The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana. Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every week from the latest published research literature and community data submissions.
The Nottingham Arabidopsis Stock Centre (NASC) provides seed and information resources to the International Arabidopsis Genome Programme and the wider research community. It was established in April 1991 as part of the Plant Molecular Biology initiative of the Agricultural and Food Research Council (AFRC). It is based in the Plant Science Division of the School of Biosciences at the University of Nottingham, Sutton Bonington Campus, UK. The Centre is funded by the Biotechnology and Biological Sciences Research Council (BBSRC) and the University of Nottingham.
The Arabidopsis Information Portal is an online resource for plant biology research. It houses the Arabidopsis thaliana genome sequence and associated annotation. The current implementation provides an indexed database of core genomic information. Araport uses software from the InterMine and JBrowse projects to expose curated data from TAIR, GO, BAR, EBI, UniProt, PubMed and EPIC CoGe.
The SIGnAL website provides access to a number of large datasets as well as tools for accessing this data. Arabidopsis resources include: T-DNA Express; the Salk Homozygote T-DNA Collection; Arabidopsis Tiling Array Transcriptome; Arabidopsis Gene ORFeome Collection; Arabidopsis GMUCT Uncapped & Cleaved Transcripts; EIN3 –Ethylene Chip-seq/RNA-seq browser; High Resolution Arabidopsis Exosome; Arabidopsis Cyclome; Arabidopsis 1,001 Genomes Epigenomes, Transcriptomes & Physical Maps; Salk Arabidopsis 1,001 Genomes; Perlegen Arabidopsis Resequencing; Single Feature Polymorphism Database; High Resolution Arabidopsis Methylome; Transgenerational Inheritance of Methylation Variants; Single-base Resolution Epigenome Maps; Arabidopsis Population Epigenomic Diversity; Arabidopsis Biotic Stress Epigenome; Plant Cistrome /Epicistrome Atlas; Arabidopsis Root Cell-type Methylomes; Arabidopsis Seed Methylomes; Arabidopsis Interactome (AI-1); Abscisic Acid TF Network; Arabidopsis thaliana transcription factor interaction network (AtTFIN-1).
GABI-Kat was initiated at the Max Planck Institute for Plant Breeding Research (Cologne, Germany) in the year 1999. The project was moved from MPIPZ Cologne to Bielefeld University (Chair of Genome Research, Bernd Weisshaar) in late 2006. User access to the T-DNA insertion mutant collection and its Flanking Sequence Tags (FSTs) is provided by the front end SimpleSearch.
There were several motivations for the recently completed first phase of the 1001 Genomes project: to quantify genome variation in a large and representative sample of accessions; to investigate the demographic history of the species; to identify features that make specific geographic or genetic subsets particularly well suited for forward genetics, field experiments and selection scans; and to provide a powerful GWAS resource. Previous studies had shown that the ability to detect footprints of selection depended greatly on the sample (e.g., Cao et al., 2011; Long et al., 2013; Huber et al., 2014). Similarly, while GWAS have identified common alleles with major effects from as few as 96 accessions (Aranzana et al., 2005; Atwell et al., 2010), a much larger sample is required for most traits. The SNP-genotyped RegMap panel (Horton et al. 2012) provided such a collection, but did not efficiently capture all SNPs and structural variants. Fully sequencing this collection would be of limited benefit, as one could accurately impute the missing data by sequencing a subset. We therefore assembled a set of accessions that sufficiently overlap the RegMap panel for imputation of variants in all lines. The combined collection constitutes a powerful resource for determining how genetic variation translates into phenotypic variation.
The Multinational Arabidopsis Steering Committee (MASC) has its origin in the 1990s when scientists from the United States, Europe, Japan and Australia formed an ad hoc committee to promote large-scale studies in Arabidopsis thaliana. One of the main aims of the committee was and still is to strengthen international collaboration and coordination, to reduce redundancy and to help in guiding the community in making progress on projects that can be successful only by combined international efforts. This idea of a combined and coordinated effort accompanied by the policy of open data sharing has proven successful and led to the establishment of Arabidopsis thaliana as a reference plant and the Arabidopsis community as being one of the most active research communities. MASC is composed of representatives from each country with major efforts in Arabidopsis research or coalition of countries with smaller programs. It is open to any country interested in participating.