Copia-like retrotransposons in the genus Setaria:: Sequence heterogeneity, species distribution and chromosomal organization

The presence of copia-like retrotransposons has been investigated in genus Setaria by using PCR amplification with degenerated primers to conserved motifs of the predicted reverse transcriptase (RT) Tyl-copia-like protein sequence. Amplification products from each genotype of Setaria grass species with different genomic composition (A versus B) and different ploidy levels (2n = 18 and 2n = 36) were cloned and sequenced. Sequence analysis of RT clones revealed a high degree of similarity between sequences of the deduced amino acid and RT from diverse plants including mono- and dicotyledon species. Cluster analysis of these sequences has shown a great heterogeneity among RT domains cloned from different Setaria species and even from the same species. FISH analysis using the cloned RT sequences as probes on metaphase chromosomes showed that these sequences were dispersed throughout the genome, albeit excluded from the nucleolus-organizing regions. These characteristics make copia-like retrotransposon clones good candidates to study the genetic structure of the S. italica (foxtail millet) gene pool.