Apis mellifera
1 Bioinformatics Research Center (BiRC), Department of Genetics and Ecology, University of Aarhus, Aarhus, Denmark
2 Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
* Corresponding author: email: frank{at}birc.au.dk, phone: (45) 89423131, Fax: (45) 89423077. Address: BiRC - Bioinformatics Research Center, University of Aarhus, Høegh-Guldbergs Gade 10, Building 1090, DK-8000 Århus C
The honeybee (Apis mellifera) has a genome with a wide variation in GC content showing two clear modal GC values, in some ways reminiscent of an isochore-like structure. To gain insight into causes and consequences of this pattern we used a comparative approach to study the genome-wide alignment of primarily coding sequence of A. mellifera with Drosophila melanogaster and Anopheles gambiae. The latter two species show a higher average GC content than A. mellifera and no indications of bimodality, suggesting that the GC-poor mode is a derived condition in honeybee. In A. mellifera, synonymous sites of genes generally adopt the GC content of the region in which they reside. A large proportion of genes in GC-poor regions have not been assigned to the honeybee assembly because of the low sequence complexity of their genome neighborhood. The synonymous substitution rate between A. mellifera and the other species is very close to saturation, but analyses of nonsynonymous substitutions as well as amino acid substitutions indicate that the GC-poor regions are not evolving faster than the GC-rich regions. We describe the codon usage and amino acid usage and show that they are remarkably heterogeneous within the honeybee genome between the two different GC-regions. Specifically, the genes located in GC-poor regions show a much larger deviation in both codon usage bias and amino acid usage from the Dipterans than do genes located in the GC-rich regions.
Key Words: Apis mellifera • GC content • Isochore • Codon Bias • Amino Acids
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