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PMID: 17641193 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana.

Science (New York, N.Y.) ·Vol. 317 ·No. 5836 ·2007-07-20 ·Pages 338-42

Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P, Warthmann N, Hu TT, Fu G, Hinds DA, Chen H, Frazer KA, Huson DH, Schölkopf B, Nordborg M, Rätsch G, Ecker JR, Weigel D

Abstract

The genomes of individuals from the same species vary in sequence as a result of different evolutionary processes. To examine the patterns of, and the forces shaping, sequence variation in Arabidopsis thaliana, we performed high-density array resequencing of 20 diverse strains (accessions). More than 1 million nonredundant single-nucleotide polymorphisms (SNPs) were identified at moderate false discovery rates (FDRs), and approximately 4% of the genome was identified as being highly dissimilar or deleted relative to the reference genome sequence. Patterns of polymorphism are highly nonrandom among gene families, with genes mediating interaction with the biotic environment having exceptional polymorphism levels. At the chromosomal scale, regional variation in polymorphism was readily apparent. A scan for recent selective sweeps revealed several candidate regions, including a notable example in which almost all variation was removed in a 500-kilobase window. Analyzing the polymorphisms we describe in larger sets of accessions will enable a detailed understanding of forces shaping population-wide sequence variation in A. thaliana.

MeSH Terms
Algorithms Arabidopsis/genetics Base Sequence Chromosomes, Plant/genetics Computational Biology Gene Frequency Genes, Plant Genetic Variation Genome, Plant Molecular Sequence Data Polymorphism, Genetic Polymorphism, Single Nucleotide Selection, Genetic Sequence Analysis, DNA
Authors & Affiliations
18 authors, click to expand affiliations / ORCID
Clark Richard M
Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
Schweikert Gabriele
Toomajian Christopher
Ossowski Stephan
Zeller Georg
Shinn Paul
Warthmann Norman
Hu Tina T
Fu Glenn
Hinds David A
Chen Huaming
Frazer Kelly A
Huson Daniel H
Schölkopf Bernhard
Nordborg Magnus
Rätsch Gunnar
Ecker Joseph R
Weigel Detlef
Article Info
Journal
Science (New York, N.Y.)
Abbr.
Science
ISSN
1095-9203
Published
2007-07-20
Pages
338-42
Language
English
Region
United States
NLM ID
0404511
Subset
IM
Databases
GENBANK
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