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PMID: 23793030 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Nature genetics ·Vol. 45 ·No. 8 ·2013-08-00 ·Pages 884-890

Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, Zhang Q, Vilhjálmsson BJ, Korte A, Nizhynska V, Voronin V, Korte P, Sedman L, Mandáková T, Lysak MA, Seren Ü, Hellmann I, Nordborg M

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.

MeSH Terms
Arabidopsis/genetics Chromosome Mapping Chromosomes, Plant DNA Copy Number Variations Evolution, Molecular Genetic Variation Genetics, Population Genome, Plant Genome-Wide Association Study High-Throughput Nucleotide Sequencing INDEL Mutation Linkage Disequilibrium Polymorphism, Single Nucleotide Selection, Genetic Sweden
Authors & Affiliations
18 authors, click to expand affiliations / ORCID
Long Quan
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
Rabanal Fernando A
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
Meng Dazhe
Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA.
Huber Christian D
Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.
Farlow Ashley
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
Platzer Alexander
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
Zhang Qingrun
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
Vilhjálmsson Bjarni J
Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA.
Korte Arthur
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
Nizhynska Viktoria
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
Voronin Viktor
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
Korte Pamela
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
Sedman Laura
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
Mandáková Terezie
Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
Lysak Martin A
Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
Seren Ümit
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
Hellmann Ines
Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.
Nordborg Magnus
Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria. | Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA.
References (45)
45 references, click to expand
  1. Fast and accurate short read alignment with Burrows-Wheeler transform.
    Bioinformatics. 2009 Jul 15;25(14):1754-60 PMID: 19451168
  2. Specific gene amplification in oocytes. Oocyte nuclei contain extrachromosomal replicas of the genes for ribosomal RNA.
    Science. 1968 Apr 19;160(3825):272-80 PMID: 4867987
  3. Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness.
    Heredity (Edinb). 2012 Mar;108(3):285-91 PMID: 21878986
  4. Genomic scans for selective sweeps using SNP data.
    Genome Res. 2005 Nov;15(11):1566-75 PMID: 16251466
  5. Linkage disequilibrium due to random genetic drift in finite subdivided populations.
    Proc Natl Acad Sci U S A. 1982 Mar;79(6):1940-4 PMID: 16593171
  6. The extent of linkage disequilibrium in Arabidopsis thaliana.
    Nat Genet. 2002 Feb;30(2):190-3 PMID: 11780140
  7. Genome-wide detection and characterization of positive selection in human populations.
    Nature. 2007 Oct 18;449(7164):913-8 PMID: 17943131
  8. Patterns of population epigenomic diversity.
    Nature. 2013 Mar 14;495(7440):193-8 PMID: 23467092
  9. TE-Locate: A Tool to Locate and Group Transposable Element Occurrences Using Paired-End Next-Generation Sequencing Data.
    Biology (Basel). 2012 Sep 12;1(2):395-410 PMID: 24832231
  10. Disruption of the AtREV3 gene causes hypersensitivity to ultraviolet B light and gamma-rays in Arabidopsis: implication of the presence of a translesion synthesis mechanism in plants.
    Plant Cell. 2003 Sep;15(9):2042-57 PMID: 12953110
  11. Visualization of SNPs with t-SNE.
    PLoS One. 2013;8(2):e56883 PMID: 23457633
  12. A framework for variation discovery and genotyping using next-generation DNA sequencing data.
    Nat Genet. 2011 May;43(5):491-8 PMID: 21478889
  13. Multiple reference genomes and transcriptomes for Arabidopsis thaliana.
    Nature. 2011 Aug 28;477(7365):419-23 PMID: 21874022
  14. Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome.
    Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21611-6 PMID: 21115826
  15. Population differentiation as a test for selective sweeps.
    Genome Res. 2010 Mar;20(3):393-402 PMID: 20086244
  16. Increasing the multiplicity of ribosomal RNA genes in Drosophila melanogaster.
    Science. 1971 Jan 22;171(3968):294-7 PMID: 5538845
  17. The Sequence Alignment/Map format and SAMtools.
    Bioinformatics. 2009 Aug 15;25(16):2078-9 PMID: 19505943
  18. Rare variants create synthetic genome-wide associations.
    PLoS Biol. 2010 Jan 26;8(1):e1000294 PMID: 20126254
  19. Recombination and linkage disequilibrium in Arabidopsis thaliana.
    Nat Genet. 2007 Sep;39(9):1151-5 PMID: 17676040
  20. Genome size variation among accessions of Arabidopsis thaliana.
    Ann Bot. 2004 Mar;93(3):317-21 PMID: 14724121
  21. Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines.
    Nature. 2010 Jun 3;465(7298):627-31 PMID: 20336072
  22. Conditions under which genome-wide association studies will be positively misleading.
    Genetics. 2010 Nov;186(3):1045-52 PMID: 20813880
  23. The control of natural variation in cytosine methylation in Arabidopsis.
    Genetics. 2002 Sep;162(1):355-63 PMID: 12242246
  24. Loss of DNA polymerase zeta causes chromosomal instability in mammalian cells.
    Cancer Res. 2006 Jan 1;66(1):134-42 PMID: 16397225
  25. A small number of cistrons for ribosomal RNA in the germinal nucleus of a eukaryote, Tetrahymena pyriformis.
    Proc Natl Acad Sci U S A. 1974 Aug;71(8):3082-6 PMID: 4606151
  26. RFLP and physical mapping with an rDNA-specific endonuclease reveals that nucleolus organizer regions of Arabidopsis thaliana adjoin the telomeres on chromosomes 2 and 4.
    Plant J. 1996 Feb;9(2):259-72 PMID: 8820610
  27. Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region.
    Cell. 2000 Feb 4;100(3):367-76 PMID: 10676818
  28. Adaptation to climate across the Arabidopsis thaliana genome.
    Science. 2011 Oct 7;334(6052):83-6 PMID: 21980108
  29. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change.
    Nat Genet. 2011 May;43(5):476-81 PMID: 21478890
  30. Low levels of DNA polymerase alpha induce mitotic and meiotic instability in the ribosomal DNA gene cluster of Saccharomyces cerevisiae.
    PLoS Genet. 2008 Jun 27;4(6):e1000105 PMID: 18584028
  31. The pattern of polymorphism in Arabidopsis thaliana.
    PLoS Biol. 2005 Jul;3(7):e196 PMID: 15907155
  32. Reference-guided assembly of four diverse Arabidopsis thaliana genomes.
    Proc Natl Acad Sci U S A. 2011 Jun 21;108(25):10249-54 PMID: 21646520
  33. Eukaryotic MCM proteins: beyond replication initiation.
    Microbiol Mol Biol Rev. 2004 Mar;68(1):109-31 PMID: 15007098
  34. Naturally occurring genetic variation in Arabidopsis thaliana.
    Annu Rev Plant Biol. 2004;55:141-72 PMID: 15377217
  35. A map of local adaptation in Arabidopsis thaliana.
    Science. 2011 Oct 7;334(6052):86-9 PMID: 21980109
  36. The 1001 genomes project for Arabidopsis thaliana.
    Genome Biol. 2009;10(5):107 PMID: 19519932
  37. The scale of population structure in Arabidopsis thaliana.
    PLoS Genet. 2010 Feb 12;6(2):e1000843 PMID: 20169178
  38. The nature of confounding in genome-wide association studies.
    Nat Rev Genet. 2013 Jan;14(1):1-2 PMID: 23165185
  39. Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel.
    Nat Genet. 2012 Jan 08;44(2):212-6 PMID: 22231484
  40. Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness.
    Nature. 2010 Mar 11;464(7286):279-82 PMID: 20182427
  41. Histone methyltransferases regulating rRNA gene dose and dosage control in Arabidopsis.
    Genes Dev. 2012 May 1;26(9):945-57 PMID: 22549957
  42. Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana.
    BMC Plant Biol. 2007 Aug 16;7:44 PMID: 17705842
  43. Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana.
    Science. 2007 Jul 20;317(5836):338-42 PMID: 17641193
  44. Natural variation in DNA methylation in ribosomal RNA genes of Arabidopsis thaliana.
    BMC Plant Biol. 2008 Sep 10;8:92 PMID: 18783613
  45. Whole-genome sequencing of multiple Arabidopsis thaliana populations.
    Nat Genet. 2011 Aug 28;43(10):956-63 PMID: 21874002
Article Info
Journal
Nature genetics
Abbr.
Nat Genet
ISSN
1546-1718
DOI
10.1038/ng.2678
Published
2013-08-00
Epub
2013-00-23
Pages
884-890
Language
English
Region
United States
NLM ID
9216904
PMCID
PMC3755268
Subset
IM
Grants
European Research Council · 268962 · International
External Links
PubMed source DOI: 10.1038/ng.2678 PMC Full Text View journal details
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