Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators
文献类型：期刊论文
| 作者 | Lin, Shen1,2,3; Haas, Stefan2; Zemojtel, Tomasz2; Xiao, Peng1,2,3; Vingron, Martin2; Li, Renhui1 |
| 刊名 | GENE
 |
| 出版日期 | 2011-03-01 |
| 卷号 | 473期号:2页码:139-149 |
| 关键词 | Transposable element Insert sequence IS diversity Cyanobacterial genomes IS family IS subfamily |
| ISSN号 | 0378-1119 |
| 通讯作者 | Li, RH, Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat Biol, Wuhan 430072, Peoples R China ; biolin@ihb.ac.cn ; haas@molgen.mpg.de ; zemojtel@molgen.mpg.de ; xp@ihb.ac.cn ; vingron@molgen.mpg.de ; reli@ihb.ac.cn |
| 中文摘要 | Transposable elements are widely distributed in archaea, bacteria and eukarya domains. Considerable discrepancies of transposable elements in eukaryotes have been reported, however, the studies focusing on the diversity of transposable element systems in prokaryotes were scarce. Understanding the transposable element system in cyanobacteria by the genome-wide analysis will greatly improve the knowledge of cyanobacterial diversity. In this study, the transposable elements of seventeen cyanobacterial genomes were analyzed. The abundance of insertion sequence (IS) elements differs significantly among the cyanobacterial genomes examined. In particular, water bloom forming Microcystis aeruginosa NIES843 was shown to have the highest abundance of IS elements reaching 10.85% of the genome. IS family is a widely acceptable IS classification unit, and IS subfamily, based on probe sequences, was firstly proposed as the basic classification unit for IS element system therefore both IS family and IS subfamily were suggested as the two hierarchical units for evaluating the IS element system diversity. In total, 1980 predicted IS elements, within 21 IS families and 132 subfamilies, were identified in the examined cyanobacterial genomes. Families IS4, IS5, IS630 and IS200-605 are widely distributed, and therefore supposed to be the ancestral IS families. Analysis on the intactness of IS elements showed that the percentage of the intact IS differs largely among these cyanobacterial strains. Higher percentage of the intact IS detected in the two hot spring cyanobacterial strains implied that the intactness of IS elements may be related to the genomic stabilization of cyanobacteria inhabiting in the extreme environments. The frequencies between IS elements and miniature inverted-repeat transposable elements (MITEs) were shown to have a linear positive correlation. The transposable element system in cyanobacterial genomes is of hypervariabilty. With characterization of easy definition and stability, IS subfamily is considered as a reliable lower classification unit in IS element system. The abundance of intact IS, the composition of IS families and subfamilies, the sequence diversity of IS element nucleotide and transposase amino acid are informative and suitable as the indicators for studies on cyanobacterial diversity. Practically, the transposable system may provide us a new perspective to realize the diversity and evolution of populations of water bloom forming cyanobacterial species. (C) 2010 Elsevier B.V. All rights reserved. |
| 英文摘要 | Transposable elements are widely distributed in archaea, bacteria and eukarya domains. Considerable discrepancies of transposable elements in eukaryotes have been reported, however, the studies focusing on the diversity of transposable element systems in prokaryotes were scarce. Understanding the transposable element system in cyanobacteria by the genome-wide analysis will greatly improve the knowledge of cyanobacterial diversity. In this study, the transposable elements of seventeen cyanobacterial genomes were analyzed. The abundance of insertion sequence (IS) elements differs significantly among the cyanobacterial genomes examined. In particular, water bloom forming Microcystis aeruginosa NIES843 was shown to have the highest abundance of IS elements reaching 10.85% of the genome. IS family is a widely acceptable IS classification unit, and IS subfamily, based on probe sequences, was firstly proposed as the basic classification unit for IS element system therefore both IS family and IS subfamily were suggested as the two hierarchical units for evaluating the IS element system diversity. In total, 1980 predicted IS elements, within 21 IS families and 132 subfamilies, were identified in the examined cyanobacterial genomes. Families IS4, IS5, IS630 and IS200-605 are widely distributed, and therefore supposed to be the ancestral IS families. Analysis on the intactness of IS elements showed that the percentage of the intact IS differs largely among these cyanobacterial strains. Higher percentage of the intact IS detected in the two hot spring cyanobacterial strains implied that the intactness of IS elements may be related to the genomic stabilization of cyanobacteria inhabiting in the extreme environments. The frequencies between IS elements and miniature inverted-repeat transposable elements (MITEs) were shown to have a linear positive correlation. The transposable element system in cyanobacterial genomes is of hypervariabilty. With characterization of easy definition and stability, IS subfamily is considered as a reliable lower classification unit in IS element system. The abundance of intact IS, the composition of IS families and subfamilies, the sequence diversity of IS element nucleotide and transposase amino acid are informative and suitable as the indicators for studies on cyanobacterial diversity. Practically, the transposable system may provide us a new perspective to realize the diversity and evolution of populations of water bloom forming cyanobacterial species. (C) 2010 Elsevier B.V. All rights reserved. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine |
| 学科主题 | Genetics & Heredity |
| 类目[WOS] | Genetics & Heredity |
| 研究领域[WOS] | Genetics & Heredity |
| 关键词[WOS] | INSERTION POLYMORPHISM ; SEQUENCE ; POPULATIONS ; CHROMOSOME ; DNA ; EVOLUTION ; SYSTEM ; NUMBER ; FAMILY ; MITES |
| 收录类别 | SCI |
| 资助信息 | National Key Basic Research Program (973) [2008CB418002]; FEBL fund [2011FB17]; CAS-MPG joint doctoral program |
| 语种 | 英语 |
| WOS记录号 | WOS:000288305600011 |
| 公开日期 | 2011-06-30 |
| 源URL | [http://ir.ihb.ac.cn/handle/342005/15676]  |
| 专题 | 水生生物研究所_水生生物分子与细胞生物学研究中心_期刊论文 |
| 作者单位 | 1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Aquat Biodivers & Conservat Biol, Wuhan 430072, Peoples R China 2.Max Planck Inst Mol Genet, Dept Computat Mol Biol, D-14195 Berlin, Germany 3.Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China |
| 推荐引用方式 GB/T 7714 | Lin, Shen,Haas, Stefan,Zemojtel, Tomasz,et al. Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators[J]. GENE,2011,473(2):139-149. |
| APA | Lin, Shen,Haas, Stefan,Zemojtel, Tomasz,Xiao, Peng,Vingron, Martin,&Li, Renhui.(2011).Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators.GENE,473(2),139-149. |
| MLA | Lin, Shen,et al."Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators".GENE 473.2(2011):139-149. |
入库方式： OAI收割
来源：水生生物研究所
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