Brachypodium Genome Resources

Welcome to the Brachypodium resource page of the Genomics and Gene Discovery Research Unit at the USDA-ARS Western Regional Research Center in Albany, CA, USA. Brachypodium distachyon (Brachypodium) is a small annual grass that is being developed as a model for the grasses in much the same way as Arabidopsis thaliana (Arabidopsis) has been developed as a model for dicotyledenous plants (dicots). Over the past several years we have put considerable effort into developing the tools necessary to use Brachypodium as a modern model organism. Some background information about Brachypodium may be found HERE. In order to aid researchers interested in using Brachypodium for in their laboratories, we have compiled a list of resources and methods we, along with collaborators, have developed over the past few years. We have also included a list of our publications that you may download as PDFs and links to other Brachypodium sites for even more information. We hope you find this information useful and if you have any questions feel free to contact us.

METHODS

RESOURCES

Genome sequence: The entire Brachypodium genome has been sequenced and the assembly was of very high quality. We are currently working on a manuscript describing the genome sequencing project. The 8X genome assembly and the version 1.0 annotation is now available at: www.brachypodium.org and www.phytozome.org.

Germplasm: In collaboration with colleagues from Turkey, we recently described over 200 new inbred lines. For more information please see our publication in BMC Plant Biology (in press).

T-DNA mutants: We are currently generating >7,500 T-DNA mutants as part of a DOE-funded grant to create 3,000 lines and have started sequencing the flanking DNA. We are in the process of creating a website where you can search for knockouts and order seeds.

High-density SNP map: We have created a genetic linkage map using a Bd21 X Bd3-1 mapping population created by David Garvin containing 562 markers. This map has been used to assemble the whole genome into chromosome scale assemblies (more details coming soon).

CMap viewer: We have loaded the final Brachypodium genome into the GrainGenes CMap viewing tool to enable comparative genomics. The sequence will be available soon.

Physical Map: (a link will be provided soon).

Publications

Vogel, J.P., Tuna, M., Budak, H., Huo, N., Gu, Y.Q., Steinwand, M.A. 2009 Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC Plant Biology. (in press)

Wei B., Cai T., Zhang R., Li A., Huo N., Li S., Gu Y.Q., Vogel J., Jia J, Qi Y., Mao, L. 2009 Novel microRNAs uncovered by deep sequencing of small RNA transcriptomes in bread wheat (Triticum aestivum L.) and Brachypodium distachyon (L.) Beauv. Functional and Integrative Genomics (in press)

Huo, N., Vogel, J., Lazo, G.R.., You, F., Ma, Y., McMahon, S., Dvorak, J., Anderson, O., Luo, M., and Gu, Y. 2009 Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat. Plant Molecular Biology 70: 47

Vogel, J., and Bragg, J. 2009 Brachypodium distachyon, a New Model for the Triticeae. in Genetics and Genomics of the Triticeae. Springer. in press

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

Vogel, J., Hill, T. 2008 High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3. Plant Cell Rep. 27: 471-478.

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. 2008. The nuclear genome of Brachypodium distachyon : analysis of BAC end sequences. Functional and Integrative Genomics. 8:135-147.

Vogel, J. 2008 Unique aspects of the grass cell wall. Current Opinion in Plant Biology. 11: 301-307

Garvin, D., Gu, Y., Hasterok, R., Hazen, S., Jenkins, G., Mockler, T., Mur, L. J., and Vogel, J. P. 2008. Development of genetic and genomic research resources for Brachypodium distachyon, a new model for grass crop research. Crop Science 48: S69-S84.

Huo, N., Gu, Y., Lazo, G., Vogel, J., Coleman-Derr, D., Luo, M., Thilmony, R., Garvin, D., and Anderson, O. 2006 Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome 49:1099-1108.

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.

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.

Analysis of BAC-ends used for physical map assembly and anchoring shotgun sequencing effort:
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

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