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Extremely High Copy Numbers and Polymorphisms of the rDNA Operon Estimated from Single Cell Analysis of Oligotrich and Peritrich Ciliates

文献类型：期刊论文

作者Gong, Jun1,2; Dong, Jun1,3; Liu, Xihan1,3; Massana, Ramon4
刊名PROTIST
出版日期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
ISSN号1434-4610
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
文献子类Article
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.
学科主题Microbiology
URL标识查看原文
WOS关键词RIBOSOMAL-RNA GENES ; OPERATIONAL TAXONOMIC UNITS ; REAL-TIME PCR ; TETRAHYMENA-PYRIFORMIS ; INTRAGENOMIC VARIATION ; ENVIRONMENTAL-SAMPLES ; QUANTITATIVE PCR ; GENOME SIZE ; DIVERSITY ; DNA
WOS研究方向Microbiology
语种英语
WOS记录号WOS:000319716700005
资助机构CAS; Natural Science Foundation of China [40976099, 41176143]; Natural Science Foundation for Distinguished Young Scholars of Shandong [JQ201210]; FANEDD [2007B27]
公开日期2013-08-14
源URL[http://ir.yic.ac.cn/handle/133337/6435]  
专题烟台海岸带研究所_海岸带生物学与生物资源利用所重点实验室
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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