title: Insertion Sequences show diverse recent activities in Cyanobacteria and Archaea.
abstract: BACKGROUND
  Mobile genetic elements (MGEs) play an essential role in genome rearrangement and evolution, and are widely used as an important genetic tool.
  
  
  RESULTS
  In this article, we present genetic maps of recently active Insertion Sequence (IS) elements, the simplest form of MGEs, for all sequenced cyanobacteria and archaea, predicted based on the previously identified ~1,500 IS elements. Our predicted IS maps are consistent with the NCBI annotations of the IS elements. By linking the predicted IS elements to various characteristics of the organisms under study and the organism's living conditions, we found that (a) the activities of IS elements heavily depend on the environments where the host organisms live; (b) the number of recently active IS elements in a genome tends to increase with the genome size; (c) the flanking regions of the recently active IS elements are significantly enriched with genes encoding DNA binding factors, transporters and enzymes; and (d) IS movements show no tendency to disrupt operonic structures.
  
  
  CONCLUSIONS
  This is the first genome-scale maps of IS elements with detailed structural information on the sequence level. These genetic maps of recently active IS elements and the several interesting observations would help to improve our understanding of how IS elements proliferate and how they are involved in the evolution of the host genomes.
authors.affiliation: Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA. ffzhou@csbl.bmb.uga.edu
authors.forename: Fengfeng
authors.initials: F
authors.lastname: Zhou
authors.forename: Victor
authors.initials: V
authors.lastname: Olman
authors.forename: Ying
authors.initials: Y
authors.lastname: Xu
mesh_terms: D001105:Archaea / Q000235:genetics* / Q000378:metabolism*; D001483:Base Sequence; D002874:Chromosome Mapping; D002876:Chromosomes, Bacterial; D000458:Cyanobacteria / Q000235:genetics* / Q000378:metabolism*; D004251:DNA Transposable Elements; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D008957:Models, Genetic; D016254:Mutagenesis, Insertional; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid; D013698:Templates, Genetic; D020079:Terminal Repeat Sequences
chemical_list: D004251:DNA Transposable Elements