期刊
G3-GENES GENOMES GENETICS
卷 7, 期 8, 页码 2695-2703出版社
OXFORD UNIV PRESS INC
DOI: 10.1534/g3.117.044016
关键词
concerted evolution; genome sequencing; RIP; phylogeny; fungi
资金
- National Natural Science Foundation of China [31170017, 31400018, 30025002]
- Ministry of Science and Technology of China [2013BAD16B013, 2007BAI32B03]
- Qinghai Science and Technology Department [2014-NS-524, 2014-NS-525]
- Chinese Academy of Sciences [KSCX2-YW-G-076, KSCX2-SW-101C]
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, i.e., 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.
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