Genetics, Vol. 166, 1437-1450, March 2004, Copyright © 2004

Large Retrotransposon Derivatives: Abundant, Conserved but Nonautonomous Retroelements of Barley and Related Genomes

Ruslan Kalendara, Carlos M. Vicienta, Ofer Pelegb, Kesara Anamthawat-Jonssonc, Alexander Bolshoyb, and Alan H. Schulmana,d
a MTT/BI Plant Genomics Laboratory, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, FIN-00014 Helsinki, Finland,
b Genome Diversity Center, Institute of Evolution, University of Haifa, 31905 Haifa, Israel,
c Faculty of Sciences, University of Iceland, 108 Reykjavík, Iceland
d Plant Breeding Biotechnology, Plant Production Research, MTT Agrifood Research Finland, 31600 Jokioinen, Finland

Corresponding author: Alan H. Schulman, Institute of Biotechnology, University of Helsinki, P.O. Box 56, Viikinkaari 4, FIN-00014 Helsinki, Finland., alan.schulman{at}helsinki.fi (E-mail)

Communicating editor: D. F. VOYTAS

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, ~4.4-kb LTRs formerly called Sukkula elements. The ~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 103 full-length copies and 1.16 x 104 solo LTRs, indicating frequent recombinational loss of internal domains as demonstrated also for the BARE-1 barley retrotransposon.




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