The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genomes: an example from freshwater stingrays.
The 5S rDNA family evolves through concerted and birth-and-death evolution in fish genomes: an example from freshwater stingrays.
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DOI：
10.1186/1471-2148-11-151
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发表时间：
2011-05-31
影响因子：
3.4
通讯作者：
Martins C
中科院分区：
文献类型：
--
作者：
Pinhal D;Yoshimura TS;Araki CS;Martins C
众所周知，核糖体5S基因在核糖体折叠和功能中起着关键作用。这些基因被认为以一种协调一致的方式进化，具有较高的基因拷贝同质化率。然而，之前大多数关于rDNA重复序列进化过程的分析都是在无脊椎动物和植物中进行的。对脊椎动物也进行了研究，但这些分析通常仅限于18S、5.8S和28S rRNA基因。最近在板鳃鱼和硬骨鱼基因组中发现了不同的5S rRNA基因同源物，这表明真核生物5S rRNA基因家族的基因组组织比以前认为的要复杂得多。来自硬骨鱼和板鳃动物等低等脊椎动物的新序列数据的可用性，使5S rDNA在脊椎动物之间的进化特征得到增强。我们在黄貂鱼基因组中发现了两个5S rDNA序列变异类，与其他脊椎动物的基因组相似。其中一类5S rRNA基因仅为板鳃虫所共有。一项对100种脊椎动物的广泛比较研究表明，鱼类5S rRNA基因变异起源于几轮基因组重复。在激烈的净化选择下，这些变异通过生与死机制得以维持或消除。5S rDNA变异的聚集性多拷贝可能是由于不平等杂交机制而产生的。同时，不同的基因组簇被独立均质化，导致通过协同进化维持高度相似重复的簇。我们认为，鱼类基因组5S rDNA的分子进化是由生与死和协同进化相结合的混合机制驱动的。
Ribosomal 5S genes are well known for the critical role they play in ribosome folding and functionality. These genes are thought to evolve in a concerted fashion, with high rates of homogenization of gene copies. However, the majority of previous analyses regarding the evolutionary process of rDNA repeats were conducted in invertebrates and plants. Studies have also been conducted on vertebrates, but these analyses were usually restricted to the 18S, 5.8S and 28S rRNA genes. The recent identification of divergent 5S rRNA gene paralogs in the genomes of elasmobranches and teleost fishes indicate that the eukaryotic 5S rRNA gene family has a more complex genomic organization than previously thought. The availability of new sequence data from lower vertebrates such as teleosts and elasmobranches enables an enhanced evolutionary characterization of 5S rDNA among vertebrates. We identified two variant classes of 5S rDNA sequences in the genomes of Potamotrygonidae stingrays, similar to the genomes of other vertebrates. One class of 5S rRNA genes was shared only by elasmobranches. A broad comparative survey among 100 vertebrate species suggests that the 5S rRNA gene variants in fishes originated from rounds of genome duplication. These variants were then maintained or eliminated by birth-and-death mechanisms, under intense purifying selection. Clustered multiple copies of 5S rDNA variants could have arisen due to unequal crossing over mechanisms. Simultaneously, the distinct genome clusters were independently homogenized, resulting in the maintenance of clusters of highly similar repeats through concerted evolution. We believe that 5S rDNA molecular evolution in fish genomes is driven by a mixed mechanism that integrates birth-and-death and concerted evolution.
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