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Celebrating the Eucalyptus Reference Genome

New Phytologist dedicates an entire issue to various research directions based on the tree genome. The Science: Building off the Eucalyptus grandis tree genome that researchers at the DOE Joint Genome Institute helped sequence and analyze, several researchers demonstrate the utility of the reference genome in the June 2015 special issue of New Phytologist. The… [Read More]

Charting Short-Term Results of Wetlands Restoration

Patterns in carbon sequestration and emissions are charted in the San Joaquin Delta. The Science: Researchers at the DOE Joint Genome Institute sequenced and analyzed the microbial communities in restored wetlands in the Sacramento-San Joaquin Delta and combined the data with greenhouse gas measurements from the area to track patterns in methane emissions. The Impact:… [Read More]

The Most Complete Functional Map of an Entire Enzyme Family

DOE-funded researchers develop a new process for annotating cellulose-degrading enzymes. The Science: Researchers at two Department of Energy-funded Scientific User Facilities collaborated with one of three Bioenergy Research Centers to develop and analyze high-resolution crystal structures of an enzyme from the cellulose-degrading GH55 family. They then went further and were able to apply a variety… [Read More]

Understanding the [Non-Coding] Spaces Between

DOE JGI researchers sequenced and analyzed a cyanobacterium with known nitrogen-fixing capabilities. The Science: Researchers sequenced and analyzed the uncommonly large genome of a nitrogen-fixing cyanobacterial strain, comparing it to the more than 150 extant cyanobacterial genomes. The Impact: Unlike many of the existing cyanobacterial genome sequences, the genome of Trichodesmium erythaeum IMS 101 is… [Read More]

Big Plant Genomes: Formerly Intractable, No Longer Insurmountable

DOE JGI researchers have developed an assembly and mapping strategy for any species, including large and complex genomes. The Science: Through a combination of high-throughput sequencing, high performance computing, and genetic mapping, DOE JGI researchers have derived a sequence assembly for the highly repetitive plant genome of bread wheat (Triticum aestivum). The Impact: The researchers… [Read More]

Targeted Sorting of Microbial Cells

DOE JGI is enabling collaborators to develop a universally applicable technique for studying microbial metabolic activities. The Science: A team led by University of Vienna researchers has developed a way to identify and sort single microbial cells through a probe-independent process that uses heavy water (laced with deuterium) which is then incorporated into mostly lipids… [Read More]

Identifying causes of poplar canker

A comparative fungal genome analysis could help bioenergy researchers develop disease-resistant poplar plantations. The Science: A team including DOE JGI researchers conducted a comparative analysis of two fungal tree pathogens to find out how one of them has gained the capability to significantly damage hybrid poplar plantations. The Impact: The development of poplar plantations for… [Read More]

Complete Genomes from Single Cells Still Elusive

DOE JGI researchers describe the current challenges in single-cell genomics. The Science: DOE JGI researchers review the status of single-cell genomics, and how close scientists are to being able to reconstruct an individual cell’s genome. The Impact: As an alternative method of studying microbial communities, single-cell genomics allows researchers to link function to phylogeny without… [Read More]

Enhancing Microbial Pathways for Biofuel Production

DOE JGI, JBEI researchers collaborate on improving terpene production in E. coli. Science: Researchers from the DOE JGI and the Joint Bioenergy Institute identified genes in an E. coli microbial metabolism pathway that could improve the production of terpenes. The Impact: Terpenes are high-energy compounds produced in microbes and plants that could be used for… [Read More]

How a White Rot Tackles Freshly-Cut Wood

Unlike many other white rot fungi, P. gigantea prefers to colonize freshly-harvested wood. The Science: Researchers sequenced and analyzed the white rot fungus Phlebiopsis gigantea, which can break down fresh-cut conifer sapwood. They also sequenced and analyzed the set of P. gigantea’s secreted proteins (secretome) and the set of all of its RNA molecules (transcriptome)…. [Read More]