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Background  The transposable element (TE) content of the genomes of plant species varies from near zero in the genome of  Utricularia gibba  to more than 80 % in many species. It is not well understood whether this variation in genome composition results from common mechanisms or stochastic variation. The major obstacles to investigating mechanisms of TE evolution have been a lack of comparative genomic data sets and efficient computational methods for measuring differences in TE composition between species. In this study, we describe patterns of TE evolution in 14 species in the flowering plant family Asteraceae and 1 outgroup species in the Calyceraceae to investigate phylogenetic patterns of TE dynamics in this important group of plants.    Results  Our findings indicate that TE families in the Asteraceae exhibit distinct patterns of non-neutral evolution, and that there has been a directional increase in copy number of  Gypsy  retrotransposons since the origin of the Asteraceae. Specifically, there is marked increase in  Gypsy  abundance at the origin of the Asteraceae and at the base of the tribe Heliantheae. This latter shift in genome composition has had a significant impact on the diversity and abundance distribution of TEs in a lineage-specific manner.    Conclusions  We show that the TE-driven expansion of plant genomes can be facilitated by just a few TE families, and is likely accompanied by the modification and/or replacement of the TE community. Importantly, large shifts in TE composition may be correlated with major of phylogenetic transitions.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1830-8) contains supplementary material, which is available to authorized users.

Evolutionary transitions in the Asteraceae coincide with marked shifts in transposable element abundance