Molecular structure of the copia-like retrotransposable element Yokozuna on the W chromosome of the silkworm, Bombyx mori

We discovered a novel retrotransposable element, designated Yokozuna, on the W chromosome of Bombyx mori. The size of this element is 4738 bp, including a 208-bp long terminal repeat (LTR) on one side and a 183-bp LTR on the other. This retrotransposable element is flanked by a 5-bp target site duplication, TAATT. Yokozuna contains a single long open reading frame (ORF) and the whole deduced amino acid sequence of ORF reveals strong homology with copia of Drosophila. Moreover, an alignment analysis of the reverse transcriptase (RT) sequences suggested that the Yokozuna element is the first Bombyx retrotransposable element belonging to the Ty1-copia group. The number of Yokozuna per haploid genome is approximately four copies. Although Yokozuna was discovered on the W chromosome, it is not specific for the W chromosome.