Evolution of a Distinct Genomic Domain in Drosophila: Comparative Analysis of the Dot Chromosome in Drosophila melanogaster and Drosophila virilis
Evolution of a Distinct Genomic Domain in Drosophila: Comparative Analysis of the Dot Chromosome in Drosophila melanogaster and Drosophila virilis
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DOI：
10.1534/genetics.110.116129
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发表时间：
2010-08-01
期刊：
影响因子：
3.3
通讯作者：
Elgin, Sarah C. R.
中科院分区：
文献类型：
--
作者：
Leung, Wilson;Shaffer, Christopher D.;Elgin, Sarah C. R.
黑腹果蝇第四条染色体的远臂（“点”）是不寻常的，因为它表现出异染色质的混合特性（例如，例如，在一个实施例中，致密包装、后期复制）和常色性（例如，例如，在一个实施例中，基因密度类似于常染色质结构域，在多聚化期间复制）。为了研究这个不寻常的结构域的进化，我们通过生成高质量的序列数据和手动管理D. virilis（Tucson菌株15010-1051.88）。我们的分析表明，D. melanogaster和D.与参考常染色质结构域相比，男性化具有更高的重复密度、更大的基因大小、更低的密码子偏好性和更高的基因重排率。对8个“流浪者”基因（存在于一个物种的常染色质染色体臂上，另一个物种的点染色体上）的分析表明，它们的特征与同一结构域中的其他基因相似，这表明这些特征是结构域的特征，而不是这些基因发挥功能所必需的。对该菌株进行了比较。virilis与果蝇12基因组联盟测序的菌株（Tucson菌株15010-1051.87）的比较表明，点上的大多数基因处于弱纯化选择下。总的来说，尽管这个结构域具有异染色质样的特性，但点上的基因在进化的同时对局部环境的变化做出反应，以维持功能。
The distal arm of the fourth ("dot") chromosome of Drosophila melanogaster is unusual in that it exhibits an amalgamation of heterochromatic properties (e. g., dense packaging, late replication) and euchromatic properties (e. g., gene density similar to euchromatic domains, replication during polytenization). To examine the evolution of this unusual domain, we undertook a comparative study by generating high-quality sequence data and manually curating gene models for the dot chromosome of D. virilis (Tucson strain 15010-1051.88). Our analysis shows that the dot chromosomes of D. melanogaster and D. virilis have higher repeat density, larger gene size, lower codon bias, and a higher rate of gene rearrangement compared to a reference euchromatic domain. Analysis of eight "wanderer" genes (present in a euchromatic chromosome arm in one species and on the dot chromosome in the other) shows that their characteristics are similar to other genes in the same domain, which suggests that these characteristics are features of the domain and are not required for these genes to function. Comparison of this strain of D. virilis with the strain sequenced by the Drosophila 12 Genomes Consortium (Tucson strain 15010-1051.87) indicates that most genes on the dot are under weak purifying selection. Collectively, despite the heterochromatin-like properties of this domain, genes on the dot evolve to maintain function while being responsive to changes in their local environment.