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Speciation and allopolyploidization in cereals may be accompanied by dramatic changes in abundance of centromeric repeated transposable elements. Here we demonstrate that the reverse transcriptase part of Ty3/gypsy centromeric retrotransposon (RT-CR) is highly conservative in the segmental hexaploid  Thinopyrum intermedium  (J r J vs St) and its possible diploid progenitors  Th .  bessarabicum  (J b ),  Pseudoroegneria spicata  (St) and  Dasypyrum villosum  (V) but the abundance of the repeats varied to a large extent. Fluorescence  in situ  hybridization (FISH) showed hybridization signals in centromeric region of all chromosomes in the studied species, although the intensity of the signals drastically differed. In  Th .  intermedium , the strongest signal of RT-CR probe was detected on the chromosomes of J v , intermediate on J r  and faint on J s  and St subgenome suggesting different abundance of RT-CR on the individual chromosomes rather than the sequence specificity of RT-CRs of the subgenomes. RT-CR quantification using real-time PCR revealed that its content per genome in  Th .  bessarabicum  is ~ 2 times and  P .  spicata  is ~ 1,5 times higher than in genome of  D .  villosum . The possible burst of Ty3/gypsy centromeric retrotransposon in  Th .  intermedium  during allopolyploidization and its role in proper mitotic and meiotic chromosome behavior in a nascent allopolyploid is discussed.

Variation in Copy Number of Ty3/Gypsy Centromeric Retrotransposons in the Genomes of Thinopyrum intermedium and Its Diploid Progenitors