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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]

A highly adaptable bacterium that can thrive alone or in symbiosis

Variovorax paradoxus is a β-proteobacterium typically found in the region where the plant roots interact with soil and has the ability to engage in mutually beneficial interactions with both plants and other bacterial species. The bacterium also has the ability to break down a wide range of contaminants including pesticides and crude oil compounds, and… [Read More]

Making Science’s Insights of the Decade list – twice

The December 17 issue of Science includes a special feature called “Insights of the Decade” and two of them feature work done by DOE JGI researchers. (Note: Free registration is required to read the articles online.) Genome research features prominently in Science’s Insights of the Decade list. (DNA helix image by DS from Flickr via… [Read More]

Breaking the Petabit barrier, a Tweet at a time

Earlier this year, the DOE JGI teamed with the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory to scale up its computing infrastructure to meet increasing user needs and the rising amount of data being generated. ESnet traffic map by Jon Dugan, ESnet Network Engineering Group, LBNL On Dec. 14, the… [Read More]

Unpredictable MDA biases in metagenomic analyses

Genomic studies of low-biomass environments is often limited by the amount of DNA available, and one solution has been to use a whole genome amplification technique that uses phi29 DNA polymerase known as multiple displacement amplification (MDA). When used in single cell genomic studies, one noted drawback of the procedure has been amplification bias that… [Read More]

Methanotroph Methylosinus trichosporium

Considered the second most important greenhouse gas, methane is 21 times more potent than carbon dioxide. Methane-oxidizing bacteria called methanotrophs help reduce levels of atmospheric methane. To better understand the bacteria involved in the global methane cycle, the DOE JGI sequenced, assembled and annotated the genome of Methylosinus trichosporium OB3b. The project was led by… [Read More]