Identification of Bilby, a diverged centromeric Ty1-copia retrotransposon family from cereal rye (Secale cereale L.)

A diminutive rye chromosome (midget) in wheat was used as a model system to isolate a highly reiterated centromeric sequence from a rye chromosome. Fl uorescence in situ hybridization (FISH) shows this sequence localized withi n all rye centromeres and no signal was detected on wheat chromosomes. DNA sequencing of the repetitive element has revealed the presence of some cata lytic domains and signature motifs typical of retrotransposon genes and has been called the Bilby family, representing a diverged family of retrotrans poson-like elements. Extensive DNA database searching revealed some sequenc e similarity to centromeric retrotransposons from wheat, barley, and centro meric repetitive sequences from rice. Very low levels of signal were observ ed when Bilby was used as a probe against barley, and no signal was detecte d with rice DNA during Southern hybridization. The abundance of Bilby in ry e indicates that this family may have diverged from other distantly related centromeric retrotransposons or incorporated in the centromere but rapidly evolved in rye during speciation. The isolation of a rye retrotransposon a lso allowed the analysis of centromeric breakpoints in wheat-rye translocat ion lines. A quantitative analysis shows that the breakpoint in 1DS.1RL and 1DL.1RS and recombinant lines containing proximal rye chromatin have a por tion of the rye centromere that may contribute to the normal function of th e centromeric region.