Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes
Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes
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DOI：
10.1101/gr.6249707
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发表时间：
2007-12-01
期刊：
影响因子：
7
通讯作者：
Ponting, Chris P.
中科院分区：
文献类型：
--
作者：
Heger, Andreas;Ponting, Chris P.
新近测序的11个果蝇物种的基因组序列为研究近亲物种进化速率的变化提供了第一次机会。利用已建立的黑腹果蝇基因作为模板预测蛋白质编码基因，根据物种差异和基因组组装质量，回收率在81%-97%之间。在不同的果蝇物种中，正畸和类群分配是自洽的，并且与保守基因顺序（synteny blocks）的区域一致。接下来，我们研究了这些物种的基因库在氨基酸替换和基因复制方面的多样化率。氨基酸序列的限制似乎在D. ananassae上最明显，而在D. simulans和D. erecta末端谱系上最不明显。研究发现，在免疫反应和RNA代谢中发挥作用的基因中，预测受到正选择影响的密码子明显过多，后者包括Dicer-2/r2d2异源二聚体的每个亚基。绝大多数基因重复（96.5%）和同源重排发生在单个Muller元件中。我们表明，古代基因复制的速率是相对统一的。然而，末端谱系中的基因复制强烈倾向于最近发生的事件，这与快速出生和快速死亡模型相一致，或者在这些果蝇种群中存在大量拷贝数可变基因。胰蛋白酶样蛋白酶和DM8假定的脂质结合结构域蛋白之间的重复更为频繁。
The newly sequenced genome sequences of 11 Drosophila species provide the first opportunity to investigate variations in evolutionary rates across a clade of closely related species. Protein-coding genes were predicted using established Drosophila melanogaster genes as templates, with recovery rates ranging from 81%-97% depending on species divergence and on genome assembly quality. Orthology and paralogy assignments were shown to be self-consistent among the different Drosophila species and to be consistent with regions of conserved gene order ( synteny blocks). Next, we investigated the rates of diversification among these species' gene repertoires with respect to amino acid substitutions and to gene duplications. Constraints on amino acid sequences appear to have been most pronounced on D. ananassae and least pronounced on D. simulans and D. erecta terminal lineages. Codons predicted to have been subject to positive selection were found to be significantly over-represented among genes with roles in immune response and RNA metabolism, with the latter category including each subunit of the Dicer-2/r2d2 heterodimer. The vast majority of gene duplications ( 96.5%) and synteny rearrangements were found to occur, as expected, within single Muller elements. We show that the rate of ancient gene duplications was relatively uniform. However, gene duplications in terminal lineages are strongly skewed toward very recent events, consistent with either a rapid-birth and rapid-death model or the presence of large proportions of copy number variable genes in these Drosophila populations. Duplications were significantly more frequent among trypsin-like proteases and DM8 putative lipid-binding domain proteins.