ISOLATION AND CHARACTERIZATION OF LTR RETROTRANSPOSONS FROM STRAWBERRY GENOME

Abstract

Strawberry (Fragaria spp.) is a kind of herbaceous perennial plant that propagates vegetatively. The conserved domains of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy groups of LTR retrotransposons were amplified from the cultivated and wild strawberry genomes. In the cultivated strawberry, sequence analysis of clones demonstrated that 5 of 19 Ty1-copia group unique sequences and 2 of 10 Ty3-gypsy unique sequences possessed either stop codon or frameshift. Ty1-copia group sequences are highly heterogeneous (divergence ranged from 1 to 69.8%), but the Ty3-gypsy group sequences are less variable (divergence ranged from 1 to 10%). In wild strawberry, sequence analysis of clones demonstrated that 11 of 34 Ty1-copia group unique sequences and 6 of 14 Ty3-gypsy unique sequences possessed either stop codon or frameshift. Southern dot blot hybridization result suggested that both of the LTR retrotransposons are present in the genome of cultivated strawberry (Fragaria × ananassa) with high copy number (Ty1-copia group 2,875; Ty3-gypsy group 348). Both types of LTR retrotransposons contributed to 15.8% of the cultivated strawberry genome of which the contribution of Ty1-copia retrotransposons being higher (13.5%) than that of Ty3-gypsy (2.3%). RT-PCR amplification from total RNA, which was extracted from callus induced from strawberry leaves cultured on MS medium supplemented with 2,4-D, yield the RT fragments of Ty1-copia retrotransposons.