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Background  Relatively few species of flowering plants are dioecious and even fewer are known to have sex chromosomes. Current theory posits that homomorphic sex chromosomes, such as found in  Bryonia dioica  (Cucurbitaceae), offer insight into the early stages in the evolution of sex chromosomes from autosomes. Little is known about these early steps, but an accumulation of transposable element sequences has been observed on the Y-chromosomes of some species with heteromorphic sex chromosomes. Recombination, by which transposable elements are removed, is suppressed on at least part of the emerging Y-chromosome, and this may explain the correlation between the emergence of sex chromosomes and transposable element enrichment.    Findings  We sequenced 2321 bp of the Y-chromosome in  Bryonia dioica  that flank a male-linked marker,  BdY1 , reported previously. Within this region, which should be suppressed for recombination, we observed a solo-LTR nested in a  Copia -like transposable element. We also found other, presumably paralogous, solo-LTRs in a consensus sequence of the underlying  Copia -like transposable element.    Conclusions  Given that solo-LTRs arise via recombination events, it is noteworthy that we find one in a genomic region where recombination should be suppressed. Although the solo-LTR could have arisen before recombination was suppressed, creating the male-linked marker  BdY1 , our previous study on  B. dioica  suggested that  BdY1  may not lie in the recombination-suppressed region of the Y-chromosome in all populations. Presence of a solo-LTR near  BdY1  therefore fits with the observed correlation between retrotransposon accumulation and the suppression of recombination early in the evolution of sex chromosomes. These findings further suggest that the homomorphic sex chromosomes of  B. dioica , the first organism for which genetic XY sex-determination was inferred, are evolutionarily young and offer reference information for comparative studies of other plant sex chromosomes.

A specific insertion of a solo-LTR characterizes the Y-chromosome of Bryonia dioica (Cucurbitaceae)