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

BMC Genomics
Vasantika SuryawanshiUte Krämer

Abstract

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 a...Continue Reading

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Citations

Mar 27, 2018·PloS One·Sara Monzerrat Ramírez-OlveraFernando Carlos Gómez-Merino
Jun 8, 2018·Plant, Cell & Environment·Hassan AhmadiStephan Clemens
Nov 10, 2018·Molecular Ecology·Alessia GuggisbergAlex Widmer
Jun 4, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Veronica PreiteLevi Yant
Jun 6, 2019·The Biochemical Journal·Amelie DetterbeckStephan Clemens
May 21, 2020·Metallomics : Integrated Biometal Science·Massimiliano Corso, Vanesa S García de la Torre
Jul 21, 2020·Journal of Experimental Botany·Pierre-Nicolas Boulc'hIvan Couée
Nov 22, 2018·Frontiers in Plant Science·Jachym SumanTomas Macek
Feb 6, 2017·BMC Genomics·Christian SchönbachShoba Ranganathan
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Jul 14, 2020·Frontiers in Genetics·Vellaichamy Gandhimeyyan RenganathanJegadeesan Ramalingam

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Methods Mentioned

BETA
chip
electrophoresis

Software Mentioned

MAS5
lyrata
MapMan
Limma package
Limma
Matlab
R
Harshlight package
lmFit
Ensembl Plants

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