title: 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.
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Quan
authors.initials: Q
authors.lastname: Long
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Fernando A
authors.initials: FA
authors.lastname: Rabanal
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA.
authors.forename: Dazhe
authors.initials: D
authors.lastname: Meng
authors.affiliation: Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.
authors.forename: Christian D
authors.initials: CD
authors.lastname: Huber
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Ashley
authors.initials: A
authors.lastname: Farlow
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Alexander
authors.initials: A
authors.lastname: Platzer
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Qingrun
authors.initials: Q
authors.lastname: Zhang
authors.affiliation: Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA.
authors.forename: Bjarni J
authors.initials: BJ
authors.lastname: Vilhjálmsson
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Arthur
authors.initials: A
authors.lastname: Korte
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Viktoria
authors.initials: V
authors.lastname: Nizhynska
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Viktor
authors.initials: V
authors.lastname: Voronin
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Pamela
authors.initials: P
authors.lastname: Korte
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Laura
authors.initials: L
authors.lastname: Sedman
authors.affiliation: Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
authors.forename: Terezie
authors.initials: T
authors.lastname: Mandáková
authors.affiliation: Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
authors.forename: Martin A
authors.initials: MA
authors.lastname: Lysak
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.
authors.forename: Ümit
authors.initials: Ü
authors.lastname: Seren
authors.affiliation: Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.
authors.forename: Ines
authors.initials: I
authors.lastname: Hellmann
authors.affiliation: Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria.|Molecular and Computational Biology, University of Southern California, Los Angeles, California, USA.
authors.forename: Magnus
authors.initials: M
authors.lastname: Nordborg
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D056915:DNA Copy Number Variations; D019143:Evolution, Molecular; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D054643:INDEL Mutation; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D013548:Sweden