About Brachypodium distachyon
Brachypodium distachyon, like Arabidopsis thaliana, has several features that recommend it as a model plant for functional genomic studies, especially in the grasses. It has a small, diploid genome (~355 Mbp), small physical size, a short life-cycle and few growth requirements. Brachypodium is related to the major cereal grain species but is understood to be more closely related to the Triticeae (wheat and barley) than to the other cereals.
What can I find? Homologues, gene trees, and whole genome alignments across multiple species.
Download alignments (EMF)
|Brachypodium distachyon : Arabidopsis thaliana||BLASTZ_NET | stats|
|Brachypodium distachyon : Hordeum vulgare||LASTZ_NET | stats|
|Brachypodium distachyon : Oryza sativa Indica||BLASTZ_NET | stats|
|Brachypodium distachyon : Oryza sativa Japonica||LASTZ_NET | stats|
|Brachypodium distachyon : Triticum aestivum||LASTZ_NET | stats|
Brachypodium sylvaticum transcriptome
De novo gene models from the RNA-Seq analysis of three Brachypodium sylvaticum populations  were mapped to the B. distachyon reference genome. Click here for example. Assembled data is available from the Jaiswal lab and raw reads are available from INSDC project PRJNA182761.
Triticum aestivum transcriptome
Wheat RNA-Seq, EST and UniGene datasets have been aligned to the Brachypodium distachyon genome:
- 454 Wheat RNA-seq data, from the study, ERP001415, were aligned using GMAP. Click here for example.
- All publicly available Wheat EST data were aligned using Exonerate, following the standard Ensembl pipeline. Click here for example.
- Wheat UniGene cluster sequence data were aligned using Exonerate, following the standard Ensembl pipeline. Click here for example.
Links (Brachypodium distachyon)
- Gramene species page for Brachypodium
- The International Brachypodium Initiative (IBI) community portal
- The John Innes Centre ModelCrop.org
- MIPS Brachypodium genome database
- Phytozome entry page for Brachypodium distachyon
- Jaiswal Lab at Oregon State University
- INSDC project PRJNA182761
Links (Triticum aestivum)
- MIPS Wheat Genome Database
- ENA study ERP000319: 454 pyrosequencing of the Triticum aestivum (bread wheat) genome to 5X coverage
- ENA study ERP001415: 454 sequencing of Triticum aestivum (bread wheat) cv. Chinese spring cDNA samples from a pool of tissues, from plants under drought stress and from circadian-sampled leaves
- Triticum aestivum ESTs at ENA
- Triticum aestivum UniGene cluster sequences at NCBI