GC-Biased Gene Conversion Impacts Ribosomal DNA Evolution in Vertebrates, Angiosperms, and Other Eukaryotes
GC-Biased Gene Conversion Impacts Ribosomal DNA Evolution in Vertebrates, Angiosperms, and Other Eukaryotes
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DOI：
10.1093/molbev/msr079
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发表时间：
2011-09-01
影响因子：
10.7
通讯作者：
Galtier, Nicolas
中科院分区：
文献类型：
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作者：
Escobar, Juan S.;Glemin, Sylvain;Galtier, Nicolas
核糖体DNA（rDNA）是真核生物中最保守的基因之一。基因组中rDNA的多个拷贝以协调一致的方式进化，通过不平等的交换和/或基因转换，这两种机制与同源重组有关。在几种生物体中，降解通过一种称为GC偏向基因转换（gBGC）的过程增加了局部GC含量。gBGC在哺乳动物、鸟类和草类中已得到很好的表征，但其在生命树中的系统发育分布知之甚少。在这里，我们测试的假设，重组影响18 S rDNA的碱基组成的演变，并检查这个彻底研究的分子作为真核生物中的gBGC标记的可靠性。脊椎动物和被子植物的18 S rDNA的系统发育分析显示，在这两个群体的基础组成的演变显着的异质性。哺乳动物、鸟类和草的18 S rDNA GC含量增加，与以前的全基因组分析一致。此外，我们观察到在Ostariophysi射线鳍鱼类和鸭嘴兽科单子叶植物中GC含量增加（即，包括禾本科植物在内的进化枝），表明这两个类群的基因组已经受到gBGC的影响。rDNA的多态性分析证实，gBGC，而不是突变偏倚，是这些模式的最合理的解释。我们还发现，核糖体RNA的二级结构的螺旋和环的网站不以相同的速度进化：环比螺旋进化得更快，而螺旋比环GC丰富。我们扩展分析的主要谱系的真核生物，并建议gBGC也可能影响基地组成贾第鞭毛虫（Diplomonadina），裸鳃腹足类（软体动物），和Asterozoa（Echinodermata）。
Ribosomal DNA (rDNA) is one of the most conserved genes in eukaryotes. The multiples copies of rDNA in the genome evolve in a concerted manner, through unequal crossing over and/or gene conversion, two mechanisms related to homologous recombination. Recombination increases local GC content in several organisms through a process known as GC-biased gene conversion (gBGC). gBGC has been well characterized in mammals, birds, and grasses, but its phylogenetic distribution across the tree of life is poorly understood. Here, we test the hypothesis that recombination affects the evolution of base composition in 18S rDNA and examine the reliability of this thoroughly studied molecule as a marker of gBGC in eukaryotes. Phylogenetic analyses of 18S rDNA in vertebrates and angiosperms reveal significant heterogeneity in the evolution of base composition across both groups. Mammals, birds, and grasses experience increases in the GC content of the 18S rDNA, consistent with previous genome-wide analyses. In addition, we observe increased GC contents in Ostariophysi ray-finned fishes and commelinid monocots (i.e., the clade including grasses), suggesting that the genomes of these two groups have been affected by gBGC. Polymorphism analyses in rDNA confirm that gBGC, not mutation bias, is the most plausible explanation for these patterns. We also find that helix and loop sites of the secondary structure of ribosomal RNA do not evolve at the same pace: loops evolve faster than helices, whereas helices are GC richer than loops. We extend analyses to major lineages of eukaryotes and suggest that gBGC might have also affected base composition in Giardia (Diplomonadina), nudibranch gastropods (Mollusca), and Asterozoa (Echinodermata).