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Background  Gene copy number divergence between species is a form of genetic polymorphism that contributes significantly to both genome size and phenotypic variation. In plants, copy number expansions of single genes were implicated in cultivar- or species-specific tolerance of high levels of soil boron, aluminium or calamine-type heavy metals, respectively.  Arabidopsis halleri  is a zinc- and cadmium-hyperaccumulating extremophile species capable of growing on heavy-metal contaminated, toxic soils. In contrast, its non-accumulating sister species  A. lyrata  and the closely related reference model species  A. thaliana  exhibit merely basal metal tolerance.    Results  For a genome-wide assessment of the role of copy number divergence (CND) in lineage-specific environmental adaptation, we conducted cross-species array comparative genome hybridizations of three plant species and developed a global signal scaling procedure to adjust for sequence divergence. In  A. halleri , transition metal homeostasis functions are enriched twofold among the genes detected as copy number expanded. Moreover, biotic stress functions including mostly disease  Resistance  ( R ) gene-related genes are enriched twofold among genes detected as copy number reduced, when compared to the abundance of these functions among all genes.    Conclusions  Our results provide genome-wide support for a link between evolutionary adaptation and CND in  A. halleri  as shown previously for  Heavy metal ATPase4 . Moreover our results support the hypothesis that elemental defences, which result from the hyperaccumulation of toxic metals, allow the reduction of classical defences against biotic stress as a trade-off.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-016-3319-5) contains supplementary material, which is available to authorized users.

Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri