title: Whole-genome sequencing of multiple Arabidopsis thaliana populations.
abstract: The plant Arabidopsis thaliana occurs naturally in many different habitats throughout Eurasia. As a foundation for identifying genetic variation contributing to adaptation to diverse environments, a 1001 Genomes Project to sequence geographically diverse A. thaliana strains has been initiated. Here we present the first phase of this project, based on population-scale sequencing of 80 strains drawn from eight regions throughout the species' native range. We describe the majority of common small-scale polymorphisms as well as many larger insertions and deletions in the A. thaliana pan-genome, their effects on gene function, and the patterns of local and global linkage among these variants. The action of processes other than spontaneous mutation is identified by comparing the spectrum of mutations that have accumulated since A. thaliana diverged from its closest relative 10 million years ago with the spectrum observed in the laboratory. Recent species-wide selective sweeps are rare, and potentially deleterious mutations are more common in marginal populations.
authors.affiliation: Max Planck Institute for Developmental Biology, Tübingen, Germany.
authors.forename: Jun
authors.initials: J
authors.lastname: Cao
authors.forename: Korbinian
authors.initials: K
authors.lastname: Schneeberger
authors.forename: Stephan
authors.initials: S
authors.lastname: Ossowski
authors.forename: Torsten
authors.initials: T
authors.lastname: Günther
authors.forename: Sebastian
authors.initials: S
authors.lastname: Bender
authors.forename: Joffrey
authors.initials: J
authors.lastname: Fitz
authors.forename: Daniel
authors.initials: D
authors.lastname: Koenig
authors.forename: Christa
authors.initials: C
authors.lastname: Lanz
authors.forename: Oliver
authors.initials: O
authors.lastname: Stegle
authors.forename: Christoph
authors.initials: C
authors.lastname: Lippert
authors.forename: Xi
authors.initials: X
authors.lastname: Wang
authors.forename: Felix
authors.initials: F
authors.lastname: Ott
authors.forename: Jonas
authors.initials: J
authors.lastname: Müller
authors.forename: Carlos
authors.initials: C
authors.lastname: Alonso-Blanco
authors.forename: Karsten
authors.initials: K
authors.lastname: Borgwardt
authors.forename: Karl J
authors.initials: KJ
authors.lastname: Schmid
authors.forename: Detlef
authors.initials: D
authors.lastname: Weigel
mesh_terms: D000483:Alleles; D017360:Arabidopsis / Q000235:genetics*; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D018744:DNA, Plant / Q000235:genetics; D056426:Genetic Loci; D005828:Genetics, Population; D018745:Genome, Plant; D005843:Geography; D015810:Linkage Disequilibrium; D009154:Mutation; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D018744:DNA, Plant