Cronn R C, Zhao X, Paterson A H, Wendel J F
Department of Botany, Iowa State University, Ames, IA 50011, USA.
J Mol Evol. 1996 Jun;42(6):685-705. doi: 10.1007/BF02338802.
5S RNA genes and their nontranscribed spacers are tandemly repeated in plant genomes at one or more chromosomal loci. To facilitate an understanding of the forces that govern 5S rDNA evolution, copy-number estimation and DNA sequencing were conducted for a phylogenetically well-characterized set of 16 diploid species of cotton (Gossypium) and 4 species representing allopolyploid derivatives of the diploids. Copy number varies over twentyfold in the genus, from approximately 1,000 to 20,000 copies/2C genome. When superimposed on the organismal phylogeny, these data reveal examples of both array expansion and contraction. Across species, a mean of 12% of nucleotide positions are polymorphic within individual arrays, for both gene and spacer sequences. This shows, in conjunction with phylogenetic evidence for ancestral polymorphisms that survive speciation events, that intralocus concerted evolutionary forces are relatively weak and that the rate of interrepeat homogenization is approximately equal to the rate of speciation. Evidence presented also shows that duplicated 5S rDNA arrays in allopolyploids have retained their subgenomic identity since polyploid formation, thereby indicating that interlocus concerted evolution has not been an important factor in the evolution of these arrays. A descriptive model, one which incorporates the opposing forces of mutation and homogenization within a selective framework, is outlined to account for the empirical data presented. Weak homogenizing forces allow equivalent levels of sequence polymorphism to accumulate in the 5S gene and spacer sequences, but fixation of mutations is nearly prohibited in the 5S gene. As a consequence, fixed interspecific differences are statistically underrepresented for 5S genes. This result explains the apparent paradox that despite similar levels of gene and spacer diversity, phylogenetic analysis of spacer sequences yields highly resolved trees, whereas analyses based on 5S gene sequences do not.
5S核糖体RNA基因及其非转录间隔区在植物基因组中的一个或多个染色体位点上串联重复。为了便于理解控制5S核糖体DNA进化的力量，对一组系统发育特征明确的16个二倍体棉花（棉属）物种和4个代表二倍体异源多倍体衍生物的物种进行了拷贝数估计和DNA测序。该属的拷贝数变化超过20倍，从大约1000个拷贝/2C基因组到20000个拷贝/2C基因组。当这些数据叠加在生物系统发育树上时，揭示了阵列扩张和收缩的例子。在所有物种中，基因和间隔区序列的单个阵列内平均有12%的核苷酸位置是多态的。结合物种形成事件中幸存的祖先多态性的系统发育证据来看，这表明基因座内协同进化力量相对较弱，重复序列间的同质化速率大约等于物种形成速率。所提供的证据还表明，异源多倍体中重复的5S核糖体DNA阵列自多倍体形成以来保留了它们的亚基因组特性，从而表明基因座间协同进化在这些阵列的进化中并不是一个重要因素。本文概述了一个描述性模型，该模型在一个选择性框架内纳入了突变和同质化的相反力量，以解释所呈现的实证数据。较弱的同质化力量使得5S基因和间隔区序列中能够积累同等水平的序列多态性，但5S基因中几乎禁止突变的固定。因此，5S基因的种间固定差异在统计学上代表性不足。这一结果解释了一个明显的悖论，即尽管基因和间隔区的多样性水平相似，但基于间隔区序列的系统发育分析产生的树分辨率很高，而基于5S基因序列的分析则不然。
