The evolution of ribosomal DNA in Daphnia

已经观察到，基因组中多次出现的基因拷贝（多基因家族）在物种内彼此非常相似，即使不同物种中拷贝之间的相似性非常低。 这种现象被称为“协同进化”。核糖体DNA（rDNA）是一个多基因家族，在植物和动物细胞中存在数百至数千个拷贝，并编码构成核糖体的结构RNA分子（rRNA）：所有细胞中蛋白质合成的位点。 一个rDNA单元由3个编码rRNA分子的基因组成，这些基因被“间隔区”隔开。间隔区包含控制rRNA产生速率的序列。rDNA单元的某些区域在物种之间分化非常缓慢，而其他区域（如间隔区）分化非常迅速，即使在密切相关的物种之间也是如此。尽管这种快速的分歧，序列仍然保留了它们的功能。 我使用小型甲壳动物（水蚤）作为模型系统来研究rDNA的分子进化。我的工作目标是了解导致协同进化的分子过程与自然选择之间的相互作用，以维持rDNA和rRNA序列的功能。 我将研究rDNA拷贝数差异的影响，并在rDNA的分子重组率，水蚤物种之间的协同进化的速度，以及这些差异如何影响物种内rDNA拷贝之间的变化水平。 我还将确定自然选择作用于rDNA单元不同区域变异的相对强度。间隔区序列在物种之间差异非常迅速，但对它们与必须与它们结合以控制rRNA产生的蛋白质共同进化的方式知之甚少。 我计划鉴定这些蛋白质，并研究遗传变异对蛋白质与它们所结合的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.