Ty1-copia-like retrotransposons of tomato (Lycopersicon esculentum Mill.)

We have used a PCR and cloning strategy to identify Ty1-copia-like retrotransposons in tomato, Lycopersicon esculentum Mill. Using degenerate oligonucleotide primers corresponding to conserved domains of the Ty1-copia retrotransposon reverse transcriptase (RT), fragments of about 260 bp were obtained by PCR amplification. Sequences of 20 cloned amplification fragments showed similarity to retrotransposon sequences. The copy number for total tomato Ty1-copia-like RT population was estimated to be approximately 2500 and may account for about 1.5% of the tomato genome. Copy numbers for four of the individual RT clones ranged from 20 to 1400 copies. A comparison of the conceptual translations of the RT sequences identified four clusters as well as three sequences which were ungrouped. When compared to RT sequences reported from several other sources, the tomato RT population was found to be widely dispersed with the majority of the RT sequences from Lycopersicon species delineated by the four tomato cluster groups. The gag region of a tomato retrotransposon was cloned from PCRs with primers based on the Tnt1 retrotransposon of tobacco. The tomato clone (pTom1.1) had 81% sequence similarity to the Tntl gag region. Several pTom1.1 sequences are present in other solanaceous species as indicated by Southern hybridization.