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  Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators

Lin, S., Haas, S., Zemojtel, T., Xiao, P., Vingron, M., & Li, R. (2011). Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators. Gene, 473(2), 139-49. doi:10.1016/j.gene.2010.11.011.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7918-1 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-791B-C
Genre: Journal Article

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Lin, S., Author
Haas, S.1, Author              
Zemojtel, T.2, Author              
Xiao, P., Author
Vingron, M.3, Author              
Li, R., Author
Affiliations:
1Gene Structure and Array Design (Stefan Haas), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479640              
2Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              
3Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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Free keywords: Chromosome Mapping; Cyanobacteria/*genetics; DNA Copy Number Variations; *DNA Transposable Elements; Evolution, Molecular; *Genetic Variation; Phylogeny; Sequence Analysis; Sequence Analysis, Protein
 Abstract: 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 hypervariability. 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.

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 Dates: 2011
 Publication Status: Published in print
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Title: Gene
Source Genre: Journal
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Pages: - Volume / Issue: 473 (2) Sequence Number: - Start / End Page: 139 - 49 Identifier: ISSN: 1879-0038 (Electronic) 0378-1119 (Print)