title: Population dynamics of miniature inverted-repeat transposable elements (MITEs) in Medicago truncatula.
abstract: Miniature inverted-repeat transposable elements (MITEs) are small and high copy number transposons, related to and mobilized by some class II autonomous elements. New MITE families can be identified by computer-based mining of sequenced genomes. We describe four MITE families related to MtPH transposons mined de novo in the genome of Medicago truncatula, together with one previously described family MITRAV. Different levels of their intra-family sequence diversity and insertion polymorphism indicate that they were active at different evolutionary periods. MetMIT1 and MITRAV families were uniform in sequence and produced highly polymorphic insertion sites in 26 ecotypes representing a M. truncatula core collection. A subset of insertions was present only in the reference genome of A17 'Jemalong', suggesting that the two families might have been active in the course of domestication. In contrast, all investigated insertions of the MetMIT2 family were fixed, showing that it was not active after M. truncatula speciation. MetMIT1 elements were divided into three clusters, i.e. (I) relatively heterogenous copies fixed in the genome of M. truncatula, (II) uniform but also mostly fixed, and (III) uniform and polymorphic among the investigated accessions. It might reflect the evolutionary history of the MetMIT1 family, showing multiple bursts of activity. A number of MetMIT1 and MITRAV insertions were present within 1 kb upstream or downstream the ORF. A high proportion of insertions proximal to coding regions was unique to A17 'Jemalong'.
authors.affiliation: Department of Genetics, Plant Breeding and Seed Science, University of Agriculture in Krakow, Al. 29 Listopada 54, 31-425 Krakow, Poland. dgrzebel@ogr.ar.krakow.pl
authors.forename: Dariusz
authors.initials: D
authors.lastname: Grzebelus
authors.forename: Mirosława
authors.initials: M
authors.lastname: Gładysz
authors.forename: Alicja
authors.initials: A
authors.lastname: Macko-Podgórni
authors.forename: Tomasz
authors.initials: T
authors.lastname: Gambin
authors.forename: Barbara
authors.initials: B
authors.lastname: Golis
authors.forename: Roksana
authors.initials: R
authors.lastname: Rakoczy
authors.forename: Anna
authors.initials: A
authors.lastname: Gambin
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D004251:DNA Transposable Elements / Q000235:genetics*; D018628:Gene Dosage; D018745:Genome, Plant / Q000235:genetics; D055029:Inverted Repeat Sequences / Q000235:genetics*; D046913:Medicago truncatula / Q000235:genetics*; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional / Q000502:physiology; D016366:Open Reading Frames / Q000235:genetics; D011110:Polymorphism, Genetic; D012689:Sequence Homology, Nucleic Acid
chemical_list: D004251:DNA Transposable Elements