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Structure and evolution of Cyclops: a novel giant retrotransposon of the Ty3/Gypsy family highly amplified in pea and other legume species

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Abstract

We characterized a novel giant Gypsy-like retrotransposon, Cyclops, present in about 5000 copies in the genome of Pisum sativum. The individual element Cyclops-2 measures 12 314 bp including long terminal repeats (LTRs) of 1504 bp and 1594 bp, respectively, showing 4.1% sequence divergence between one another. Cyclops-2 carries a polypurine tract (PPT) and an unusual primer binding site (PBS) complementary to tRNA-Glu. The element is bounded by 5 bp target site duplications and harbors three successive internal regions with homology to retroviral genes gag (424 codons) and pol (1382 codons) and an additional open reading frame (423 codons) of unknown function indicating the element's potential capacity for gene transduction. The pol region contains sequence motifs related to the enzymes protease, reverse transcriptase, RNAse H and integrase in the same typical order (5′-PR-RT-RH-IN-3′) known for retroviruses and Gypsy-like retrotransposons. The reading frame of the pol region is disrupted by several mutations suggesting that Cyclops-2 does not encode functional enzymes. A phylogenetic analysis of the reverse transcriptase domain confirms our differential genetic assessment that Cyclops from pea is a novel element with no specific relationship to the previously described Gypsy-like elements from plants. Genomic Southern hybridizations show that Cyclops is abundant not only in pea but also in common bean, mung bean, broad bean, soybean and the pea nut suggesting that Cyclops may be an useful genetic tool for analyzing the genomes of agronomically important legumes.

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Author notes

  1. Franz Chavanne

    Present address: Consiglio Nazionale delle Ricerche, Istituto di Genetica Biochimica ed Evoluzionistica, Via Abbiategrasso 207, 27100, Pavia, Italy

  2. De-Xing Zhang

    Present address: School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK

Authors and Affiliations

  1. Institut für Genetik, Technische, Universität Braunschweig, [Spielmannstr. 7, D-38106, Braunschweig, Germany

    Franz Chavanne, Marie-Françoise Liaud & Rüdiger Cerff

  2. Moléculaire Végétale, Université Joseph Fourier, F-38041, Grenoble, France

    De-Xing Zhang

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Chavanne, F., Zhang, DX., Liaud, MF. et al. Structure and evolution of Cyclops: a novel giant retrotransposon of the Ty3/Gypsy family highly amplified in pea and other legume species. Plant Mol Biol 37, 363–375 (1998). https://doi.org/10.1023/A:1005969626142

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