1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 highquality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the finescale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes

Understanding global patterns of structural variation in Arabidopsis thaliana: Future of the 1001 Genome project

The recently released map of polymorphism of 1,135 re-sequenced A. thaliana natural inbred lines provides an invaluable resource to understand global genetic patterns in a large collection of wild individuals that are products of natural selection under diverse ecological conditions. Our work clarified prior hypotheses such as the strong impact of the last ice age on population structure and in addition revealed that modern A. thaliana is a mixture of stationary relicts and fast expanding survivors from different glacial refugia. In the future the resource will enable researchers to decipher more accurately how genetic variation translates into phenotypic variation. However, connecting hits from genome-wide association studies (GWAS) to causal sequences is still challenging since previous analysis approaches mostly rely on mapping to a single reference, which insufficiently captures structural variations (SVs) or the presence of sequences not found in the reference. Discovery and genotyping of such sequences remains computationally difficult with short read data, since they are often in repetitive regions and because they can the changes can be complex. The next objective for the 1001 Genomes project is to discover and genotype major classes of SVs in the global set of A. thaliana accessions. By reanalyzing the 1001 Genomes Project whole-genome sequencing (WGS) data together with long-read DNA technologies, we will survey SV mutation hotspots throughout the worldwide population and target so far undescribed patterns and classes of SV complexity. Here we present strategies, pilot studies and first results of our upcoming work that will provide struc- tural variations and polymorphisms as an integrated resource alongside with detailed information about epigenomes as well as molecular and nonmolecular phenotypes to understand how traits are connected to genomes and epigenomes

1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana

Arabidopsis thaliana serves as a model organism for the study of fundamental physiological, cellular, and molecular processes. It has also greatly advanced our understanding of intraspecific genome variation. We present a detailed map of variation in 1,135 high-quality re-sequenced natural inbred lines representing the native Eurasian and North African range and recently colonized North America. We identify relict populations that continue to inhabit ancestral habitats, primarily in the Iberian Peninsula. They have mixed with a lineage that has spread to northern latitudes from an unknown glacial refugium and is now found in a much broader spectrum of habitats. Insights into the history of the species and the fine-scale distribution of genetic diversity provide the basis for full exploitation of A. thaliana natural variation through integration of genomes and epigenomes with molecular and non-molecular phenotypes.ISSN:0092-8674ISSN:1097-417