Xu Jianpeng, Zhang Quanqi, Xu Xiaofei, Wang Zhigang, Qi Jie
Key Lab of Marine Genetics and Gene Resource Exploitation, Ministry of Education, College of Marine Life Science, Ocean University of China, No. 5 Yushan Road, Qingdao 266003, PR China.
Mol Phylogenet Evol. 2009 Jul;52(1):157-66. doi: 10.1016/j.ympev.2009.03.031. Epub 2009 Apr 5.
Molecular study of Stone flounder Kareius bicoloratus revealed a high level of intra-individual polymorphism of ribosomal DNA (18S rDNA, ITS1 and 5.8S rDNA). This polymorphism includes not only multiple functional genes but also putative pseudogenes and recombinants. Three major types (Type I, II and III) of 18S rDNA differing in lengths coexisted in the genome of each studied individual. Type II and Type III have a 15-bp-deletion and Type III has an additional 7-bp-deletion relative to Type I. Expression analyses gave clear evidence that Type I 18S rDNA was abundantly expressed. In contrast, transcription of Type II and III 18S rDNA were not detected. Further sequence analysis revealed that Type I was the expected and functional 18S rDNA in K. bicoloratus, while Type II and Type III were pseudogenes. Phylogeny of the ITS1 sequences formed three groups (Group I, II and III), of which Group I linking with Type I 18S rDNA were functional, whereas the remaining two Groups (II and III) linking with Type II and Type III 18S rDNA were pseudogenes. Groups II and III ITS1 sequences were shorter (685-717bp in length) than Group I ITS1 (762-776bp), but had much higher sequence divergence (9.8%) than the later ones did (4.9%). Group II sequences were recombinants between Group I and Group III sequences, providing the possibility that the rDNA of K. bicoloratus is in a transition stage of concerted evolution. In addition, by comparing standard PCR and high-stringency PCR, we concluded that DMSO might prevent functional ITS1 sequences from being amplified instead of enhancing its amplification efficiency. The analysis suggests a non-concerted evolution of rDNA in K. bicoloratus. Features of rDNA functional genes and pseudogenes are described. Possible causes for the lack of homogenization of rDNA paralogues within individuals are discussed.
对石鲽（Kareius bicoloratus）的分子研究表明，核糖体DNA（18S rDNA、ITS1和5.8S rDNA）存在高度的个体内多态性。这种多态性不仅包括多个功能基因，还包括假定的假基因和重组体。在每个研究个体的基因组中，共存着三种长度不同的主要类型（I型、II型和III型）的18S rDNA。相对于I型，II型和III型有一个15bp的缺失，III型还有一个额外的7bp缺失。表达分析提供了明确的证据，表明I型18S rDNA大量表达。相比之下，未检测到II型和III型18S rDNA的转录。进一步的序列分析表明，I型是石鲽中预期的功能性18S rDNA，而II型和III型是假基因。ITS1序列的系统发育形成了三组（I组、II组和III组），其中与I型18S rDNA相连的I组是功能性的，而其余两组（II组和III组）与II型和III型18S rDNA相连的是假基因。II组和III组的ITS1序列（长度为685 - 717bp）比I组的ITS1（762 - 776bp）短，但序列差异（9.8%）比后者（4.9%）高得多。II组序列是I组和III组序列之间的重组体，这表明石鲽的rDNA可能处于协同进化的过渡阶段。此外，通过比较标准PCR和高严谨度PCR，我们得出结论，二甲基亚砜（DMSO）可能会阻止功能性ITS1序列的扩增，而不是提高其扩增效率。该分析表明石鲽的rDNA存在非协同进化。描述了rDNA功能基因和假基因的特征。讨论了个体内rDNA旁系同源物缺乏同质化的可能原因。
