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Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

Abstract

Despite advances in sequencing, the goal of obtaining a comprehensive view of genetic variation in populations is still far from reached. We sequenced 180 lines of A. thaliana from Sweden to obtain as complete a picture as possible of variation in a single region. Whereas simple polymorphisms in the unique portion of the genome are readily identified, other polymorphisms are not. The massive variation in genome size identified by flow cytometry seems largely to be due to 45S rDNA copy number variation, with lines from northern Sweden having particularly large numbers of copies. Strong selection is evident in the form of long-range linkage disequilibrium (LD), as well as in LD between nearby compensatory mutations. Many footprints of selective sweeps were found in lines from northern Sweden, and a massive global sweep was shown to have involved a 700-kb transposition.

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Figure 1: Polymorphism detection.
Figure 2: Genome size variation.
Figure 3: Compensatory indels.
Figure 4: Long-range LD.
Figure 5: Characterization of selective sweeps on chromosome 1.

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Acknowledgements

We thank O. Mittelsten Scheid for comments on the manuscript, J. Dolezel for providing a size standard for flow cytometry, G. Schmauss for technical assistance with flow cytometry, N. Lettner for help with sample preparation, A. Sommer for help with sequencing and the Gregor Mendel Institute IT team (in particular, P. Forai) for excellent cluster support. This work was supported by European Research Council grant 268962 MAXMAP and European Community Framework Programme 7 grant 283496 transPLANT to M.N., by the Austrian Science Fund (Vienna Graduate School of Population Genetics, FWF W1225) to I.H. and by Czech Science Foundation grants P501/12/G090 and P506/12/0668 to M.A.L.

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Authors and Affiliations

Authors

Contributions

M.N. supervised the project. V.N. generated the sequencing data. Q.L., D.M. and A.P. performed primary analysis of the sequencing data, including all polymorphism detection and quality control. D.M. carried out de novo assembly. F.A.R. and L.S. performed the genome size analyses. M.A.L. and T.M. carried out FISH analyses. Q.L., D.M., Q.Z. and B.J.V. analyzed the pattern of LD. C.D.H. and I.H. carried out population structure and selective sweep analyses. A.F., D.M., A.K., P.K. and V.V. analyzed the chromosome 1 transposition. Ü.S. contributed web tools and helped with data management. M.N. wrote the manuscript with major input from Q.L., F.A.R., D.M., C.D.H., A.F. and I.H.

Corresponding author

Correspondence to Magnus Nordborg.

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The authors declare no competing financial interests.

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Supplementary Figures 1–25, Supplementary Tables 1–5 and Supplementary Note (PDF 7381 kb)

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Long, Q., Rabanal, F., Meng, D. et al. Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet 45, 884–890 (2013). https://doi.org/10.1038/ng.2678

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