Between-species differences in gene copy number are enriched among functions critical for adaptive evolution in Arabidopsis halleri. (December 2016)

• Record Type: Journal Article
• Authors: Suryawanshi, Vasantika; Talke, Ina; Weber, Michael; Eils, Roland; Brors, Benedikt; Clemens, Stephan; Krämer, Ute
• Is Part Of: BMC genomics. Volume 17:Number 13(2016)
• Page Start: 43
• Page End: 64
• Publication Date: 2016-12
• Subjects: Cross-species -- Array-CGH -- Metal hyperaccumulation -- CNV -- Arabidopsis halleri -- Toll-Interleukin Receptor-Nucleotide Binding Site-Leucine Rich Repeat (TIR-NBS-LRR) protein family -- Resistance genes (R genes); Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-016-3319-5
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract 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 speciesA. lyrata and the closely related reference model speciesA. 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. InA. halleri, transition metal homeostasis functions are enriched twofold among the genes detected as copy number expanded. Moreover, biotic stress functions including mostly diseaseResistance (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 inA. halleri as shown previously forHeavy 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.