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Background  Miniature inverted repeat transposable elements (MITEs) are small non-autonomous DNA transposons that are ubiquitous in plant genomes, and are mobilised by their autonomous relatives.  Stowaway  MITEs are derived from and mobilised by elements from the  mariner  superfamily. Those elements constitute a significant portion of the carrot genome; however the variation caused by  Daucus carota Stowaway  MITEs ( DcSto s), their association with genes and their putative impact on genome evolution has not been comprehensively analysed.    Results  Fourteen families of  Stowaway  elements  DcSto s occupy about 0.5% of the carrot genome. We systematically analysed 31 genomes of wild and cultivated  Daucus carota , yielding 18.5 thousand copies of these elements, showing remarkable insertion site polymorphism.  DcSto  element demography differed based on the origin of the host populations, and corresponded with the four major groups of  D. carota,  wild European, wild Asian, eastern cultivated and western cultivated. The  DcSto s elements were associated with genes, and most frequently occurred in 5′ and 3′ untranslated regions (UTRs). Individual families differed in their propensity to reside in particular segments of genes. Most importantly,  DcSto  copies in the 2 kb regions up- and downstream of genes were more frequently associated with open reading frames encoding transcription factors, suggesting their possible functional impact. More than 1.5% of all  DcSto  insertion sites in different host genomes contained different copies in exactly the same position, indicating the existence of insertional hotspots. The  DcSto 7b family was much more polymorphic than the other families in cultivated carrot. A line of evidence pointed at its activity in the course of carrot domestication, and identified  Dcmar 1 as an active carrot  mariner  element and a possible source of the transposition machinery for  DcSto 7b.    Conclusion   Stowaway  MITEs have made a substantial contribution to the structural and functional variability of the carrot genome.

Stowaway miniature inverted repeat transposable elements are important agents driving recent genomic diversity in wild and cultivated carrot