Arabidopsis thaliana
Arabidopsis thaliana is a small flowering plant in the Brassicaceae family and one of the principal model organisms in plant genetics, genomics, development, epigenetics, and molecular biology. Its compact genome, short generation time, extensive mutant collections, and well-developed community resources have made it a central reference species for functional plant research.
AraBase provides browser-based access to two major Arabidopsis reference resources. TAIR12 represents the current genome and annotation release used by AraBase, while TAIR10 together with Araport11 provides a widely used historical reference assembly and community annotation. These resources are presented separately to prevent ambiguity between assemblies and annotation releases.
This page summarizes the available genome assemblies, annotations, downloadable files, tools, external resources, and citation information. AraBase is implemented as a static genomic database, with lightweight searches, sequence retrieval, and genome browsing performed in the user’s browser.
Genome Information
| Metric | TAIR12 | TAIR10 / Araport11 |
|---|---|---|
| Assembly / release | TAIR12 | TAIR10 assembly with Araport11 annotation |
| Reference species | Arabidopsis thaliana | Arabidopsis thaliana |
| Nuclear chromosomes | 5 | 5 |
| Organelle sequences | Chloroplast and mitochondrial sequences included | Chloroplast and mitochondrial sequences included |
| Genome FASTA | Athaliana_TAIR12_genomic_Chr_softmasked.fa.gz | TAIR10_chr_all.fa.gz |
| Primary gene annotation | TAIR12 protein-coding gene annotation | Araport11 protein-coding gene annotation |
| Non-coding RNA annotation | TAIR12 non-coding RNA annotation | Araport11 non-coding RNA annotation |
| Transposable-element annotation | TAIR12 transposable elements, TE subclasses, and non-TE repeats | Araport11 classified transposable elements and TE genes |
| Genome browser | Available | Available |
| Sequence extraction | Gene, transcript, CDS, and protein where supported | Gene, transcript, CDS, protein, and TE/repeat where supported |
Main Data
| Resource | TAIR12 | TAIR10 / Araport11 | Description |
|---|---|---|---|
| Genome assembly | Athaliana_TAIR12_genomic_Chr_softmasked.fa.gz | TAIR10_chr_all.fa.gz | BGZF-compressed reference genome FASTA. |
| Gene annotation | TAIR12_protein_coding_with_UTRs.gff3.gz | Araport11_GFF3_genes_transposons.20250813_protein_coding.gff3.gz | Protein-coding gene annotation in BGZF-compressed GFF3 format. |
| Non-coding RNA annotation | TAIR12_non_coding_RNA.gff3.gz | Araport11_GFF3_genes_transposons.20250813.gff3.all_ncRNAs.gff3.gz | Araport11 non-coding RNA annotation. |
| TE annotation | TAIR12_All_TE.gff3.gz | Araport11_GFF3_genes_transposons.20250813_classified_transposable_element.gff3.gz | Classified transposable-element annotation. |
| Complete annotation | TAIR12_genome_annotation_TAIR.gff3.gz | Araport11_GFF3_genes_transposons.20250813.gff3.gz | Combined Araport11 genes and transposable-element annotation. |
External Resources
| Resource | Description |
|---|---|
| TAIR | The Arabidopsis Information Resource: genome annotation, gene information, literature, stocks, and community resources. |
| Araport | Arabidopsis community portal and data resources. |
| Ensembl Plants | Genome browser, gene annotation, comparative genomics, and plant variation resources. |
| NCBI Taxonomy: Arabidopsis thaliana | NCBI taxonomy record for Arabidopsis thaliana. |
| CoGe | Comparative genomics and genome evolution analysis platform. |
| Phytozome | Plant comparative genomics portal with genome assemblies, annotations, and gene-family resources. |
Citation
Please cite AraBase together with the relevant genome assembly, annotation release, and software used in your analysis.
AraBase
Chen, H., Emmerson, R., and Mosher, R. 2026. Near-gapless and haplotype-resolved Capsella genomes enable investigation into genomic consequences of mating system shifts. bioRxiv, 2026.07.10.737683. https://doi.org/10.64898/2026.07.10.737683
TAIR12
Reiser, L., Proia, A., Bakker, E., Subramaniam, S., Khosa, K., Sawant, S., Chen, X., Prithvi, T., and Berardini, T. Z. 2026. Recent major changes to TAIR: updates to the database, website, and Arabidopsis genome. Genetics 232(4):iyaf248. https://doi.org/10.1093/genetics/iyaf248
Wlodzimierz, P., Rabanal, F. A., Burns, R., et al. 2023. Cycles of satellite and transposon evolution in Arabidopsis centromeres. Nature 618:557–565. https://doi.org/10.1038/s41586-023-06062-z
TAIR10
Lamesch, P., Berardini, T. Z., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R., Muller, R., Dreher, K., Alexander, D. L., Garcia-Hernandez, M., Karthikeyan, A. S., Lee, C. H., Nelson, W. D., Ploetz, L., Singh, S., Wensel, A., and Huala, E. 2012. The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools. Nucleic Acids Research 40(D1):D1202–D1210. https://doi.org/10.1093/nar/gkr1090
Araport11
Cheng, C.-Y., Krishnakumar, V., Chan, A. P., Thibaud-Nissen, F., Schobel, S., and Town, C. D. 2017. Araport11: a complete reannotation of the Arabidopsis thaliana reference genome. The Plant Journal 89(4):789–804. https://doi.org/10.1111/tpj.13415
JBrowse 2
Diesh, C., Stevens, G. J., Xie, P., De Jesus Martinez, T., Hershberg, E. A., Leung, A., Guo, E., Dider, S., Zhang, J., Bridge, C., Hogue, G., Wang, X., Liu, G., Dunn, M., Holmes, I. H., and Buels, R. M. 2023. JBrowse 2: a modular genome browser with views of synteny and structural variation. Genome Biology 24:74. https://doi.org/10.1186/s13059-023-02914-z
BAR / ePlant
Sullivan, A., Lombardo, M. N., Pasha, A., Lau, V., Zhuang, J. Y., Christendat, A., Pereira, B., Zhao, T., Li, Y., Wong, R., Qureshi, F. Z., and Provart, N. J. 2025. 20 years of the Bio-Analytic Resource for Plant Biology. Nucleic Acids Research 53(D1):D1576-D1586. https://doi.org/10.1093/nar/gkae920