This is the development site for the Brachypodium Genome Resources Project
The Brachypodium Genome Resources Project is part of the United States Department of Agriculture (USDA), Agricultural Research Service (ARS),
Genomics and Gene Discovery (GGD) Research Unit, located at the Western Regional Research Center
(WRRC) in Albany, CA. One of the efforts of this research unit is directed at Biofuels research. To best characterize the genomes of plants
being used for biofuels research, a model plant species is being adapted for this purpose; the model plant species is Brachypodium distachyon.
This is a companion site to the wEST (wheat EST) site and is thus named the bEST (brachypodium EST) site.
Oct, 2007 : The 4X Brachypodium distachyon genome sequence done at JGI is now available at brachypodium.org
This laboratory is beginning to characterize this genome both locally and in collaboration with others on several fronts:
- Developing a Brachypodium distachyon transformation system.
- A successful Agrobacterium-mediated transformation system was developed by GGD scientists.
- Developing a Brachypodium distachyon genetic map.
- GGD scientists are collaborating in this effort with other ARS (MN) scientists making SSLP markers from EST and BAC-end sequences.
- Developing a Brachypodium distachyon mutant population.
- in progress.
- Characterization of Brachypodium distachyon expressed genes via Expressed Sequence Tag (EST) analysis.
- 20,449 Brachypodium distachyon ESTs from five cDNA libraries were sequenced at GGD and deposited to NCBI dbEST.
Additional cDNA libraries will be sequenced by the DOE Joint Genome Institute.
- Develop a Brachypodium distachyon large-insert BAC libraries for genome manipulation.
- Three BAC libraries (HindIII and BamHI) were picked and arrayed onto high-density colony filters by scientists at GGD.
- Characterization of the Brachypodium distachyon genome sequence via BAC-end sequences.
- A publication is under review and some preliminary data is noted below.
- Develop a physical map of the Brachypodium distachyon genome.
- in progress at GGD and UC Davis.
- Sequence the Brachypodium distachyon genome.
- The DOE Joint Genome Institute has added the 320MB genome of Brachypodium distachyon
to their list of genomes to be sequenced.
- Integration of project data into the wEST-SQL and GrainGenes databases.
- Currently in progress at GGD.
Available Data and Links
July 31, 2008
The sequences genome of the Brachypodium chlorplast is made available:
Bortiri, E., Coleman-Derr, D., Lazo, G.R., Anderson, O.D., and Gu, Y.Q. 2008. The complete chloroplast genome sequence of Brachypodium distachyon: sequence comparison and phylogenetic analysis of eight grass plastomes. BMC Research Notes 2008, 1:61. DOI:10.1186/1756-0500-1-61
June 27, 2008
Molecular Markers from the GrainGenes Resource were compared against the rice genome (TIGR Release 5, 2007) and the 4X JGI pre-release genome sequence of Brachypodium distachyon. These markers and their map positions are now available from GrainGenes from the CMap Viewing Tool.
A nice view of the resolved map correspondences between Brachypodium and Rice can be seen in this image (Apologies: image removed by request until publication), but please take note that these correspondences were only generated from the available molecular markers in GrainGenes and not using the sequence itself.
Try out the GrainGenes CMap Viewing Tool and build your own comparisons (Apologies: Brachypodium map will be added again after publication).
November 7, 2007:
Analysis of BAC-ends used for physical map assembly and anchoring shotgun sequencing effort:
Huo, N., Lazo, G.R., Vogel, J.P., You, F.M., Ma, Y., Hayden, D.M., Coleman-Derr, D., Hill, T.A., Dvorak, J, Anderson, O.D., Luo, M.-C., and Gu, Y.Q. 2007.
The nuclear genome of Brachypodium distachyon : analysis of BAC end sequences. Functional and Integrative Genomics. DOI 10.1007/s10142-007-0062-7.
October 19, 2006:
Brachypodium distachyon BAC libraries are constructed:
Gu, Y., Lazo, G., Vogel, J., Coleman-Derr, D., Luo, M.C., Thilmony, R., Garvin, D., Anderson, O., Huo, N. 2006. Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome. 49(9):1099-1108.
January 11, 2006:
A Brachypodium distachyon tissue culture method is available:
Vogel, J.P., Garvin, D.F., Leong, O.M., and Hayden, D.M. 2006. Agrobacterium-mediated transformation and inbred line development in the model grass brachypodium distachyon. Plant Cell Tissue And Organ Culture. 84:199-211.
October 21, 2005:
Brachypodium distachyon, a close relative of wheat and possibly a model system for the study of wheat genes has over 20,000 EST sequences contributed to dbEST:
Vogel, J.P., Gu, Y.Q., Twigg, P., Lazo, G.R., Chingcuanco, D.L., Hayden, D.M., Donze, T., Vivia-Lindsay, A., Stamova, B., and Coleman-Derr, D. 2006. EST sequencing and phylogenetic analysis of the model grass brachypodium distachyon. Theoretical and Applied Genetics. 113: 186-195.
While the Brachypodium distachyon sequences may be downloaded from NCBI [HERE], the FASTA sequence files and their corresponding QUAL quality files generated from the USDA-ARS (Albany, CA) project are available below:
There were five cDNA libraries created from:
Additional sequences from the Triticeae can be obtained from the wEST web site, or the
wEST Tracefile Server.
Links to other Brachypodium distachyon Research Sites
BLAST Databases
This database is maintained locally and serves local research activities. Custom databases
are set up to screen against Triticeae and related sequences, Assemblies, cDNA libraries, and other
specialty formatted databases.
The wEST resource is a USDA-ARS sponsored server of nucleic acid sequence data for
Triticeae-associated research projects located at the USDA-ARS Western Regional Research Center,
Albany, California. Other associated projects which use resources located at this site are:
E-mail inquiries to: curator@wheat.pw.usda.gov