Jørgensen Frank Grønlund, Schierup Mikkel Heide, Clark Andrew G
Bioinformatics Research Center, Department of Genetics and Ecology, University of Aarhus, Aarhus, Denmark.
Mol Biol Evol. 2007 Feb;24(2):611-9. doi: 10.1093/molbev/msl190. Epub 2006 Dec 5.
The honeybee (Apis mellifera) has a genome with a wide variation in GC content showing 2 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 2 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 2 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 the genes located in the GC-rich regions.
蜜蜂（西方蜜蜂）的基因组在GC含量上有很大差异，呈现出2个明显的模态GC值，在某些方面让人联想到等容线样结构。为了深入了解这种模式的成因和后果，我们采用了一种比较方法来研究西方蜜蜂主要编码序列与黑腹果蝇和冈比亚按蚊的全基因组比对。后两个物种的平均GC含量高于西方蜜蜂，且没有双峰性的迹象，这表明GC含量低的模式是蜜蜂的一种衍生状态。在西方蜜蜂中，基因的同义位点通常采用其所在区域的GC含量。由于基因组邻域的序列复杂性低，GC含量低区域的很大一部分基因尚未被分配到蜜蜂基因组组装中。西方蜜蜂与其他物种之间的同义替换率非常接近饱和，但非同义替换以及氨基酸替换的分析表明，GC含量低的区域进化速度并不比GC含量高的区域快。我们描述了密码子使用和氨基酸使用情况，并表明在蜜蜂基因组中，这两个不同GC区域之间它们存在显著差异。具体而言，与位于GC含量高区域的基因相比，位于GC含量低区域的基因在密码子使用偏好和氨基酸使用方面与双翅目昆虫的偏差要大得多。
