title: Transposon diversity in Arabidopsis thaliana.
abstract: Recent availability of extensive genome sequence information offers new opportunities to analyze genome organization, including transposon diversity and accumulation, at a level of resolution that was previously unattainable. In this report, we used sequence similarity search and analysis protocols to perform a fine-scale analysis of a large sample ( approximately 17.2 Mb) of the Arabidopsis thaliana (Columbia) genome for transposons. Consistent with previous studies, we report that the A. thaliana genome harbors diverse representatives of most known superfamilies of transposons. However, our survey reveals a higher density of transposons of which over one-fourth could be classified into a single novel transposon family designated as Basho, which appears unrelated to any previously known superfamily. We have also identified putative transposase-coding ORFs for miniature inverted-repeat transposable elements (MITEs), providing clues into the mechanism of mobility and origins of the most abundant transposons associated with plant genes. In addition, we provide evidence that most mined transposons have a clear distribution preference for A + T-rich sequences and show that structural variation for many mined transposons is partly due to interelement recombination. Taken together, these findings further underscore the complexity of transposons within the compact genome of A. thaliana.
authors.affiliation: Department of Biology, McGill University, 1205 Docteur Penfield Avenue, Montreal, Quebec H3A 1B1, Canada.
authors.forename: Q H
authors.initials: QH
authors.lastname: Le
authors.forename: S
authors.initials: S
authors.lastname: Wright
authors.forename: Z
authors.initials: Z
authors.lastname: Yu
authors.forename: T
authors.initials: T
authors.lastname: Bureau
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D004251:DNA Transposable Elements / Q000235:genetics*; D014644:Genetic Variation; D018745:Genome, Plant; D008969:Molecular Sequence Data; D016415:Sequence Alignment
chemical_list: D004251:DNA Transposable Elements