A new family of site-specific retrotransposons, SART1, is inserted into telomeric repeats of the silkworm, Bombyx mori

The telomeres of the silkworm, Bombyx mori, consist of pentanucleotide repeats (TTAGG)(n). We previously characterized the non-LTR element TRAS1, which terminates with oligo (A) in a head to tail orientation at the exact position (between A and C) of the (CCTAA)(n) repeats. Here we characterized another family of telomere-specific non-LTR retrotransposon named SART1. The SART1 family was inserted at another site of the (TTAGG)(n) in a reverse orientation from that of TRAS1, The complete unit of SART1, 6.7 kb in length with a poly (A) stretch, contains two open reading frames encoding putative gag and pol products, overlapping by 54 bp in the -1 reading frame. Most of the 600 SART1 copies in the silkworm haploid genome are completely conserved in structure without 5' truncation, All SART1 sequences analyzed were inserted at the same position (between T and A) within the (TTAGG)(n) repeats, Fluorescence in situ hybridization showed that many of the SART1 copies were localized in the chromosomal ends. A phylogenetic tree showed that the SART1, TRAS1 and two other site-specific elements, R1 and RT, which insert into 28S ribosomal RNA genes in insects, belong to the same group. Based on the orientation for the chromosomal insertion and structural similarities, these elements could be further classified into two subgroups, R2/TRAS1 and RT/SART1, suggesting that the target specificity of the two telomere-associated elements was changed independently.