Ty3/Gypsy retrotransposons in the Pacific abalone Haliotis discus hannai: characterization and use for species identification in the genus Haliotis

Transposable elements are highly abundant elements that are present in all eukaryotic species. Here, we present a molecular description of abalone retrotransposon ( Abret ) elements. The genome of Haliotis discus hannai contains 130 Abret elements which were all Ty3 /Gypsy retrotransposons. The Ty1 /Copia elements were absent in the H. discus hannai genome. Most of the elements were not complete due to sequence truncation or coding region decay. However, three elements Abret -296, Abret -935, and Abret -3259 had most of the canonical features of LTR (long terminal repeat)-retrotransposons. There were several reading frame shifts in Abret- 935 and Abret- 3259 elements. Surprisingly, phylogenetic analysis indicated that all of the elements belonged to the Osvaldo lineage. The sequence divergence between LTRs revealed that the Abret elements were mostly active within 2 million years ago. Abre t elements were used as molecular markers in SSAP analyses, which allowed clear distinction of different species in the genus Haliotis . The polymorphic markers were converted into SCAR markers for use in species identification by simple PCR in the Haliotis genus.