Low codon bias and high rates of synonymous substitution in Drosophila hydei and D. melanogaster histone genes.
Low codon bias and high rates of synonymous substitution in Drosophila hydei and D. melanogaster histone genes.
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DOI：
10.1093/oxfordjournals.molbev.a040011
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发表时间：
1993-03
影响因子：
10.7
通讯作者：
D. Fitch;L. Strausbaugh
中科院分区：
文献类型：
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作者：
D. Fitch;L. Strausbaugh
我们对果蝇组蛋白基因的密码子使用偏好性进行了评估，并获得了5,161个碱基组蛋白基因重复单位的核苷酸序列。该重复序列包含所有五种组蛋白(H1、H_2A、H_2B、H_3和H_4)的基因，与以前报道的不同之处在于有第二个EcoRI位点。这些D.hydei重复序列已经相互比对，并与来自D.Blackogaster的5.0kb(即长的)和4.8kb(即短的)组蛋白重复类型比对。在每个物种中，同义位点的碱基组成与平均基因组组成相似，并接近组蛋白基因重复序列的小基因间隔区的碱基组成。在物种分化后，同义位置的同义变化累积相当高。这两个特征与与其他果蝇基因相比，在这些基因中观察到的相对较低的密码子使用偏向是一致的。因此，在果蝇中大量表达的基因具有高度的密码子偏好性和低的沉默替换率的概括并不适用于组蛋白基因。
We have evaluated codon usage bias in Drosophila histone genes and have obtained the nucleotide sequence of a 5,161-bp D. hydei histone gene repeat unit. This repeat contains genes for all five histone proteins (H1, H2a, H2b, H3, and H4) and differs from the previously reported one by a second EcoRI site. These D. hydei repeats have been aligned to each other and to the 5.0-kb (i.e., long) and 4.8-kb (i.e., short) histone repeat types from D. melanogaster. In each species, base composition at synonymous sites is similar to the average genomic composition and approaches that in the small intergenic spacers of the histone gene repeats. Accumulation of synonymous changes at synonymous sites after the species diverged is quite high. Both of these features are consistent with the relatively low codon usage bias observed in these genes when compared with other Drosophila genes. Thus, the generalization that abundantly expressed genes in Drosophila have high codon bias and low rates of silent substitution does not hold for the histone genes.