Yokozuna is the first Ty1/Copia LTR retrotransposon characterized in the genome of the domestic silkworm, Bombyx mori (Ohbayashi et al. 1998). This element is part of a nested structure containing at least seven mobile elements, it is located in the Kabuki Ty3/Gypsy-like retroelement (Ohbayashi et al. 1998; Abe et al. 2000). Yokozuna is closely related (or tentatively belongs) to Copia clade within Branch 2 of the Ty1/Copia family (Llorens et al. 2009). Yokozuna genome is 4738 bp in size, including a 208-bp 5’-LTR and a 183-bp 3’LTR. The different size is due to an insertion (or deletion) of 25 bp. These LTRs differ from other retrotransposable element LTRs in that they do not terminate in CA (Ohbayashi et al. 1998). The internal region of this element contains a Primer Binding Site (PBS), a single long Open Reading Frame (ORF) displaying the typical Ty1/Copia-like gag and pol domains (gag, protease, integrase, reverse transcriptase and ribonuclease H) and a Polypurine Tract (PPT) adjacent to the 3’ LTR (Ohbayashi et al. 1998).
Figure not to scale. If present, long terminal repeats (LTRs) have been highlighted in blue. Amino acid motifs noted with lines indicate the conserved residues in each protein domain, abbreviations below mean:
||DU or DUT=dUTPase
||TAV or IBMP=transactivator/viroplasmin or inclusion body matrix protein
||PBS=primer binding site
||ATF=aphid transmission factor
||VAP=virion associated protein
Mobile DNA II. (Craig et al. 2002)