title: Diversification, evolution and methylation of short interspersed nuclear element families in sugar beet and related Amaranthaceae species.
abstract: Short interspersed nuclear elements (SINEs) are non-autonomous non-long terminal repeat retrotransposons which are widely distributed in eukaryotic organisms. While SINEs have been intensively studied in animals, only limited information is available about plant SINEs. We analysed 22 SINE families from seven genomes of the Amaranthaceae family and identified 34 806 SINEs, including 19 549 full-length copies. With the focus on sugar beet (Beta vulgaris), we performed a comparative analysis of the diversity, genomic and chromosomal organization and the methylation of SINEs to provide a detailed insight into the evolution and age of Amaranthaceae SINEs. The lengths of consensus sequences of SINEs range from 113 nucleotides (nt) up to 224 nt. The SINEs show dispersed distribution on all chromosomes but were found with higher incidence in subterminal euchromatic chromosome regions. The methylation of SINEs is increased compared with their flanking regions, and the strongest effect is visible for cytosines in the CHH context, indicating an involvement of asymmetric methylation in the silencing of SINEs.
authors.affiliation: Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
authors.forename: Katrin
authors.initials: K
authors.lastname: Schwichtenberg
authors.affiliation: Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
authors.forename: Torsten
authors.initials: T
authors.lastname: Wenke
authors.affiliation: Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
authors.forename: Falk
authors.initials: F
authors.lastname: Zakrzewski
authors.affiliation: Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
authors.forename: Kathrin M
authors.initials: KM
authors.lastname: Seibt
authors.affiliation: Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.|Garvan Institute of Medical Research, 2010, Sydney, NSW, Australia.
authors.forename: André
authors.initials: A
authors.lastname: Minoche
authors.affiliation: Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.|Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), 1190, Vienna, Austria.
authors.forename: Juliane C
authors.initials: JC
authors.lastname: Dohm
authors.affiliation: CeBiTec & Department of Biology, University of Bielefeld, 33615, Bielefeld, Germany.
authors.forename: Bernd
authors.initials: B
authors.lastname: Weisshaar
authors.affiliation: Garvan Institute of Medical Research, 2010, Sydney, NSW, Australia.|Department of Biotechnology, University of Natural Resources and Life Sciences (BOKU), 1190, Vienna, Austria.
authors.forename: Heinz
authors.initials: H
authors.lastname: Himmelbauer
authors.affiliation: Institute of Botany, Technische Universität Dresden, 01069, Dresden, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Schmidt
mesh_terms: D027703:Amaranthaceae / Q000235:genetics*; D027461:Beta vulgaris / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D020086:Short Interspersed Nucleotide Elements / Q000235:genetics*
keywords: Amaranthaceae; DNA methylation; non-long terminal repeat retrotransposon; short interspersed nuclear elements (SINEs); sugar beet