Undergraduate lab assistant, Rebecca Lamonthe, awarded HHMI Research Intership.

Having recently completed a very competitive NSF supported Research Experience for Undergraduates in Integrative and Evolutionary Biology summer program at UMass Boston, she will continue her research in our laboratory with the support of the Howard Hughes Medical Institute. Rebecca will functionally characterize noncoding RNAs predicted to target genes involved in cell wall biosynthesis. 10/15/2009.

The Brachypodium genome is now available.

Version 4.0 of Phytozome is now available and includes JGI v1.0 8x assembly of strain Brachypodium Bd21 with JGI/MIPS PASA annotation. 5/13/2009.

Sam Hazen presents at Dartmouth College 

Sam Hazen will present a seminar entitled 'Transcriptional Landscape of Plant Circadian Rhythms' at the Department of Biological Sciences, Dartmouth College on April 22.

Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays.

This study revealed widespread circadian clock regulation of the Arabidopsis genome extending well beyond the protein coding transcripts measured to date. This suggests a greater level of structural and temporal dynamics than previously known. View at Genome Biology

Biologists Identify Genes Controlling Rhythmic Plant Growth. 
The University of California San Diego, The Salk Institute for Biological Studies and Oregon State University has identified the genes that enable plants to undergo bursts of rhythmic growth at night and allow them to compete when their leaves are shaded by other plants. They reported that that these genes control the complex interplay of plant growth hormones, plant light sensors and circadian rhythms that permit plants to undergo rhythmic growth spurts at specific times of the day or year in response to varying levels of light and other environmental conditions.   9/15/2008. View at PloS Biology

DOE and USDA Announce More than $10 Million in Bioenergy Plant Feedstock Research.

Agriculture Under Secretary for Research, Education and Economics Gale Buchanan and Energy Department (DOE) Under Secretary for Science Raymond Orbach and today announced plans to award 10 grants totaling more than $10 million to accelerate fundamental research in the development of cellulosic biofuels.  8/7/2008. View summary

Network discovery pipeline elucidates conserved time of day specific cis-regulatory modules.

Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study we describe a hypothesis driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility we applied the pipeline to a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition tested and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover we show that the three transcription modules are conserved across Arabidopsis, poplar and rice. These results confirm the complex interplay between thermocycles, photocycles and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation.  View at PLoS Genetics

The DOE Joint Genome Institute has selected Brachypodium distachyon as a target for resequencing.

Energy-rich Portfolio of New Genome Sequencing Targets for DOE JGI. 
Bioenergy crop plants switchgrass and cassava, other important agricultural commodities such as cotton, and microbes geared to break down plant material to render biofuels, round out the roster of more than 40 projects to be tackled by the U.S. Department of Energy Joint Genome Institute (DOE JGI) over the next year.   7/11/2006

Why sequence Brachypodium?