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POPSEQ for Plant Genome Assembly

New approach allows researchers to work on many species regardless of sequence resources The Science Plant genomics researchers evaluated POPSEQ, a method for assembling complex plant genomes using next-generation sequencing. The Impact Using a large, complex and highly-repetitive plant genome, the findings yielded results comparable to the previously assembled sequence. The proof of principle demonstrates… [Read More]

Subsurface Sediment Yields Novel Organism

Metagenomic analysis emphasizes the “extraordinary microbial novelty” of poorly-explored subsurface ecosystems The Science Through metagenomics, researchers reconstructed a dominant organism and member of a new phylum-level lineage from an aquifer sediment in Colorado. The Impact Analysis of the complete microbial genome led to a detailed metabolic model with evidence for multiple new enzymes and pathways…. [Read More]

Hope for Re-establishing Gulf of Mexico Microbial Populations

Comparative Analysis Shows Petroleum Reduced Species Diversity The Science Researchers used metatranscriptomic analyses to compare the microbial populations in the Gulf of Mexico before and after the Deepwater Horizon oil spill to learn more about the impact of adding petroleum to the waters. The Impact Though the oil spill reduced the diversity of the microbial… [Read More]

Solving the Secrets of Sedimentary Microbes

Microbes from Phylum Chloroflexi Provide Clues to Carbon Cycling, Respiration in Sediments The Science Through metagenomics, researchers sequenced 86 organisms from the phylum Chloroflexi that represent 15 distinct lineages in order to discover the secrets of microbial life within terrestrial aquifer sediment deposits. The Impact These Chloroflexi microbes were found to have metabolic processes involved… [Read More]

Moss Sequencing “Ennobles” Flagship Genome

Physcomitrella Genome Expected to Provide Help with Global Climate Change The Science An international team of scientists has annotated all 32,275 genes of Physcomitrella patens, a moss sequenced by the DOE Joint Genome Institute that contains about 10,000 more genes than humans. The Impact It is widely believed that the P. patens genome contains information… [Read More]

Breaking Down Biomass with Thermophilic Bacteria

The deconstruction of biomass is a pivotal process in the biofuel industry, but the enzymes that possess a significant role in the breakdown of biomass remain relatively unexplored. To this end, DOE researchers at several national labs and user facilities are studying thermophilic bacteria, organisms that survive and thrive in high-temperature environments, that contain these… [Read More]

The Importance and Function of Nitrogen-Fixing Microbes

All organisms on Earth require nitrogen to survive, but most cannot use nitrogen unless it is combined with other elements. These compounds are formed by the process known as nitrogen fixation, which can only be carried out in nature with the help of microorganisms. In agriculture, fertilizers are often deployed to supplement nitrogen levels in… [Read More]

Solving Microbial “Dark Matter” With Single-Cell Genomics

Microbes facilitate many of the natural cycles in plant growth and health, and play roles in  many processes in nutrient cycles that control certain environments and climates. Though thousands of these microbes have been identified, the majority of these microbes are still a mystery to scientists and are referred to as microbial “dark matter.” Steps… [Read More]

Noncoding DNA Map Provides Insight to Plant Gene Regulation

Widely used as a model for plant research, Arabidopsis thaliana was the first plant to have its genome completely sequenced. However, there is still much to learn about this plant, including the function of its many DNA conserved noncoding sequences (CNSs). These regions hold key roles in activating certain traits during plant development, but why… [Read More]

Genome Streamlining a Survival Strategy in Marine Microbes

The ocean’s surface or photic zone, where sufficient light enables photosynthesis, harbors vast amounts of life-sustaining microbes that attach themselves to plankton. A large portion of the carbon in the ocean is processed by these microbes, which helps sustain the abundance of diverse marine life. But these microbes can be exceedingly difficult to culture in… [Read More]