Buckler E S, Ippolito A, Holtsford T P
Division of Biological Sciences, University of Missouri, Columbia 65211, USA.
Genetics. 1997 Mar;145(3):821-32. doi: 10.1093/genetics/145.3.821.
Although nuclear ribosomal DNA (rDNA) repeats evolve together through concerted evolution, some genomes contain a considerable diversity of paralogous rDNA. This diversity includes not only multiple functional loci but also putative pseudogenes and recombinants. We examined the occurrence of divergent paralogues and recombinants in Gossypium, Nicotiana, Tripsacum, Winteraceae, and Zea ribosomal internal transcribed spacer (ITS) sequences. Some of the divergent paralogues are probably rDNA pseudogenes, since they have low predicted secondary structure stability, high substitution rates, and many deamination-driven substitutions at methylation sites. Under standard PCR conditions, the low stability paralogues amplified well, while many high-stability paralogues amplified poorly. Under highly denaturing PCR conditions (i.e., with dimethylsulfoxide), both low- and high-stability paralogues amplified well. We also found recombination between divergent paralogues. For phylogenetics, divergent ribosomal paralogues can aid in reconstructing ancestral states and thus serve as good outgroups. Divergent paralogues can also provide companion rDNA phylogenies. However, phylogeneticists must discriminate among families of divergent paralogues and recombinants or suffer from muddled and inaccurate organismal phylogenies.
尽管核糖体DNA（rDNA）重复序列通过协同进化共同演化，但一些基因组含有大量同源rDNA的多样性。这种多样性不仅包括多个功能位点，还包括假定的假基因和重组体。我们研究了棉属、烟草属、摩擦禾属、林仙科和玉米核糖体内部转录间隔区（ITS）序列中不同的旁系同源物和重组体的出现情况。一些不同的旁系同源物可能是rDNA假基因，因为它们预测的二级结构稳定性低、替换率高，并且在甲基化位点有许多脱氨基驱动的替换。在标准PCR条件下，低稳定性的旁系同源物扩增良好，而许多高稳定性的旁系同源物扩增不佳。在高度变性的PCR条件下（即使用二甲基亚砜），低稳定性和高稳定性的旁系同源物都扩增良好。我们还发现了不同旁系同源物之间的重组。对于系统发育学来说，不同的核糖体旁系同源物有助于重建祖先状态，因此可作为良好的外类群。不同的旁系同源物也可以提供伴随的rDNA系统发育。然而，系统发育学家必须区分不同旁系同源物和重组体的家族，否则会得出混乱和不准确的生物系统发育。
