Chromosomal organization of centromeric Ty3/gypsy retrotransposons in Allium cepa L. and Allium fistulosum L.

This is the first report on the presence of Ty3/gypsy-like retrotransposons in the centromeric region of Allium cepa and Allium fistulosum. We identified the putative Ty3/gypsy centromeric retrotransposons (CR) among the DNA sequences of A. cepa present in the NCBI database and evaluated their copy number in the genomes of A. cepa and A. fistulosum. The putative copy number of Ty3/gypsy CR constituted about 26000 for A. cepa and about 7000 for A. fistulosum. The chromosomal organization of Ty3/gypsy CR was analyzed with fluorescent in situ hybridization (FISH). Primers were designed using the sequence ET645811 of A. cepa (Genome Survey Sequence database), and a 300 bp product was obtained from genomic DNA of A. cepa and A. fistulosum. The PCR product displayed similarity to the reverse transcriptase of the CR Ty3/gypsy family and was used as a probe for FISH. Hybridization signals were mainly localized in the centromeric regions of A. cepa chromosomes. On the chromosomes of A. fistulosum, however, the hybridization patterns were less specific. The evolution of the CR Ty3/gypsy in these two closely related Allium species is discussed.