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Comparative genomics of social amoebae

Found in soils worldwide, slime molds such as Dictyosteliumdiscoideumare perhaps best known by their behaviors in the presence or absence of food. When food is plentiful, the social amoeba behave as individuals, but when food is scarce, they come together to form multicellular “fruiting bodies” that look like a flower bud atop a single stalk… [Read More]

First analysis of Trichoderma species as biocontrol agents

Trichodermaatroviride and T. virens are filamentous fungi commonly found in the soil and are good at protecting crops such as beans, tomatoes, strawberries and cotton against a range of fungal pathogens. Their ability to do so could offer bioenergy crop growers an alternative to chemical pesticide treatment. Both were selected for sequencing by the DOE… [Read More]

Arabidopsis lyrata reference genome now available

Arabidopsis thaliana is a small flowering plant often used as a model system by researchers. As part of the 2006 Community Sequencing Program portfolio, the DOE JGI selected A. thaliana’s close relative A. lyrata for sequencing. By comparing their genomes and the genomes of other, related species, researchers could gain insight into plant genetics, specifically… [Read More]

ORNL collaboration to understand methylmercury production

Mercury pollution in aquatic environments has been a concern, though the contaminants are mainly sourced from industrial processes and fossil fuel combustion. Isolated from Chesapeake Bay sediment, the sulfate-reducing bacterium, Desulfovibriodesulfuricansstrain ND132, can also produce the human neurotoxin methylmercury. “What is not known are the genes or the proteins that allow these bacteria to mediate… [Read More]

Finding cellulases in sediment from a paper mill

During the DOE JGI User Meeting held in Walnut Creek, Calif. from March 22-24, 2011, collaborator Daniel Distel noted that more than 20 enzymes are needed to break down cellulose. To assist in identifying novel cellulose degraders and thus improve cellulosic biofuel production processes, a team of DOE JGI researchers including Microbial Program head TanjaWoyke… [Read More]

Toward a Genomic Encyclopedia of Fungi

Fungi are key components of terrestrial ecosystems and help maintain the interactions between a myriad of species of animals, plants and bacteria that make up these environments. With the ability to thrive in a wide variety of ecological niches, fungi are essential to the global carbon cycle, and the enzymes and metabolites they produce are… [Read More]

DOE JGI Highlight: First genome of a Harmful Algal Bloom species

Algae play key roles in the global carbon cycle, helping trap carbon emissions. But some algal species can bloom, discoloring coastal waters and reduce the amount of light and oxygen available in the ecosystem. To describe these events, the term “harmful algal blooms” (HABs) was introduced two decades ago to note that accumulation of algal… [Read More]

Daphnia pulex, the first crustacean genome

A keystone species in freshwater ecosystems, the water flea Daphnia pulex, is roughly the size of the equal sign on a keyboard. In the February 4 issue of Science, the nearly decade-long collaboration between the Daphnia Genomics Consortium and the DOE JGI culminated with a report on this first crustacean genome. “Daphnia is one of… [Read More]

Rumenating on improving biofuel production

Developing alternative fuels from plants has been challenging in part due to the high costs associated with processing plant biomass to more easily convert it into sugars and from there into biofuels. Ruminants such as the cow, however, can eat more than a hundred pounds of plant matter a day and break it down.  Switchgrass… [Read More]

JGI Highlight: More Caldicellulosiruptor bacterial genome sequences

The Caldocellulosiruptor genus contain bacteria that are capable of producing hydrogen and degrading plant biomass. Found all over the world, such as in geothermal hot springs in Russia and Iceland to solar-heated mud flats in California, the bacteria thrive in high temperatures. C. saccharolyticus (Image courtesy of A. Pereira & M. Verhaart, Wageningen University, Netherlands)… [Read More]