title: Genome-wide analysis of the Emigrant family of MITEs of Arabidopsis thaliana.
abstract: Miniature inverted-repeat transposable elements (MITEs) are structurally similar to defective class II elements, but their high copy number and the size and sequence conservation of most MITE families suggest that they can be amplified by a replicative mechanism. Here we present a genome-wide analysis of the Emigrant family of MITEs from Arabidopsis thaliana. In order to be able to detect divergent ancient copies, and low copy number subfamilies with a different internal sequence we have developed a computer program to look for Emigrant elements based solely on the terminal inverted-repeat sequence. We have detected 151 Emigrant elements of different subfamilies. Our results show that different bursts of amplification, probably of few active, or master, elements, have occurred at different times during Arabidopsis evolution. The analysis of the insertion sites of the Emigrant elements shows that recently inserted Emigrant elements tend to be located far from open reading frames, whereas more ancient Emigrant subfamilies are preferentially found associated to genes.
authors.affiliation: Department of Genètica Molecular, IBMB-CSIC, Jordi Girona 18, 08034 Barcelona, Spain.
authors.forename: Néstor
authors.initials: N
authors.lastname: Santiago
authors.forename: Cristina
authors.initials: C
authors.lastname: Herráiz
authors.forename: J Ramón
authors.initials: JR
authors.lastname: Goñi
authors.forename: Xavier
authors.initials: X
authors.lastname: Messeguer
authors.forename: Josep M
authors.initials: JM
authors.lastname: Casacuberta
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D004251:DNA Transposable Elements / Q000235:genetics*; D018744:DNA, Plant; D018745:Genome, Plant; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010802:Phylogeny
chemical_list: D004251:DNA Transposable Elements; D018744:DNA, Plant