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



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.



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.
Department of Plant Physiology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, 44801, Germany.|BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany.
Vasantika
V
Suryawanshi
Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam, 14476, Germany.
Ina N
IN
Talke
Department of Plant Physiology, University of Bayreuth, Universitätsstrasse 30, Bayreuth, 95447, Germany.
Michael
M
Weber
Division of Theoretical Bioinformatics, DKFZ, Im Neuenheimer Feld 280, Heidelberg, 69121, Germany.|BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany.|Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, Heidelberg, 69120, Germany.
Roland
R
Eils
Division of Theoretical Bioinformatics, DKFZ, Im Neuenheimer Feld 280, Heidelberg, 69121, Germany.
Benedikt
B
Brors
Department of Plant Physiology, University of Bayreuth, Universitätsstrasse 30, Bayreuth, 95447, Germany.
Stephan
S
Clemens
Department of Plant Physiology, Ruhr University Bochum, Universitätsstrasse 150, Bochum, 44801, Germany. ute.kraemer@ruhr-uni-bochum.de.|BioQuant, University of Heidelberg, Im Neuenheimer Feld 267, Heidelberg, 69120, Germany. ute.kraemer@ruhr-uni-bochum.de.
Ute
U
Krämer
D000220:Adaptation, Biological / Q000235:genetics*; D017360:Arabidopsis / Q000235:genetics*; D005075:Biological Evolution; D055028:Comparative Genomic Hybridization; D019143:Evolution, Molecular; D017353:Gene Deletion; D018628:Gene Dosage; D020440:Gene Duplication; D017343:Genes, Plant; D014644:Genetic Variation; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D010641:Phenotype; D015203:Reproducibility of Results; D013045:Species Specificity
Arabidopsis halleri; Array-CGH; CNV; Cross-species; Metal hyperaccumulation; Resistance genes (R genes); Toll-Interleukin Receptor-Nucleotide Binding Site-Leucine Rich Repeat (TIR-NBS-LRR) protein family