Abstract
Abstract Background: 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 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. Results: 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 10.95% 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. Both of IS family and IS subfamily were set as the two hierarchical units for evaluating the IS element system diversity. Totally, 1982 predicted IS elements, within 21 IS families and 133 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. Conclusions: The transposable element system in cyanobacterial genomes is of hypervariabilty. With characterization of easy definition and stability, IS subfamily is considered as a reliable 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.
Highlights
Transposable elements are widely distributed in archaea, bacteria and eukarya domains.Considerable discrepancies of transposable elements in eukaryotes have been reported; the studies focusing on the diversity of transposable systems in prokaryotes were scarce
The transposable element system in cyanobacterial genomes is of hypervariabilty
Insert sequences (IS) and miniature inverted-repeat transposable elements (MITEs) are two principal types of transposable elements, which can move from place to place via a DNA intermediate by a cut and paste mechanism [9] or spread to other organisms by horizontal gene transfer [10, 11]
Summary
Transposable elements are widely distributed in archaea, bacteria and eukarya domains.Considerable discrepancies of transposable elements in eukaryotes have been reported; the studies focusing on the diversity of transposable systems in prokaryotes were scarce. Transposable elements ( called mobile element or jumping genes) are widely distributed in a variety of organisms including prokaryotes and eukaryotes [1]. Much is known about the transposable element system, including the element structure, transposition mechanisms, copy number variance (CNVs) and evolutionary history of transposable elements [7, 8]. Insert sequences (IS) and miniature inverted-repeat transposable elements (MITEs) are two principal types of transposable elements, which can move from place to place via a DNA intermediate by a cut and paste mechanism (class II element) [9] or spread to other organisms by horizontal gene transfer [10, 11]. The evolutionary dynamics of insertion sequences in Rhizobium etli populations were shown to be related to the evolutionary histories of the chromosome and symbiotic plasmid [14]
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