Li Yi, Yang Rui-Heng, Jiang Lan, Hu Xiao-Di, Wu Zu-Jian, Yao Yi-Jian
Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agricultural and Forestry University, 350002 Fuzhou, China.
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China.
G3 (Bethesda). 2017 Aug 7;7(8):2695-2703. doi: 10.1534/g3.117.044016.
The nuclear ribosomal DNA (rDNA) is considered as a paradigm of concerted evolution. Components of the rDNA tandem repeats (45S) are widely used in phylogenetic studies of different organisms and the internal transcribed spacer (ITS) region was recently selected as a fungal DNA bar code. However, rRNA pseudogenes, as one kind of escape from concerted evolution, were reported in a wide range of organisms, especially in plants and animals. Moreover, large numbers of 5S rRNA pseudogenes were identified in several filamentous ascomycetes. To study whether rDNA evolves in a strict concerted manner and test whether rRNA pseudogenes exist in more species of ascomycetes, intragenomic rDNA polymorphisms were analyzed using whole genome sequences. Divergent rDNA paralogs were found to coexist within a single genome in seven filamentous ascomycetes examined. A great number of paralogs were identified as pseudogenes according to the mutation and secondary structure analyses. Phylogenetic analyses of the three rRNA coding regions of the 45S rDNA repeats, , 18S, 5.8S, and 28S, revealed an interspecies clustering pattern of those different rDNA paralogs. The identified rRNA pseudogenic sequences were validated using specific primers designed. Mutation analyses revealed that the repeat-induced point (RIP) mutation was probably responsible for the formation of those rRNA pseudogenes.
核糖体DNA（rDNA）被认为是协同进化的范例。rDNA串联重复序列（45S）的组成部分被广泛用于不同生物的系统发育研究，内部转录间隔区（ITS）最近被选作真菌DNA条形码。然而，rRNA假基因作为一种从协同进化中逃逸的类型，在广泛的生物中被报道，尤其是在植物和动物中。此外，在几种丝状子囊菌中鉴定出大量5S rRNA假基因。为了研究rDNA是否以严格的协同方式进化，并测试rRNA假基因是否存在于更多种类的子囊菌中，利用全基因组序列分析了基因组内rDNA多态性。在所检测的7种丝状子囊菌中，发现不同的rDNA旁系同源物共存于单个基因组中。根据突变和二级结构分析，大量旁系同源物被鉴定为假基因。对45S rDNA重复序列的三个rRNA编码区（18S、5.8S和28S）进行系统发育分析，揭示了这些不同rDNA旁系同源物的种间聚类模式。使用设计的特异性引物验证了鉴定出的rRNA假基因序列。突变分析表明，重复诱导点（RIP）突变可能是这些rRNA假基因形成的原因。
