The genome browser used is Jbrowse2. You can find the general user guide here: https://jbrowse.org/jb2/docs/user_guide/
Below are some tips relevant for our dataset.
Fig. 1. An example session showing different tracks of the browser.
The genome browser allows flexible visualization and exploration of genomic data across multiple tracks.
You can hide tracks, or make them visible from the menu in the left upper corner of the genome tracks (1 and 2 in Fig.1). There are several tracks available - genome annotation, variation data for all the populations and the outgroups for A. lyrata, expression data - both short and long reads for Siberian selfer lineage NT1 (reference), expression and methylation data from Hämälä et al. 2022 (https://doi.org/10.7554/eLife.83115)
You can navigate through the genome using either genomic coordinates or A. thaliana gene ID (3 in Fig. 1). Genome location for A. lyrata and A. arenosa genomes are navigated independently.
You can change the track display settings according to your needs by clicking the three dots near the track name.
Samples in the VCF track (8 in Fig. 1) are colored by the lineage by default (10 in Fig. 1). You can change the colors or color them by another column in the metadata, such as ploidy level.
The variation track menu includes an option "cluster by genotype", which sorts the samples based on the genotypes in the displayed genomic region. This can help to see if there are distinct haplotypes in this region and if their distribution is population-specific.
By selecting "save track data" in the track menu you can download the VCF file of the displayed genomic region.
The population maps are constructed using the implementation developed by the 1001 genomes project (http://1001genomes.org/).
Piecharts summarize all samples within a geographic area. The size of the area depends on the current map scale. Colors in the piecharts represent ADMIXTURE clusters for A. lyrata and Entropy clusters for A. arenosa. The number of the clusters (K) can be changed by clicking on the gear icon in the top left corner of the map.
To access a more detailed help message press the "i" icon in the top right corner.
With the VCF selector you can download a VCF file for a selected genome region.
0. Choose either A. lyrata or A. arenosa genome from the top menu.
1. Choose the VCF file type.
You can download a VCF file of Biallelic SNPs only, 4-fold biallelic sites, or full VCF with all positions. Be aware that the full VCF has all positions, including invariant sites as well, therefore, the file is pretty big. So, please, try to avoid using this option on large genomic regions.
2. Choose the region of the genome in the format chromosome:start-end.
If you want to find the position of a certain gene, you can use the genome browser. For example, you can download the GFF file of a certain gene using "save track data" on the annotation track.
After that click "Apply", the system will check if the coordinates exist.
3. You can select the whole lineages to add them to your VCF. When you click on the lineage name all samples from this lineage will appear in your VCF. The name of the lineage and the corresponding samples will move to the right box.
4. You can also select samples individually by clicking on their names. If you want to cancel a selected sample or lineage, click its name in the box on the right.
5. Press submit and wait for your file to be processed.
This resource publication.
Glushkevich, Anna, Laura Steinmann, Nikita Tikhomirov, et al. 2026. “A Global Genomic Resource for Outcrossing Arabidopsis Lyrata and Arabidopsis Arenosa.” In bioRxiv. BioRxiv, March 3. https://doi.org/10.64898/2026.03.02.709016.
Publications of used sequencing data. You can find information about individual samples in the metadata tables.
A. lyrata
Bohutínská, Magdalena, Eliška Petříková, Tom R. Booker, et al. 2024. “Polyploids Broadly Generate Novel Haplotypes from Trans-Specific Variation in Arabidopsis Arenosa and Arabidopsis Lyrata.” PLoS Genetics 20 (12): e1011521.
Guggisberg, Alessia, Xuanyu Liu, Léonie Suter, et al. 2018. “The Genomic Basis of Adaptation to Calcareous and Siliceous Soils in Arabidopsis Lyrata.” Molecular Ecology 27 (24): 5088–5103.
Hämälä, Tuomas, Tiina M. Mattila, and Outi Savolainen. 2018. “Local Adaptation and Ecological Differentiation under Selection, Migration, and Drift in Arabidopsis Lyrata.” Evolution; International Journal of Organic Evolution 72 (7): 1373–1386.
Hämälä, Tuomas, and Outi Savolainen. 2019. “Genomic Patterns of Local Adaptation under Gene Flow in Arabidopsis Lyrata.” Molecular Biology and Evolution 36 (11): 2557–2571.
Kolesnikova, Uliana K., Alison Dawn Scott, Jozefien D. Van de Velde, et al. 2023. “Transition to Self-Compatibility Associated With Dominant S-Allele in a Diploid Siberian Progenitor of Allotetraploid Arabidopsis Kamchatica Revealed by Arabidopsis Lyrata Genomes.” Molecular Biology and Evolution 40 (7). https://doi.org/10.1093/molbev/msad122.
Marburger, Sarah, Patrick Monnahan, Paul J. Seear, et al. 2019. “Interspecific Introgression Mediates Adaptation to Whole Genome Duplication.” Nature Communications 10 (1): 5218.
Novikova, P. Y., N. Hohmann, V. Nizhynska, et al. 2016. “Sequencing of the Genus Arabidopsis Identifies a Complex History of Nonbifurcating Speciation and Abundant Trans-Specific Polymorphism.” Nature Genetics 48 (9): 1077–1082.
Scott, Alison D., Uliana K. Kolesnikova, Anna Glushkevich, et al. 2025. “Multiple Autopolyploid Arabidopsis Lyrata Populations Stabilized by Long-Range Adaptive Introgression across Eurasia.” Molecular Biology and Evolution 42 (8): msaf153.
Takou, Margarita, Tuomas Hämälä, Evan M. Koch, et al. 2021. “Maintenance of Adaptive Dynamics and No Detectable Load in a Range-Edge Outcrossing Plant Population.” Molecular Biology and Evolution 38 (5): 1820–1836.
Willi, Yvonne, Kay Lucek, Olivier Bachmann, and Nora Walden. 2022. “Recent Speciation Associated with Range Expansion and a Shift to Self-Fertilization in North American Arabidopsis.” Nature Communications 13 (1): 7564.
A. lyrata outgroups
Paape, Timothy, Roman V. Briskine, Gwyneth Halstead-Nussloch, et al. 2018. “Patterns of Polymorphism and Selection in the Subgenomes of the Allopolyploid Arabidopsis Kamchatica.” Nature Communications 9 (1): 3909.
The 1001 Genomes Consortium. 2016. “1,135 Genomes Reveal the Global Pattern of Polymorphism in Arabidopsis Thaliana.” Cell 166 (2): 481–491.
A. arenosa
Arnold, B. J., B. Lahner, J. M. DaCosta, et al. 2016. “Borrowed Alleles and Convergence in Serpentine Adaptation.” Proceedings of the National Academy of Sciences of the United States of America 113 (29): 8320–8325.
Bohutínská, Magdalena, Eliška Petříková, Tom R. Booker, et al. 2024. “Polyploids Broadly Generate Novel Haplotypes from Trans-Specific Variation in Arabidopsis Arenosa and Arabidopsis Lyrata.” PLoS Genetics 20 (12): e1011521.
Bohutínská, Magdalena, Jakub Vlček, Sivan Yair, et al. 2021. “Genomic Basis of Parallel Adaptation Varies with Divergence in Arabidopsis and Its Relatives.” Proceedings of the National Academy of Sciences of the United States of America 118 (21). https://doi.org/10.1073/pnas.2022713118.
Hollister, J. D., B. J. Arnold, E. Svedin, K. S. Xue, B. P. Dilkes, and K. Bomblies. 2012. “Genetic Adaptation Associated with Genome-Doubling in Autotetraploid Arabidopsis Arenosa.” PLoS Genetics 8 (12): e1003093. Originally published as PLoS Genetics.
Konečná, Veronika, Sian Bray, Jakub Vlček, et al. 2021. “Parallel Adaptation in Autopolyploid Arabidopsis Arenosa Is Dominated by Repeated Recruitment of Shared Alleles.” Nature Communications 12 (1): 4979.
Monnahan, Patrick, Filip Kolář, Pierre Baduel, et al. 2019. “Pervasive Population Genomic Consequences of Genome Duplication in Arabidopsis Arenosa.” Nature Ecology & Evolution 3 (3): 457–468.
Novikova, P. Y., N. Hohmann, V. Nizhynska, et al. 2016. “Sequencing of the Genus Arabidopsis Identifies a Complex History of Nonbifurcating Speciation and Abundant Trans-Specific Polymorphism.” Nature Genetics 48 (9): 1077–1082.
Preite, Veronica, Christian Sailer, Lara Syllwasschy, et al. 2019. “Convergent Evolution in Arabidopsis Halleri and Arabidopsis Arenosa on Calamine Metalliferous Soils.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 374 (1777): 20180243.
Weitz, Andrew P., Marinela Dukic, Leo Zeitler, and Kirsten Bomblies. 2021. “Male Meiotic Recombination Rate Varies with Seasonal Temperature Fluctuations in Wild Populations of Autotetraploid Arabidopsis Arenosa.” Molecular Ecology 30 (19): 4630–4641.
Yant, L., J. D. Hollister, K. M. Wright, et al. 2013. “Meiotic Adaptation to Genome Duplication in Arabidopsis Arenosa.” Current Biology: CB 23 (21): 2151–2156. Originally published as Current Biology : CB.