Structural and phylogenetic analysis of TRAS, telomeric repeat-specific non-LTR retrotransposon families in Lepidopteran insects

TRAS1 is a non-LTR retrotransposon inserted specifically into the telomeric repeat (TTAGG)(n) in the silkworm, Bombyx mori. To characterize the evolut ionary origin of TRAS-like elements, we identified seven TRAS families (TRA S3, TRAS4, TRAS5, TRAS6, TRASY, TRASZ, and TRASW) from B. mori and four ele ments from two Lepidoptera, Dictyoploca japonica (TRASDJ) and Samia cynthia ricini (TRASSC3, TRASSC4, and TRASSC9). More than 2,000 copies of various Bombyx TRAS elements accumulated within (TTAGG)(n) sequences as unusual but orderly tandem repeats. The 5' and 3' regions were highly conserved within each class of Bombyx TRAS elements without truncation. This suggests that distinct classes of TRAS have been maintained independently by retrotranspo sition into (TTAGG)(n). The phylogenetic tree of site-specific retroelement s showed that nine TRAS families in Lepidoptera constitute a single phyloge netic group that is closely related to the R1 family that inserts specifica lly into arthropod 28S rDNA. The higher amino acid sequence identity from e ndonuclease (EN) to reverse transcriptase (RT) domains between TRAS groups (about 37%-70%) than among TRAS elements and R1Bm (about 25%-30%), may refl ect the presence of some DNA structure responsible for their target specifi city. Sequence comparison from EN to RT domains among non-LTR elements reve aled several regions conserved only within TRAS elements. We found a highly conserved region that resembles the Myb-like DNA-binding structure, betwee n the EN and RT domains. These regions may be involved in site-specific int egration of TRAS elements into the (TTAGG)(n) telomeric repeats.