Isolation of a transcriptionally active element of high copy number retrotransposons in sweetpotato genome

Many plant retrotransposons have been characterized, but only three families (Tnt1, Tto1 and Tos17) have been demonstrated to be transpositionally competent. We followed a novel approach that enabled us to identify an active element of the Ty1-copia retrotransposon family with estimated 400 copies in the sweetpotato genome. DNA sequences of Ty1 -copia reverse transcriptase (RTase) from the sweetpotato genome were analyzed, and a group of retrotransposon copies probably formed by recent transposition events was further analyzed. 3’RACE on callus cDNA amplified transcripts containing long terminal repeats (LTR) of this group. The sequence -specific amplification polymorphism (S-SAP) patterns of the LTR sequence in the genomic DNA were compared between a normal plant and callus lines derived from it. A callus -specific S-SAP product was found into which the retrotransposon detected by the 3’RACE had been transposed apparently during cell culture. We conclude that our approach provides an effective way to identify active elements of retrotransposons with high copy numbers.