STRUCTURE AND EVOLUTION OF CYCLOPS - A NOVEL GIANT RETROTRANSPOSON OFTHE TY3 GYPSY FAMILY HIGHLY AMPLIFIED IN PEA AND OTHER LEGUME SPECIES/

We characterized a novel giant Gypsy-like retrotransposon, CE,clops, p resent in about 5000 copies in the genome of Pisum sativum. The indivi dual element Cyclops-2 measures 12 314 bp including long terminal repe ats (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-G lu. The element is bounded by 5 bp target site duplications and harbor s 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 potent ial capacity for gene transduction. The pol region contains sequence m otifs 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 r everse transcriptase domain confirms our differential genetic assessme nt that Cyclops from pea is a novel element with no specific relations hip to the previously described Gypsy-like elements from plants. Genom ic Southern hybridizations show that Cyclops is abundant not only in p ea but also in common bean, mung bean, broad bean, soybean and the pea nut suggesting that Cyclops may be an useful genetic tool for analyzi ng the genomes of agronomically important legumes.