The evolution of ribosomal DNA in Daphnia

人们观察到，在基因组(多基因家族)中多次出现的基因拷贝在物种内彼此非常相似，即使不同物种中的拷贝之间的相似性很低。核糖体DNA(RDNA)是一个多基因家族，在植物和动物细胞中以数百到数千个拷贝存在，编码组成核糖体的结构RNA分子(RRNA)：所有细胞中蛋白质合成的场所。一个rDNA单位由3个基因组成，这些基因编码由间隔分子隔开的rRNA分子。间隔区含有控制rRNA产生速率的序列。RDNA单位的一些区域在不同物种之间分化非常缓慢，而其他区域，如间隔区，即使在关系密切的物种之间也会非常迅速地分化。尽管出现了这种快速的分化，但这些序列仍然保留了它们的功能。我使用小型甲壳类动物(水蚤)作为模型系统来研究rDNA的分子进化。我工作的目的是了解导致协同进化的分子过程与维持rDNA和rRNA序列功能的自然选择之间的相互作用。我将研究rDNA拷贝数和rDNA中分子重组速度的差异对水蚤物种间协同进化速率的影响，以及这些差异如何影响物种内rDNA拷贝之间的变异水平。我还将确定自然选择对rDNA单位不同区域变异的相对强度。间隔区序列在不同物种之间差异很大，但人们对它们与必须结合到它们上的蛋白质共同进化的方式知之甚少，以控制rRNA的产生。我计划鉴定这些蛋白质，并研究遗传变异对蛋白质和它们所结合的rDNA序列之间相互作用的影响。

It has been observed that copies of genes that are present many times within genomes (multigene families) are very similar to one another within species, even when similarity among copies in different species is very low.    This phenomenon is known as "concerted evolution". Ribosomal DNA (rDNA) is a multigene family that is present in hundreds to thousands of copies in plants and animal cells, and encodes the structural RNA molecules (rRNA) that make up ribosomes: the site of protein synthesis in all cells.  One rDNA unit consists of 3 genes that encode rRNA molecules separated by "spacers". The spacers contain sequences that control the rate of rRNA production. Some regions of the rDNA unit diverge between species very slowly while others, such as the spacers, diverge very rapidly, even among closely related species. Despite this rapid divergence, the sequences still retain their function.    I use small crustaceans (Daphnia) as a model system to study the molecular evolution of rDNA. The goal of my work is to understand the interaction between the molecular processes that cause concerted evolution, and natural selection to maintain the function of the rDNA and rRNA sequences.  I will study the impact of differences in rDNA copy number, and in the rate of molecular recombination in rDNA, on rates of concerted evolution between Daphnia species, and how these differences influence levels of variation among rDNA copies within species.  I will also determine the relative intensity with which natural selection acts on variation in different regions of the rDNA unit. The spacer sequences diverge very rapidly between species but little is known about the way they co-evolve with the proteins that must bind to them in order to control rRNA production.  I plan to identify these proteins and study the impact of genetic variation on the interaction between the proteins and the rDNA sequences to which they bind.