Kbase is currently in alpha release and is targeted for full production release in early 2013.The community-driven and scalable open-source system is intended to provide a framework for evidence-based functional annotation of genome sequences. It will also enable the creation of metabolic and regulatory models that may be used to generate scientific hypotheses; as well…
Lessons from the adaptive strategies of a fungal pathogen
by ressaure Coniferous forests in Europe and North America have suffered several hundred million dollars in damages annually from the fungal pathogen Heterobasidion annosum. Aside from the economic losses, scientists are concerned by the white rot fungus that not only breaks down the wood for nutrients, but also releases the carbon dioxide trapped in the…
Foxtail Millet Genome an Improved Reference for Switchgrass
The DOE is interested in switchgrass as a prospective biofuels feedstock, but its genome is complicated because it has multiple copies of its chromosomes. As the world leader in sequencing plants and other organisms for their relevance to DOE missions, the JGI has sequenced switchgrass and several other plants that are candidate plant feedstocks; other…
Foxtail millet project in GenomeWeb Daily News
From Genomics in the Journals: “Bennetzen and colleagues from the University of Georgia, the HudsonAlpha Institute, the Department of Energy’s Joint Genome Institute, and elsewhere used Sanger sequencing complemented by high-throughput sequencing methods to generate a high-quality, 400 million base reference genome for foxtail millet. “ Read more at GenomeWeb Daily News
Foxtail millet project in Biofuels Digest
In an attempt to piece together the switchgrass genome, the DOE Joint Genome Institute (JGI) in an international partnership with includes the DOE BioEnergy Science Center (BESC) and the DOE Joint BioEnergy Institute (JBEI) has sequenced plant genomes of related candidate bioenergy crops such as sorghum and the model grass Brachypodium but may have found the missing…
Foxtail millet genome project in AgProfessional
One of the challenges in studying grasses for bioenergy applications is that they typically have long lifecycles and complex genomes. Jeremy Schmutz, head of the DOE JGI Plant Program at the HudsonAlpha Institute of Biotechnology, pointed out that foxtail millet has several advantages as a model. It’s a compact genome roughly half a billion bases…
Relative Reference: Foxtail Millet Offers Clues for Assembling the Switchgrass Genome
Arranging DNA fragments into a genome sequence that scientists can interpret is a challenge often compared to assembling a puzzle, except there is no box to provide an idea of what the picture is even supposed to be. Sometimes there’s guidance in the form of other publicly-available DNA sequences from related organisms that can be…
Microbes as the unknown variable in thawing permafrost
Permafrost covers a quarter of the Earth’s land surface and stores significant amounts of carbon. As global temperatures rise and cause the frozen soils to thaw, so have concerns on the fate of the stored carbon and on the global climate. One of the recent studies that looked at this question was conducted by researchers…
Mount Marty College students wrap first project with DOE JGI’s “Interpret a Genome” program
“Annotating genes is a lot of work, and you have to pay a lot of attention to detail,” said April Knapp, one of seven students who presented findings from the class’s research Friday. “But it’s also very interesting because bioenergy and biofuel is such a high-needs fields. To know that the research we did here…
Overcoming short-read genome sequence assembly challenges
The genome assembly challenges posed by short sequence reads from sequencing platforms such as 454/Roche and Illumina are well-documented; the lack of reference genome data can hinder attempts to put together the myriad of short DNA sequences. Researchers from the Georgia Institute of Technology and the DOE JGI wanted to determine the impact of short…