Arabidopsis 1001 Epigenomes, Genomes and Physical Maps

1001 Arabidopsis Genomes, Methylomes, Transcriptomes and Physical Maps

Genome Browser:
Group By: Accession Ecotype Id Geo Location

Note: The 1001 database contains Arabidopsis genomes, methylomes, transcriptomes and genome physical maps. The genomes have 1,227 tracks for displaying the genomic variants (SNPs and small indels) and 1,227 tracks of their read depths for 1,227 Arabidopsis accessions . The methylome data have 1,214 datasets of methylation calls, and 1,214 datasets of methylation reads in accessions, tissues, growth conditions. The transcriptome data have 1,059 datasets of transcript abundance signals. The physical maps have 19 tracks for displaying bionano data for 9 accessions. There are totally 6,062 tracks in addition to 2 gene model tracks.
It will take 0.1 second to activate a track. You might need 3-4 seconds to bring all tracks active in a 40-track folder. However, it will slow down your computer if you make too many tracks active. It is better to inactivate some tracks first before activating another tracks. You can double-click on a folder to activate all tracks in that folder. You can double-click an empty folder to inactivate all tracks from that folder. You can select 'Accession' (Accession Name), 'EcotypeID' (Ecotype Number) or 'Geo Location' to group the track paths in the "Track Selection". The default paths are based on geographic regions, and thus folders have variable tracks.

Project Description: The epigenome orchestrates genome accessibility, functionality and structure. Epigenetic variation can impact gene transcription and phenotypic diversity and may thus contribute to adaptation. Here we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Arabidopsis Genomes populations. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor both of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. We identified associations between transcription factor binding sites, methylation and nucleotide variations and co-expression modules through comparison to cistromes and epicistromes. Physical genome maps for nine of the most diverse accessions revealed how transposable elements and other structural variations shape the epigenome, with particularly dramatic effects on immunity genes. The Arabidopsis thaliana 1001 Epigenomes Project provides a comprehensive resource for understanding how epigenetic variations contribute to both molecular and non-molecular phenotypes in natural populations of the most widely studied model plant.

Publication Citation: Please cite this article as: Kawakatsu et al., Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions, Cell 166 (2), p492-505, 14 July 2016, http://dx.doi.org/10.1016/j.cell.2016.06.044
The 1001 Genomes Consortium (2016) 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana, Cell 166, 481-491, 14 July 2016

[] Schmitz et al., Patterns of population epigenomic diversity Nature Mar 14;495(7440):193-8. doi: 10.1038/nature11968. Epub 2013 Mar 6

Data Download: For methylomes:
- NCBI GEO Accession GSE43857 (Salk leaf/bud samples Illumina; Kawakatsu et al, 2016): 927 samples
- NCBI GEO Accession GSE54292 (GMI leaf samples 10C and 16C; Durbin et al., 2015): 284 samples
For transcriptomes:
- NCBI GEO Accession GSE80744 (Salk leaf samples Illumina; Kawakatsu et al, 2016): 728 samples
- NCBI GEO Accession GSE43858 (Salk leaf samples ABI SoLiD; Schmitz et al, 2013): 144 samples
- NCBI GEO Accession GSE54680 (GMI leaf samples 10C and 16C; Durbin et al., 2015): 323 samples
For gene body methylation data:
- All gene methylations

Collaboration: _10C and _16C data were generated by Nordborg lab, Gregor Mendel Institute (GMI) and _ebi data were generated by Weigel lab, Max Planck Institute (MPI). All other data were generated by Ecker lab, Salk Institute. The 1,211 genomic SNP and Indel data were from Nordborg - UChicago CRI server and 16 from 1001genomes.org.

FAQ: Open http://neomorph.salk.edu/FAQs/1001.php

Genome Browser:	Group By: Accession Ecotype Id Geo Location
	Note: The 1001 database contains Arabidopsis genomes, methylomes, transcriptomes and genome physical maps. The genomes have 1,227 tracks for displaying the genomic variants (SNPs and small indels) and 1,227 tracks of their read depths for 1,227 Arabidopsis accessions . The methylome data have 1,214 datasets of methylation calls, and 1,214 datasets of methylation reads in accessions, tissues, growth conditions. The transcriptome data have 1,059 datasets of transcript abundance signals. The physical maps have 19 tracks for displaying bionano data for 9 accessions. There are totally 6,062 tracks in addition to 2 gene model tracks. It will take 0.1 second to activate a track. You might need 3-4 seconds to bring all tracks active in a 40-track folder. However, it will slow down your computer if you make too many tracks active. It is better to inactivate some tracks first before activating another tracks. You can double-click on a folder to activate all tracks in that folder. You can double-click an empty folder to inactivate all tracks from that folder. You can select 'Accession' (Accession Name), 'EcotypeID' (Ecotype Number) or 'Geo Location' to group the track paths in the "Track Selection". The default paths are based on geographic regions, and thus folders have variable tracks.
Project Description:	The epigenome orchestrates genome accessibility, functionality and structure. Epigenetic variation can impact gene transcription and phenotypic diversity and may thus contribute to adaptation. Here we report 1,107 high-quality single-base resolution methylomes and 1,203 transcriptomes from the 1001 Arabidopsis Genomes populations. Although the genetic basis of methylation variation is highly complex, geographic origin is a major predictor both of genome-wide DNA methylation levels and of altered gene expression caused by epialleles. We identified associations between transcription factor binding sites, methylation and nucleotide variations and co-expression modules through comparison to cistromes and epicistromes. Physical genome maps for nine of the most diverse accessions revealed how transposable elements and other structural variations shape the epigenome, with particularly dramatic effects on immunity genes. The Arabidopsis thaliana 1001 Epigenomes Project provides a comprehensive resource for understanding how epigenetic variations contribute to both molecular and non-molecular phenotypes in natural populations of the most widely studied model plant.
Publication Citation:	Please cite this article as: Kawakatsu et al., Epigenomic Diversity in a Global Collection of Arabidopsis thaliana Accessions, Cell 166 (2), p492-505, 14 July 2016, http://dx.doi.org/10.1016/j.cell.2016.06.044 The 1001 Genomes Consortium (2016) 1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis thaliana, Cell 166, 481-491, 14 July 2016 [] Schmitz et al., Patterns of population epigenomic diversity Nature Mar 14;495(7440):193-8. doi: 10.1038/nature11968. Epub 2013 Mar 6
Data Download:	For methylomes: - NCBI GEO Accession GSE43857 (Salk leaf/bud samples Illumina; Kawakatsu et al, 2016): 927 samples - NCBI GEO Accession GSE54292 (GMI leaf samples 10C and 16C; Durbin et al., 2015): 284 samples For transcriptomes: - NCBI GEO Accession GSE80744 (Salk leaf samples Illumina; Kawakatsu et al, 2016): 728 samples - NCBI GEO Accession GSE43858 (Salk leaf samples ABI SoLiD; Schmitz et al, 2013): 144 samples - NCBI GEO Accession GSE54680 (GMI leaf samples 10C and 16C; Durbin et al., 2015): 323 samples For gene body methylation data: - All gene methylations
Collaboration:	_10C and _16C data were generated by Nordborg lab, Gregor Mendel Institute (GMI) and _ebi data were generated by Weigel lab, Max Planck Institute (MPI). All other data were generated by Ecker lab, Salk Institute. The 1,211 genomic SNP and Indel data were from Nordborg - UChicago CRI server and 16 from 1001genomes.org.
FAQ:	Open http://neomorph.salk.edu/FAQs/1001.php