Whole-genome sequencing of multiple Arabidopsis thaliana populations

By Jun Cao, Korbinian Schneeberger, Stephan Ossowski, Torsten Günther, S. Bender, Joffrey Fitz, Daniel Koenig, C. Lanz, Oliver Stegle, Christoph Lippert and 7 more. Nature Genetics, 2011

976 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/d518dbae17cb2f18dcb7361d61c54c30991e0413

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Citations in the corpus

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data (2014, background): “A variety of studies have begun to utilize and illustrate how to deal with extensive SNP data [5-10].”
Comprehending crystalline β-carotene accumulation by comparing engineered cell models and the natural carotenoid-rich system of citrus (2011, positive): “The selected list of genes was then screened for mismatches at the amino acid level between the resequenced Col-0 genome (Cao et al., 2011) and the Ler-0 genome (Gan et al.”
1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana (2016, methodology): “, 2008), soon followed by the analysis of larger collections (Cao et al., 2011; Gan et al., 2011; Long et al., 2013; Schmitz et al., 2013).”
Evolution of Gene Duplication in Plants1[OPEN] (2016, background): “Initiatives like the Arabidopsis 1001 Genomes Project (Cao et al., 2011) and parallel efforts in other species may soon provide some insights in this regard.”
A framework for incorporating evolutionary genomics into biodiversity conservation and management (2015, neutral): “See [107,108].”
The advantages and limitations of trait analysis with GWAS: a review (2013, background): “Recent whole-genome sequencing has revealed a much higher SNPs density in Arabidopsis [44-46], with approximately 7 Million SNPs within a worldwide sample.”
PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R (2014, background): “SNP files for 80 individuals (Cao et al. 2011) into a subdirectory named " Arabidopsis.”
Epigenomic diversity in a global collection of Arabidopsis thaliana accessions (2016, neutral): “The nearly symmetrical ‘‘gains’’ and ‘‘losses’’ relative to the reference set the optical maps apart from previous efforts based on de novo assemblies of short reads, which suffered from reference bias and therefore always reported more ‘‘losses’’ than ‘‘gains’’ (e.g., Cao et al., 2011).”
Demographic fate of Arabidopsis thaliana cohorts of autumn‐ and spring‐germinated plants along an altitudinal gradient (2012, methodology): “thaliana accessions (Cao et al. 2011; Schneeberger et al. 2011; Weigel 2012) should be complemented with equal efforts to generate long-term life cycle and population performance data across multiple environments whereA.”
The Ensembl Variant Effect Predictor (2016, background): “In other species, efforts such as Genome 10K (Koepfli et al. 2015), the 1001 Arabidopsis genomes (Cao et al. 2011) and 1000 bull genome project (Daetwyler et al. 2014) have similar goals, but operate under different funding models, often with less support than the Homo sapiens focused projects.”