Abstract
BackgroundGene 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.ResultsFor 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.ConclusionsOur 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 materialThe online version of this article (doi:10.1186/s12864-016-3319-5) contains supplementary material, which is available to authorized users.
Highlights
Gene copy number divergence between species is a form of genetic polymorphism that contributes significantly to both genome size and phenotypic variation
Singlegene and segmental duplications as well as whole-genome duplications have been hypothesized to propel adaptive evolution and speciation. This view is supported by recent reports on cultivar-specific boron tolerance in barley [15], aluminium tolerance in maize [16] and species-wide heavy metal tolerance in the wild plant Arabidopsis halleri [17, 18], all supporting the role of gene copy number expansion in plant adaptation to abiotic stress
Metal hyperaccumulation and hypertolerance in A. halleri have previously been attributed to the constitutively enhanced expression of a number of metal homeostasis genes, several of which were shown to be expanded in genomic copy number through DNA gel blots [31], BAC sequencing [18, 38] or other methods [34]
Summary
Gene copy number divergence between species is a form of genetic polymorphism that contributes significantly to both genome size and phenotypic variation. Singlegene and segmental duplications as well as whole-genome duplications have been hypothesized to propel adaptive evolution and speciation In plants, this view is supported by recent reports on cultivar-specific boron tolerance in barley [15], aluminium tolerance in maize [16] and species-wide heavy metal tolerance in the wild plant Arabidopsis halleri [17, 18], all supporting the role of gene copy number expansion in plant adaptation to abiotic stress. Betweenspecies genome comparisons have remained difficult to date, the few existing studies have supported the hypothesis that gene copy number expansions, and especially those involving tandem duplications [21], might underlie plant adaptations to environmental stress [22]. Given that novel functions are much more likely to be generated by adaptive specialization of one of several pre-existing copies of a duplicated gene than by an entirely novel gene [23, 24], such comparative studies are key to understanding the patterns of genomic polymorphisms associated with adaptation and speciation
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