February 19, 2014
Pond-dwelling powerhouse's genome points to its biofuel potential. Duckweed is a tiny floating plant that's been known to drive people daffy. It's one of the smallest and fastest-growing flowering plants that often becomes a hard-to-control weed in ponds and small lakes. But it's also been exploited to clean contaminated water and as a source to produce pharmaceuticals. Now, the genome of Greater Duckweed (Spirodela polyrhiza) has given this miniscule plant's potential as a biofuel source a big boost. In a paper published February 19, 2014 in the journal Nature Communications, researchers from Rutgers University, the Department of Energy Joint Genome Institute and several other facilities detailed the complete genome of S. polyrhiza and analyzed it in comparison to several other plants, including rice and tomatoes.
January 30, 2014
Ocean sponge-dwelling bacteria have hidden talents. The kidney-red coral reef sponge, Theonella swinhoei, is a source of several anti-fungal and anti-cancer drug candidates. These compounds aren't produced by the sponge itself, but by symbiotic bacteria that live inside it. The compounds in question are called polyketides, secondary metabolites that happen to be made by just two bacterial tenants of T. swinhoei, which have eluded researchers up to now.
December 20, 2013
A gluttonous plant reveals how its cellular power plant devours foreign DNA. Amborella trichopoda, a sprawling shrub that grows on just a single island in the remote South Pacific, is the only plant in its family and genus. It is also one of the oldest flowering plants, having branched off from others about 200 million years ago.
November 25, 2013
How Scavenging Fungi Became a Plant’s Best Friend. Glomeromycota is an ancient lineage of fungi that has a symbiotic relationship with roots that goes back nearly 420 million years to the earliest plants. More than two thirds of the world’s plants depend on this soil-dwelling symbiotic fungus to survive, including critical agricultural crops such as wheat, cassava, and rice.
November 22, 2013
The Inner Workings of a Bacterial Black Box Caught on Time-lapse Video. Cyanobacteria, found in just about every ecosystem on Earth, are one of the few bacteria that can create their own energy through photosynthesis and “fix” carbon – from carbon dioxide molecules – and convert it into fuel inside of miniscule compartments called carboxysomes.
November 18, 2013
Monkey Flower See, Monkey Flower Do — Model Plant's Legacy Highlights Gene-Shuffling Hotspots. Genomic variation is a feature of all natural populations and is vitally important in order to survive changes in their environments. Genetic variation among individuals, to which DNA recombination is an important contributor, is passed from parents to offspring and helps explain that different individuals in the population may harbor a diverse set of traits. Understanding and characterizing this variation requires both appropriate model organisms and a considerable amount of genomic sequencing capacity, on the scale of the capability of the U.S. Department of Energy Joint Genome Institute (DOE JGI).
October 28, 2013
Expanding Research Communities and Collaborations: DOE JGI 2014 Community Science Program Portfolio Announced. From the depths of ocean dead zones, to wide swaths of forests, and rising up to the troposphere, where most weather changes occur, the U.S. Department of Energy Joint Genome Institute (DOE JGI) 2014 Community Science Program portfolio seeks to parse functional information extracted from complex ecosystems to address urgent energy and environmental challenges. These massive, data-intensive undertakings require interdisciplinary approaches, many leveraging additional expertise through a new inter-DOE-Facility partnership.
September 30, 2013
Cold, Salty and Promiscuous—Gene-shuffling Microbes Dominate Antarctica’s Deep Lake. Sequestered in Antarctica’s Vestfold Hills, Deep Lake became isolated from the ocean 3,500 years ago by the Antarctic continent rising, resulting in a saltwater ecosystem that remains liquid in extreme cold, and providing researchers a unique niche for studying the evolution of the microbes that now thrive under such conditions.
July 14, 2013
Boldly Illuminating Biology’s “Dark Matter”. Is space really the final frontier, or are the greatest mysteries closer to home? In cosmology, dark matter is said to account for the majority of mass in the universe, however its presence is inferred by indirect effects rather than detected through telescopes.
July 2, 2013
Streamlining a Common Survival Strategy in Marine Microbes. Despite advances made in the fields of DNA sequencing and analysis, researchers have barely begun to scratch the tip of the iceberg in cataloging the planet’s microbial diversity, mainly because only a minute fraction of the millions of species of microbes have been cultured in the laboratory.
June 12, 2013
Chalking up a Marine Blooming Alga: Genome Fills a Gap in the Tree of Life. To World War II soldiers, “The White Cliffs of Dover” was a morale-boosting song that lifted spirits in dark times. To geographers, the white cliffs mark the point at which England is closest to continental Europe. To scientists, the white cliffs are towering structures made of the chalky, white shells that envelop the single-celled photosynthetic alga known as Emiliania huxleyi.
May 15, 2013
The DOE Joint Genome Institute Expands Capabilities via New Partnerships. With the publication last year of its strategic plan, “Forging the Future — A Ten-Year Strategic Vision” the U.S. Department of Energy Joint Genome Institute (DOE JGI) has positioned itself to provide the most current technology and expertise to their users so that they can address pressing energy and environmental scientific challenges.
May 6, 2013
A New Cost-Effective Genome Assembly Process. The U.S. Department of Energy Joint Genome Institute (DOE JGI) is among the world leaders in sequencing the genomes of microbes, focusing on their potential applications in the fields of bioenergy and environment.
March 24, 2013
Peach Genome Offers Insights into Breeding Strategies for Biofuels Crops. Rapidly growing trees like poplars and willows are candidate “biofuel crops” from which it is expected that cellulosic ethanol and higher energy content fuels can be efficiently extracted.
December 19, 2012
From the stockings decorating mantles to the new outfits in display windows calling to shoppers, cotton is woven into the fabric of the holiday season. For bioenergy researchers, however, fiber composition matters more than color and texture as each cotton strand is composed of more than two dozen coils of cellulose, a target biomass for next-generation biofuels.
November 28, 2012
Tiny Algae Shed Light on Photosynthesis as a Dynamic Property. One of the first chemical reactions children learn is the recipe for photosynthesis, combining carbon dioxide, water and solar energy to produce organic compounds. Many of the world’s most important photosynthetic eukaryotes such as plants did not develop the ability to combine these ingredients themselves.
October 16, 2012
From Form to Function: 2013 DOE JGI Community Sequencing Program Portfolio Announced. For architects, “form to function” means designing a building that best serves its intended purpose. For genomics researchers, the term could be applied to the ongoing transition from not just studying the genetic code of an organism, but also understanding what roles those genes play in the biology of the organism that encodes them.
October 8, 2012
Adaptable Button Mushroom Serves Up Biomass-Degrading Genes Critical to Managing the Planet’s Carbon Stores. The button mushroom occupies a prominent place in our diet and in the grocery store where it boasts a tasty multibillion-dollar niche, while in nature, Agaricus bisporus is known to decay leaf matter on the forest floor. Now, owing to an international collaboration of two-dozen institutions led by the French National Institute for Agricultural Research (INRA) and the U.S. Department of Energy Joint Genome Institute (DOE JGI), the full repertoire of A. bisporus genes has been determined.
August 1, 2012
Getting to the Root—Unearthing the Plant-Microbe Quid Pro Quo. While the flower may attract the bee and the admiring eye of the passerby, it is the unseen complex network of life below ground where the action is. The microbial community or microbiome that inhabits the rhizosphere and endosphere —the niches immediately surrounding and inside a plant’s root—facilitates the shuttling of nutrients and information into and out of the roots within the soil matrix.
June 28, 2012
Tracking the Remnants of the Carbon Cycle: How an Ancestral Fungus May Have Influenced Coal Formation. For want of a nail, the nursery rhyme goes, a kingdom was lost. A similar, seemingly innocuous change—the evolution of a lineage of mushrooms—may have had a massive impact on the carbon cycle, bringing an end to the 60-million year period during which coal deposits were formed.
June 21, 2012
Waves of Berkeley Lab Responders Deploy Omics to Track Deepwater Horizon Oil Spill Cleanup Microbes. In the aftermath of the Deepwater Horizon oil spill in the Gulf of Mexico two years ago, various strategies were deployed to prevent 4.9 million barrels of light crude oil from fouling the waters and reaching the shores.
May 14, 2012
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 used to guide the assembly process, but its usefulness depends on how closely related any two sequences are to one another.
March 22, 2012
Pulp NonFiction: Fungal Analysis Reveals Clues for Targeted Biomass Deconstruction. Without fungi and microbes to break down dead trees and leaf litter in nature, the forest floor might look like a scene from TV's "Hoarders." Among the fungi being studied by the DOE JGI are species that can selectively break down the cell wall components cellulose and lignin - the number one and two most abundant biopolymers on Earth.
November 23, 2011
Mite-y Genomic Resources For Bioenergy Crop Protection. For a pest that isn’t quite the size of a comma on a keyboard, the two-spotted spider mite can do a disproportionate amount of damage. These web-spinners extract the nutrients they need from leaves of more than a thousand different plant species, including bioenergy feedstocks and food staples.
November 7, 2011
Preparing for a Thaw: How Arctic Microbes Respond to a Warming World. From the North Pole to the Arctic Ocean, the frozen soils within this region keep an estimated 1,672 billion metric tons of carbon out of the Earth’s atmosphere. This sequestered carbon is more than 250 times the amount of greenhouse gas emissions attributed to the United States in the year 2009.
November 3, 2011
Trillions Served: Massive, Complex Projects Dominate DOE JGI 2012 Community Sequencing Program Portfolio. According to roadside signs, the number of burgers served has eclipsed the billion mark, while the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) will now serve up trillions of nucleotides of information from scores of newly-selected projects geared to feed the data-hungry worldwide research community.
October 2, 2011
Advancing Next Gen Biofuels by Turning Up the Heat on Biomass Pretreatment Processes. The nation’s Renewable Fuels Standard calls for annual production of 36 billion gallons of biofuel by 2022. One of the biggest hurdles to achieving this goal lies in optimizing the multistep process involved in breaking down plant biomass and then converting it into fermentable sugars that can be refined into fuel for our transportation needs.
September 16, 2011
Tringe on Popular Science’s "Brilliant 10" List. Susannah Green Tringe of the DOE Joint Genome Institute (DOE JGI) has been named one of 2011’s "Brilliant 10," the annual list compiled by Popular Science magazine of top young researchers.
September 1, 2011
Up from the Depths: How Bacteria Capture Carbon in the "Twilight Zone". Understanding the flow and processing of carbon in the world’s oceans, which cover 70 percent of Earth’s surface, is central to understanding global climate cycles, with many questions remaining unanswered.
July 25, 2011
Novel gene increases yeast's appetite for plant sugars. For thousands of years, bakers and brewers have relied on yeast to convert sugar into alcohol and carbon dioxide. Yet, University of Wisconsin-Madison researchers eager to harness this talent for brewing biofuels have found when it comes to churning through sugars, these budding microbes can be picky eaters.
July 14, 2011
Breaking down cellulose without blasting lignin: “Dry rot” genome offers lessons for biofuel pretreatment. Feared by realtors and homeowners alike, dry rot due to the fungus Serpula lacrymans causes millions of dollars worth of damage to homes and buildings around the world.
July 1, 2011
A Microbiological “Template” for Mitigating Methane Emissions. Carbon dioxide may be the most name-dropped greenhouse gas, but methane is 20 times more potent. In 2009, the U.S. Environmental Protection Agency calculated that 20 percent of the nation’s human-related methane emissions were attributable to livestock digestive processes.
June 30, 2011
Salt-loving Microbe Provides New Enzymes for the Production of Next Gen Biofuels. In order to realize the full potential of advanced biofuels that are derived from non-food sources of lignocellulosic biomass—e.g., agricultural, forestry, and municipal waste, and crops such as poplar, switchgrass and miscanthus—new technologies that can efficiently and cost-effectively break down this biomass into simple sugars are required.
May 13, 2011
Same Fungus, Different Strains: A Comparative Genomics Approach for Improved “Green” Chemical Production. Fungi play key roles in nature and are valued for their great importance in industry. Consider citric acid, a key additive in several foods and pharmaceuticals produced on a large-scale basis for decades with the help of the filamentous fungus Aspergillus niger.
May 10, 2011
JGI’s Susannah Tringe Receives Prestigious $2.5M DOE Early Career Research Award. The U.S. Department of Energy (DOE) Office of Science Early Career Research Program has awarded a grant to DOE Joint Genome Institute scientist Susannah Green Tringe to conduct genomic studies of microbial communities (metagenomes) in restored wetlands around the San Francisco Bay-Delta region of California.
May 5, 2011
Spikemoss Genome Offers New Paths for Biofuels Research--Bridges Plant Development Gap. It’s not quite Christmas, but the DNA sequence of a small plant that resembles the seasonal conifers is providing biofuels researchers with information that could influence the development of candidate biofuel feedstock plants and offering botanists long-awaited insights into plant evolution.
May 3, 2011
Formidable Fungal Force Counters Biofuel Plant Pathogens. Fungi play significant ecological and economic roles. They can break down organic matter, cause devastating agricultural blights, enter into symbiotic relationships to protect and nourish plants, or offer a tasty repast. For industrial applications, fungi provide a source of enzymes to catalyze such processes as generating biofuels from plant biomass.
February 21, 2011
Brown Tide Culprit Sequenced: Genome of the First of Algal Bloom Species. Algae play key roles in the global carbon cycle, helping sequester significant amounts of carbon. Some algal species can bloom, or become so numerous, that they discolor coastal waters and reduce the amount of light and oxygen available in the ecosystem.
February 3, 2011
Sentinel of Change: Water Flea Genome to Improve Environmental Monitoring Capabilities. A tiny crustacean that has been used for decades to develop and monitor environmental regulations is the first of its kind to have its genetic code sequenced and analyzed—revealing the most gene-packed animal characterized to date.
January 27, 2011
How Now, Inside the Cow: Nearly 30,000 Novel Enzymes for Biofuel Production Improvements. Cows eat grass—this has been observed for eons. From this fibrous diet consisting mainly of the tough to degrade plant cell wall materials cellulose and hemicellulose, substances of no nutritional value to most animals, ruminants manage to extract all they need to nourish themselves, their progeny and their keepers.
November 16, 2010
Making up the gut microbiome is a host-driven project. Baking sourdough bread requires a starter, and so do mammalian guts, which are first colonized by microbial communities from the mother and then acquire more microbes over time.
October 4, 2010
Bigger is Better: DOE JGI Announces 2011 Community Sequencing Program Portfolio. The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) has selected 35 new genomic sequencing projects for its 2011 Community Sequencing Program (CSP)—a targeted sampling of the planet’s biodiversity—to be characterized for bioenergy and environmental applications.
September 20, 2010
Beyond Genomics—DOE JGI leads method validation effort in Metatranscriptomics. Ultra-high throughput DNA sequencing platforms that allow researchers to sequence the genetic code of organisms at lightning speed for just pennies are enabling more focused genomic studies on a massive scale.
August 11, 2010
DNA Sequencing Reveals Complex Microbial Quid Pro Quo for Managing Carbon and Waste Streams. Microbial communities drive many of the important processes on the planet and DNA sequencing is emerging as a powerful tool for shedding light on their complex dynamics.
July 12, 2010
Breaking Biomass Better: DOE JGI Sequences Wood Decaying Fungus to Advance Biofuels Prospects. One of the challenges in making cellulosic biofuels commercially viable is to cost-effectively deconstruct plant material to liberate fermentable energy-rich sugars.
July 9, 2010
Genome Signatures Enable Tracking of Algal Complexity. On the long and difficult road toward a carbon-neutral source of transportation fuels, the U.S. Department of Energy (DOE) is pursuing a diversified approach.
May 24, 2010
DOE JGI Produces New QC Tool for Microbial Genomes. More than a thousand microbial genomes have been sequenced at various sequencing centers in the past 15 years to better understand their roles in tasks ranging from bioenergy to health to environmental cleanup.
April 12, 2010
JGI & NERSC Partner for Genomic High-performance Computing. The Department of Energy Joint Genome Institute (JGI) and the National Energy Research Scientific Computing Center (NERSC) Division have joined forces to create a more robust computational infrastructure for the world’s leading generator of DNA sequence information for bioenergy and environmental applications.
February 10, 2010
First Wild Grass Species and Model System for Energy Crops Sequenced. As the U.S. Department of Energy (DOE) works toward developing sustainable sources of clean renewable energy, perennial grasses have emerged as major candidates for the commercial production of cellulosic biofuels from feedstocks.
January 13, 2010
Soybean Genome Analysis Reveals Pathways for Improving Biodiesel, Disease Resistance, and Reducing Waste Runoff. Soybean, one of the most important global sources of protein and oil, is now the first legume species with a published complete draft genome sequence. The sequence and its analysis appear in the January 14 edition of the journal Nature.
December 23, 2009
Opening New Frontiers: First Volume of Microbial Encyclopedia Published in the Journal Nature by DOE JGI Collaborators. The Earth is estimated to have about a nonillion (1030) microbes in, on, around, and under it, comprised of an unknown but very large number of distinct species. Despite the widespread availability of microbial genome data—close to 2,000 microbes have been and are being decoded to date—a vast unknown realm awaits scientists intent on exploring microorganisms that inhabit this “undiscovered country.”
October 22, 2009
Model Microbial Community for Studying Expanding Dead Zones Characterized. Among the many changes in the ocean is the expansion of oxygen-deficient or oxygen minimum zones (OMZs), also known as dead zones, which affect the processes by which carbon is captured and sequestered on the seafloor and alter the microbial activities that impact the rate and magnitude of ocean carbon sequestration.
October 8, 2009
Establishing Standard Definitions for Genome Sequences. In 1996, researchers from major genome sequencing centers around the world convened on the island of Bermuda and defined a finished genome as a gapless sequence with a nucleotide error rate of one or less in 10,000 bases.
September 8, 2009
New Genomic Model Defines Microbes by Diet—Provides Tool for Tracking Environmental Change. In line with the U.S. Department of Energy (DOE) interest in characterizing the biotic factors involved in global carbon cycling, the DOE Joint Genome Institute (JGI) characterizes a diverse array of plants, microorganisms, and the communities in which they reside to inform options for reducing and stabilizing atmospheric greenhouse gases.
September 1, 2009
Fungal Map of Mutations Key to Increasing Enzyme Production for Bioenergy Use. In half a century, one fungus has gone from being the bane of the Army quartermasters’ existence in the Pacific to industry staple and someday, as part of the U.S. Department of Energy’s mission to promote national energy security through clean, renewable energy development, a biofuel producers’ best friend.
July 7, 2009
Exploring Standards to Advance Microbial Genomics. Microbes contribute to manifold human endeavors ranging from bioenergy to agriculture to medicine. Moreover, they make the Earth’s biogeochemical cycles go round, a prerequisite for all life on the planet.
June 29, 2009
Biofuel-Producing Bacteria, Insect Gut Microbes, ~ 70 other Projects Fill DOE Joint Genome Institute 2010 Pipeline. The U.S. Department of Energy (DOE) Joint Genome Institute (JGI) has selected 71 new genomic sequencing projects for its 2010 Community Sequencing Program (CSP)—a targeted sampling of the planet’s biodiversity—to be characterized for bioenergy, climate, and environmental applications.
May 28, 2009
DOE JGI Releases Expanded Version of Phytozome.net: Clearinghouse for Comparative Plant Genomics Data. An enhanced version of Phytozome.net, a web portal for comparative plant genomics geared to advance biofuel, food, feed, and fiber research, has been released by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI).
May 18, 2009
IMG ER Goes Primetime: Provides Expert-Driven QC for Microbial Genome Information. After a genome is sequenced and automatically annotated, researchers often manually review the predicted genes and their functions in order to improve accuracy and coverage across the vast genetic code of the particular target organism or community of organisms. These annotations drive the publication of high-profile science relevant to advancing bioenergy research and our understanding of biogeochemistry—the biological, chemical, physical, and geological processes that regulate our environment.
April 21, 2009
DNA of Uncultured Organisms Sequenced Using Novel Single-Cell Approach. Scientists from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Bigelow Laboratory for Ocean Sciences have assembled high quality, contamination-free draft genomes of uncultured biodegrading microorganisms using a novel single cell genome sequencing approach. This proof of principle study, published in the April 23 edition of the journal PLoS One, offers researchers a new method to access and decipher the information embedded in genomes of interest with only minute quantities of DNA.
April 9, 2009
Genes from Tiny Algae Shed Light on Big Role Managing Carbon in World’s Oceans & Coping with Environmental Change. Scientists from two-dozen research organizations led by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Monterey Bay Aquarium Research Institute (MBARI) have decoded genomes of two algal strains, highlighting the genes enabling them to capture carbon and maintain its delicate balance in the oceans.
February 12, 2009
Next Gen Sequencing Technology Pinpoint "On-Off Switches" in Genomes. Scientists from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory, and the University of California, San Diego have developed a set of molecular tools that provide important insight into the complex genomes of multicellular organisms. The strategy promises to clarify the longstanding mystery of the role played by vast stretches of DNA sequence that do not code for the functional units—genes—that nevertheless may have a powerful regulatory influence.
February 5, 2009
Rot's Unique Wood Degrading Machinery to be Harnessed for Better Biofuels Production. An international team led by scientists from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the U.S. Department of Agriculture Forest Service, Forest Products Laboratory (FPL) have translated the genetic code that explains the complex biochemical machinery making brown-rot fungi uniquely destructive to wood.
January 28, 2009
Scientists Publish Complete Genetic Blueprint of Key Biofuels Crop. Scientists at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and several partner institutions have published the sequence and analysis of the complete genome of sorghum, a major food and fodder plant with high potential as a bioenergy crop. The genome data will aid scientists in optimizing sorghum and other crops not only for food and fodder use, but also for biofuels production. The comparative analysis of the sorghum genome appears in the January 29 edition of the journal Nature.
December 8, 2008
DOE Joint Genome Institute Completes Soybean Genome—Data Released to Advance Biofuel, Food, & Feed Research. The U.S. Department of Energy Joint Genome Institute (DOE JGI) has released a complete draft assembly of the soybean (Glycine max) genetic code, making it widely available to the research community to advance new breeding strategies for one of the world’s most valuable plant commodities. Soybean not only accounts for 70 percent of the world’s edible protein, but also is an emerging feedstock for biodiesel production. Soybean is second only to corn as an agricultural commodity and is the leading U.S. agricultural export.
November 25, 2008
DOE JGI Issues Call for Genome Sequencing Proposals. The U.S. Department of Energy Joint Genome Institute (DOE JGI), through its Community Sequencing Program (CSP), is soliciting proposals related to the DOE missions of bioenergy, global carbon cycling and biogeochemical processes influencing contaminant transport. Targets include bacterial and archaeal isolates, large-scale eukaryotic or bacterial resequencing efforts that exploit next-generation sequencing technologies, eukaryotic reference genomes, and environmental microbial genomes (metagenomes). Letters of intent will be accepted beginning December 15, 2008 and are due January 30, 2009. For more details, see: http://www.jgi.doe.gov/CSP/user_guide/index.html
October 15, 2008
Diatom Genome Helps Explain Their Great Diversity and Success in Trapping Excess Carbon in Oceans. Diatoms, mighty microscopic algae, have profound influence on climate, producing 20 percent of the oxygen we breathe by capturing atmospheric carbon and in so doing, countering the greenhouse effect.
October 9, 2008
Bold traveler's journey toward the center of the Earth. The first ecosystem ever found having only a single biological species has been discovered 2.8 kilometers (1.74 miles) beneath the surface of the earth in the Mponeng gold mine near Johannesburg, South Africa. There the rod-shaped bacterium Desulforudis audaxviator exists in complete isolation, total darkness, a lack of oxygen, and 60-degree-Celsius heat (140 degrees Fahrenheit).
September 24, 2008
After the First Decade of Metagenomics--Adolescent Growth Spurt Anticipated. Mostly hidden from the scrutiny of the naked eye, microbes have been said to run the world. The challenge is how best to characterize them given that less than one percent of the estimated hundreds of millions of microbial species can be cultured in the laboratory.
September 8, 2008
DOE JGI Extends the Capabilities of the Integrated Microbial Genome (IMG) System, Updates the IMG/M Metagenome System, Launches Education Site. The U.S. Department of Energy Joint Genome Institute (DOE JGI) has extended the capabilities of the Integrated Microbial Genomes (IMG) data management system, updated the content of the IMG/M metagenome data management and analysis system, and has launched its educational companion site, IMG/EDU.
August 21, 2008
Genome of Simplest Animal Reveals Ancient Lineage, Confounding Array of Complex Capabilities. As Aesop said, appearances are deceiving—even in life’s tiniest critters. From first detection in the 1880s, clinging to the sides of an aquarium, to its recent characterization by the U.S. Department of Energy Joint Genome Institute (DOE JGI), a simple and primitive animal, Trichoplax adhaerens, appears to harbor a far more complex suite of capabilities than meets the eye. The findings, reported in the August 21 online edition of the journal Nature, establish a group of organisms as a branching point of animal evolution and identify sets of genes, or a “parts list,” employed by organisms that have evolved along particular branches.
August 18, 2008
Analysis of Lake Washington Microbes Shows the Power of Metagenomic Approaches. Today’s powerful sequencing machines can rapidly read the genomes of entire communities of microbes, but the challenge is to extract meaningful information from the jumbled reams of data. In a paper appearing in Nature Biotechnology August 17, a collaboration headed by researchers at the University of Washington and the U.S. Department of Energy Joint Genome Institute (DOE JGI) describes a novel approach for extracting single genomes and discerning specific microbial capabilities from mixed community (“metagenomic”) sequence data.
August 13, 2008
DOE JGI Director Eddy Rubin Highlights the Genomics of Plant-based Biofuels in the Journal Nature. Genomics is accelerating improvements for converting plant biomass into biofuel—as an alternative to fossil fuel for the nation’s transportation needs, reports Eddy Rubin, Director of the U.S. Department of Energy Joint Genome Institute (DOE JGI), in the August 14 edition of the journal Nature.
July 2, 2008
Pine Tree, Boat-Boring Bivalve “Bugs”, Duck Weed, Oil-Producing Microalgae, Stinkbird Gut, 40 Others Top DOE Joint Genome Institute 2009 Genome Sequencing Targets. In the continuing effort to tap the vast, unexplored reaches of the earth’s microbial and plant domains for bioenergy and environmental applications, the DOE Joint Genome Institute (DOE JGI) has announced its latest portfolio of DNA sequencing projects that it will undertake in the coming year.
May 4, 2008
Lean and Mean Biomass-Degrading Fungus Reveals Targeted Capabilities for Improved Biofuel Production. The genome analysis of a champion biomass-degrading fungus has revealed a surprisingly minimal repertoire of genes that it employs to break down plant cell walls, highlighting opportunities for further improvements in enzymes customized for biofuels production.
March 5, 2008
Mechanisms of Plant-Fungi Symbiosis Characterized by DOE Joint Genome Institute, Collaborators. Plants gained their ancestral toehold on dry land with considerable help from their fungal friends. Now, millennia later, that partnership is being exploited as a strategy to bolster biomass production for next-generation biofuels.
February 7, 2008
DOE JGI Releases a New Version of its Metagenome Data Management & Analysis System. Targeting its ever-expanding user community, the U.S. Department of Energy Joint Genome Institute (DOE JGI) has released an upgraded version of the IMG/M metagenome data management and analysis system.
January 17, 2008
DOE JGI Releases Soybean Genome Assembly. A preliminary assembly and annotation of the soybean genome, Glycine max, has been made available by the U.S. Department of Energy Joint Genome Institute (DOE JGI), to the greater scientific community to enable bioenergy research.
December 13, 2007
DOE JGI Community Sequencing Program Delivers First Moss Genome. Messages from nearly a half-billion years ago, conveyed via the inventory of genes sequenced from a present-day moss, provide clues about the earliest colonization of dry land by plants.
December 4, 2007
Latest Integrated Microbial Genomes (IMG) Data Management System Update Release. Version 2.4 of the Integrated Microbial Genomes (IMG) data management system, a resource provided to the scientific community for microbial genome data analysis, has now been released.
November 21, 2007
DOE JGI Plumbs Termite Guts to Yield Novel Enzymes for Better Biofuel Production. Termites -- notorious for their voracious appetite for wood, rendering houses to dust and causing billions of dollars in damage per year -- may provide the biochemical means to a greener biofuel future.
November 1, 2007
DOE Joint Genome Institute’s Pennacchio Wins Presidential Early Career Award. Len Pennacchio, Genetic Analysis Program Head at the U.S. Department of Energy Joint Genome Institute (JGI) and senior staff scientist in the Genomics Division of Lawrence Berkeley National Laboratory, is among this year’s recipients of The Presidential Early Career Award for Scientists and Engineers (PECASE).
October 18, 2007
Massive Reanalysis of Genome Data Solves Case of the Lethal Genes. [A JGI] survey identified genes that kill the bacteria employed in the sequencing process and throw a microbial wrench in the works. It also offers a possible strategy for the discovery of new antibiotics.
October 11, 2007
Green Alga Genome Project Catalogs Carbon Capture Machinery and Reveals Identity as Ancient Cousin of Land Plants and Animals. The genome analysis of a tiny green alga has uncovered hundreds of genes that are uniquely associated with carbon dioxide capture and generation of biomass.
September 4, 2007
Upgraded Integrated Microbial Genomes (IMG) Data Management System Released by DOE JGI to Eager User Community. A powerful set of computational tools established to ease the visualization and exploration of genomes flooding the public domain is now available in IMG Version 2.3
June 25, 2007
DOE Joint Genome Institute Secures Long-Term Lease on Production Genomics Facility. The U.S. Department of Energy Joint Genome Institute (DOE JGI) has secured a five-year extension on its lease with an option for an additional five years.
June 20, 2007
DOE JGI Upgrades its Microbial Genome Analysis System. Rising to accommodate the scientific community’s interest in harnessing the potential of the microbial world, the U.S. Department of Energy Joint Genome Institute (DOE JGI) has made Version 2.2 of the Integrated Microbial Genomes (IMG) data management system available to the public.
June 8, 2007
DOE JGI Announces 2008 Genome Sequencing Targets. Toward the goal of harnessing the power of nature through DNA sequencing, the DOE Joint Genome Institute (DOE JGI) has announced the latest Community Sequencing Program (CSP) portfolio.
May 14, 2007
DOE JGI Sets 'Gold Standard' for Metagenomic Data Analysis. The field of metagenomics is still in its infancy--the equivalent of the early days of the California Gold Rush, with labs vying to stake their claim. Amidst the prospecting, the call has been issued for methods to separate fool's gold from the real nuggets. Such a gold standard has now been provided through work led by DOE JGI.