Isolation and characterization of RNase LTR sequences of Ty1-copia retrotransposons in common bean (Phaseolus vulgaris L.)

Retroelements have proved useful for molecular marker studies and play an important role in genome evolution. Ty1-copia retrotransposons are ubiquitous and heterogeneous in plant genomes, and although many elements have been isolated and characterized, almost no information about them is available in the literature for Phaseolus vulgaris L. We report here the isolation and characterization of new RNase long terminal repeat (LTR) sections of the Ty1-copia group for this crop plant. RNAse sections showed conserved amino acids with the downstream sections corresponding to the polypurine-tract and 5' sections of 3' LTRs. The RNase sections were aligned using ClustalX to find potential relationships between sequences. A comparison with this analysis was made using the partition analysis of quasispecies package (PAQ), which is specific for quasispecies-like populations. The analysis revealed eight distinct groups. To uncover LTR variability and potential conserved promoter motifs, we also designed new primers from the presumed polypurine-tract regions. A similarity search found short stretches similar to upstream and downstream regions of some genes. Conserved motifs, corresponding to transcription factor binding sites, were discovered through MatInspector software and two sequences characterized. From a putative LTR fragment, we then designed a new primer, which, through sequence-specific amplification polymorphism (SSAP), showed numerous polymorphic bands between two distinct P. vulgaris accessions.