title: Large retrotransposon derivatives: abundant, conserved but nonautonomous retroelements of barley and related genomes.
abstract: Retroviruses and LTR retrotransposons comprise two long-terminal repeats (LTRs) bounding a central domain that encodes the products needed for reverse transcription, packaging, and integration into the genome. We describe a group of retrotransposons in 13 species and four genera of the grass tribe Triticeae, including barley, with long, approximately 4.4-kb LTRs formerly called Sukkula elements. The approximately 3.5-kb central domains include reverse transcriptase priming sites and are conserved in sequence but contain no open reading frames encoding typical retrotransposon proteins. However, they specify well-conserved RNA secondary structures. These features describe a novel group of elements, called LARDs or large retrotransposon derivatives (LARDs). These appear to be members of the gypsy class of LTR retrotransposons. Although apparently nonautonomous, LARDs appear to be transcribed and can be recombinationally mapped due to the polymorphism of their insertion sites. They are dispersed throughout the genome in an estimated 1.3 x 10(3) full-length copies and 1.16 x 10(4) solo LTRs, indicating frequent recombinational loss of internal domains as demonstrated also for the BARE-1 barley retrotransposon.
authors.affiliation: MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, FIN-00014 Helsinki, Finland.
authors.forename: Ruslan
authors.initials: R
authors.lastname: Kalendar
authors.forename: Carlos M
authors.initials: CM
authors.lastname: Vicient
authors.forename: Ofer
authors.initials: O
authors.lastname: Peleg
authors.forename: Kesara
authors.initials: K
authors.lastname: Anamthawat-Jonsson
authors.forename: Alexander
authors.initials: A
authors.lastname: Bolshoy
authors.forename: Alan H
authors.initials: AH
authors.lastname: Schulman
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D001483:Base Sequence; D017124:Conserved Sequence; D018744:DNA, Plant; D016208:Databases, Factual; D019143:Evolution, Molecular; D018745:Genome, Plant; D001467:Hordeum / Q000235:genetics*; D017404:In Situ Hybridization, Fluorescence; D020084:Long Interspersed Nucleotide Elements; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D018749:RNA, Plant / Q000737:chemistry; D018626:Retroelements; D014908:Triticum / Q000235:genetics
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D018744:DNA, Plant; D018749:RNA, Plant; D018626:Retroelements