Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana

@article{citeulike:1474652, 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 [\~{}]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. 10.1126/science.1138632}, author = {Clark, Richard M. and Schweikert, Gabriele and Toomajian, Christopher and Ossowski, Stephan and Zeller, Georg and Shinn, Paul and Warthmann, Norman and Hu, Tina T. and Fu, Glenn and Hinds, David A. and Chen, Huaming and Frazer, Kelly A. and Huson, Daniel H. and Scholkopf, Bernhard and Nordborg, Magnus and Ratsch, Gunnar and Ecker, Joseph R. and Weigel, Detlef }, citeulike-article-id = {1474652}, doi = {10.1126/science.1138632}, journal = {Science}, keywords = {population\_genomics, variation}, month = {July}, number = {5836}, pages = {338--342}, posted-at = {2008-07-01 13:20:37}, priority = {2}, title = {Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana}, url = {http://dx.doi.org/10.1126/science.1138632}, volume = {317}, year = {2007} }

TY - JOUR ID - citeulike:1474652 L3 - citeulike-article-id:1474652 TI - Common Sequence Polymorphisms Shaping Genetic Diversity in Arabidopsis thaliana JF - Science VL - 317 IS - 5836 SP - 338 EP - 342 N2 - 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 [~]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. 10.1126/science.1138632 KW - population_genomics KW - variation AU - Clark, Richard AU - Schweikert, Gabriele AU - Toomajian, Christopher AU - Ossowski, Stephan AU - Zeller, Georg AU - Shinn, Paul AU - Warthmann, Norman AU - Hu, Tina AU - Fu, Glenn AU - Hinds, David AU - Chen, Huaming AU - Frazer, Kelly AU - Huson, Daniel AU - Scholkopf, Bernhard AU - Nordborg, Magnus AU - Ratsch, Gunnar AU - Ecker, Joseph AU - Weigel, Detlef PY - 2007/07/20/ UR - http://dx.doi.org/10.1126/science.1138632 ER -