| Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates | |
Gong, Jun1,2 ; Dong, Jun1,3; Liu, Xihan1,3; Massana, Ramon4
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| 发表期刊 | PROTIST
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| ISSN | 1434-4610 |
| 2013-05-01 | |
| 卷号 | 164期号:3页码:369-379 |
| 关键词 | Ciliophora Copy Number Intragenomic Variability Rdna Quantitative Pcr Sequence Polymorphism |
| 产权排序 | [Gong, Jun; Dong, Jun; Liu, Xihan] Chinese Acad Sci, Yantai Inst Coastal Zone Res, Lab Environm Microbiol, Yantai 264003, Peoples R China; [Gong, Jun] S China Normal Univ, Coll Life Sci, Guangzhou 510631, Guangdong, Peoples R China; [Dong, Jun; Liu, Xihan] Ocean Univ China, Inst Marine Divers & Evolut, Qingdao 266003, Peoples R China; [Massana, Ramon] CSIC, Inst Ciencias Mar, Dept Marine Biol & Oceanog, E-08003 Barcelona, Catalonia, Spain |
| 通讯作者 | Gong, J (reprint author), Chinese Acad Sci, Yantai Inst Coastal Zone Res, Lab Environm Microbiol, Yantai 264003, Peoples R China. jgong@yic.ac.cn |
| 作者部门 | 海岸带生物学与生物资源利用所重点实验室 |
| 英文摘要 | The copy number and sequence variation of the ribosomal DNA (rDNA) operon are of functional significance in evolution and ecology of organisms. However, the relationship between copy number and sequence variation of rDNA in protists has been rarely studied. Here we quantified rDNA copy numbers of oligotrich and peritrich ciliate species using single-cell quantitative PCR. We also examined the rDNA sequence variation by using single-cell PCR, cloning, and sequencing of multiple clones. We found that the rDNA copy numbers per cell were extremely high and different among even congeners, with the highest record of about 310,000. There was substantial intraindividual haplotype diversity and nucleotide diversity for the rDNA markers, with sequence differences primarily characterized by single nucleotide polymorphisms. Haplotype and nucleotide diversity was positively correlated to the rDNA copy number. Our findings provide evidence that: (1) ciliates generally have much higher rDNA copy numbers than other protists and fungi, which could lead to overestimation of the relative abundance of ciliates in environmental samples when rDNA sequence-based methodologies are used; and that (2) the rDNA might not always evolve in a strictly concerted manner in ciliates, which may raise problems in rDNA-based inference of species richness and phylogeny. (C) 2012 Elsevier GmbH. All rights reserved.; The copy number and sequence variation of the ribosomal DNA (rDNA) operon are of functional significance in evolution and ecology of organisms. However, the relationship between copy number and sequence variation of rDNA in protists has been rarely studied. Here we quantified rDNA copy numbers of oligotrich and peritrich ciliate species using single-cell quantitative PCR. We also examined the rDNA sequence variation by using single-cell PCR, cloning, and sequencing of multiple clones. We found that the rDNA copy numbers per cell were extremely high and different among even congeners, with the highest record of about 310,000. There was substantial intraindividual haplotype diversity and nucleotide diversity for the rDNA markers, with sequence differences primarily characterized by single nucleotide polymorphisms. Haplotype and nucleotide diversity was positively correlated to the rDNA copy number. Our findings provide evidence that: (1) ciliates generally have much higher rDNA copy numbers than other protists and fungi, which could lead to overestimation of the relative abundance of ciliates in environmental samples when rDNA sequence-based methodologies are used; and that (2) the rDNA might not always evolve in a strictly concerted manner in ciliates, which may raise problems in rDNA-based inference of species richness and phylogeny. (C) 2012 Elsevier GmbH. All rights reserved. |
| 文章类型 | Article |
| 资助机构 | CAS; Natural Science Foundation of China [40976099, 41176143]; Natural Science Foundation for Distinguished Young Scholars of Shandong [JQ201210]; FANEDD [2007B27] |
| 收录类别 | SCI |
| 语种 | 英语 |
| 关键词[WOS] | RIBOSOMAL-RNA GENES ; OPERATIONAL TAXONOMIC UNITS ; REAL-TIME PCR ; TETRAHYMENA-PYRIFORMIS ; INTRAGENOMIC VARIATION ; ENVIRONMENTAL-SAMPLES ; QUANTITATIVE PCR ; GENOME SIZE ; DIVERSITY ; DNA |
| 研究领域[WOS] | Microbiology |
| WOS记录号 | WOS:000319716700005 |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://ir.yic.ac.cn/handle/133337/6434 |
| 专题 | 海岸带生物学与生物资源利用重点实验室_海岸带生物学与生物资源保护实验室 |
| 作者单位 | 1.Chinese Acad Sci, Yantai Inst Coastal Zone Res, Lab Environm Microbiol, Yantai 264003, Peoples R China 2.S China Normal Univ, Coll Life Sci, Guangzhou 510631, Guangdong, Peoples R China 3.Ocean Univ China, Inst Marine Divers & Evolut, Qingdao 266003, Peoples R China 4.CSIC, Inst Ciencias Mar, Dept Marine Biol & Oceanog, E-08003 Barcelona, Catalonia, Spain |
| 推荐引用方式 GB/T 7714 | Gong, Jun,Dong, Jun,Liu, Xihan,et al. Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates[J]. PROTIST,2013,164(3):369-379. |
| APA | Gong, Jun,Dong, Jun,Liu, Xihan,&Massana, Ramon.(2013).Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates.PROTIST,164(3),369-379. |
| MLA | Gong, Jun,et al."Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates".PROTIST 164.3(2013):369-379. |
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