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About Brachypodium distachyon
In common with the model plant, Arabidopsis, Brachypodium distachyon has several features that recommend it as a model plant for functional genomic studies especially in the grasses. Traits that make it an ideal model include its small genome (~355Mbp), small physical stature, a short lifecycle, 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, barley) than to the other cereals. [more].
Genome Sequencing and Gene Prediction (Brachy1.2)
Sequencing of Brachypodium distachyon inbred line Bd21 was performed by the US Department of Energy Joint Genome Institute (JGI) as part of its Community Sequencing Program. Sequencing followed a whole genome shotgun strategy and achieved an average genome coverage of 8x. The assembly has been integrated with BAC-based physical maps and genetic linkage maps to produce a final sequence assembly of 83 scaffolds. Of these, 99.6% of the sequence was contained in five scaffolds, each representing one chromosome. [more].
The Gramene release31 has updated gene annotation Brachy1.2. Genes were predicted by MIPS/JGI as follows; protein coding gene models were derived from weighted consensus predictions based on several types of evidence: ab initio gene finders, protein homology and optimal spliced alignments of expressed sequence tags (ESTs) and tentative consensus transcripts (TCs). A statistical combiner was trained and applied to the whole genome sequence to integrate experimental evidence into a consensus gene model for each locus. These gene models were rerun through the PASA pipeline to predict UTRs from EST information, to identify possible alternative splicing patterns, and to fit all predicted models to the splice sites supported by EST evidence. tRNA genes were identified by tRNA-SEscan using default parameters.
This release of the assembly (Brachy1.0) for Brachypodium distachyon is composed of 2792 chunks with a total length of 271.9 Mb assembled into:
- 5 chromosomes with a total length of 271.1 Mb
- 78 scaffolds with a total length of 0.8 Mb
Gramene/EnsemblGenomes Annotation
Additional annotations generated by the Gramene/EnsemblGenomes projects include:
- The standard set of Gramene analyses detailed here.
- Phylogenetic gene trees and whole-genome alignments with several plant and metazoan species, using Ensembl's Compara pipeline.
- Mapping to the genome of multiple sequence-based feature sets using gramene blat pipeline, see more.
Links
- 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
Data release
The Brachypodium genome has been released in pre-publication status from
the International Brachypodium Initiative. This is provided freely to be used
by anyone, but they have requested that the scientific ethics of other
groups publishing on this pre-publication data are respected. This is
outlined in detail in the Fort Lauderdale agreement
.