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论文题目: Polymorphism and evolution of ribosomal DNA in tea (Camellia sinensis, Theaceae)
英文论文题目: Polymorphism and evolution of ribosomal DNA in tea (Camellia sinensis, Theaceae)
第一作者: Xu, J; Xu, Y; Yonezawa, T; Li, LJ; Hasegawa, M; Lu, F; Chen, JK; Zhang, W
英文第一作者: Xu, J; Xu, Y; Yonezawa, T; Li, LJ; Hasegawa, M; Lu, F; Chen, JK; Zhang, W
联系作者: Zhang, W (reprint author), Fudan Univ, Sch Life Sci, Inst Biodivers Sci, Minist Educ,Key Lab Biodivers Sci & Ecol Engn, Shanghai 200433, Peoples R China.
英文联系作者: Zhang, W (reprint author), Fudan Univ, Sch Life Sci, Inst Biodivers Sci, Minist Educ,Key Lab Biodivers Sci & Ecol Engn, Shanghai 200433, Peoples R China.
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发表年度: 2015
卷: 89
期:
页码: 63-72
摘要: Ribosomal DNA (rDNA) repeats often exhibit a high level of within-species homogeneity, but intra-individual polymorphism of rDNA has been found in Camellia species. In order to reveal the evolutionary pattern of rDNA repeats in tea [Camellia sinensis (L.) O. Kuntze], we identified the 45S rDNA loci, estimated their copy number, and cloned partial regions of them from different PCR products and from digested genomic DNA. The results show that there are 3 loci (6 sites) containing 45S rDNA in the tea genome; they are located at the ends of the short arms of 6 chromosomes and consist of a maximum of 6500 repeat units. On one hand, 164 sequences of the 26S rDNA cloned from PCR products contained 147 haplotypes, consisting of 62% pseudogenes, 24% putative functional genes, and 14% PCR-mediated recombinants, suggesting that the 45S rDNA of tea maintains an extremely high level of polymorphism and divergence; on the other hand, rDNA fragments cloned directly from genomic DNA exhibited a very high level of homogeneity: only one of 33 rDNA fragments was from a pseudogene. These results demonstrate that although over 60% of the 26S rDNA sequences identified in PCR products belong to pseudogenes, most 45S rDNA repeats are functional genes and have undergone concerted evolution. In this study, strong PCR bias and PCR-mediated recombination greatly increased the apparent proportion of pseudogenes in PCR products. Phylogenetic analysis and genetic divergence values for 265 rDNA sequences obtained in this study show that many pseudogenes have originated independently from functional genes at different times, and despite thus escaping from concerted evolution, they have failed to be eliminated from the tea genome over a long period, some of them having even produced addition copies by rapid expansion. Importantly, our study suggests that in order to determine the true pattern of evolution of rDNA it is necessary to combine data from more than one method rather than relying only on sequences from PCR products. (C) 2015 Elsevier Inc. All rights reserved.
英文摘要: Ribosomal DNA (rDNA) repeats often exhibit a high level of within-species homogeneity, but intra-individual polymorphism of rDNA has been found in Camellia species. In order to reveal the evolutionary pattern of rDNA repeats in tea [Camellia sinensis (L.) O. Kuntze], we identified the 45S rDNA loci, estimated their copy number, and cloned partial regions of them from different PCR products and from digested genomic DNA. The results show that there are 3 loci (6 sites) containing 45S rDNA in the tea genome; they are located at the ends of the short arms of 6 chromosomes and consist of a maximum of 6500 repeat units. On one hand, 164 sequences of the 26S rDNA cloned from PCR products contained 147 haplotypes, consisting of 62% pseudogenes, 24% putative functional genes, and 14% PCR-mediated recombinants, suggesting that the 45S rDNA of tea maintains an extremely high level of polymorphism and divergence; on the other hand, rDNA fragments cloned directly from genomic DNA exhibited a very high level of homogeneity: only one of 33 rDNA fragments was from a pseudogene. These results demonstrate that although over 60% of the 26S rDNA sequences identified in PCR products belong to pseudogenes, most 45S rDNA repeats are functional genes and have undergone concerted evolution. In this study, strong PCR bias and PCR-mediated recombination greatly increased the apparent proportion of pseudogenes in PCR products. Phylogenetic analysis and genetic divergence values for 265 rDNA sequences obtained in this study show that many pseudogenes have originated independently from functional genes at different times, and despite thus escaping from concerted evolution, they have failed to be eliminated from the tea genome over a long period, some of them having even produced addition copies by rapid expansion. Importantly, our study suggests that in order to determine the true pattern of evolution of rDNA it is necessary to combine data from more than one method rather than relying only on sequences from PCR products. (C) 2015 Elsevier Inc. All rights reserved.
刊物名称: MOLECULAR PHYLOGENETICS AND EVOLUTION
英文刊物名称: MOLECULAR PHYLOGENETICS AND EVOLUTION
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学科: Biochemistry & Molecular Biology; Evolutionary Biology; Genetics & Heredity
英文学科: Biochemistry & Molecular Biology; Evolutionary Biology; Genetics & Heredity
影响因子: 3.916
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论文类别: Article
英文论文类别: Article
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