DNA analysis strategy aids in study of biofuel feedstocks

Biomass Magazine


By Chris Hanson | March 19, 2014


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Study of Peach Genome May Help Improve Plant Biomass Yield for Biofuels

AZOCleantech.com
Published on March 25, 2013 at 7:16 AM

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DOE Joint Genome Institute unravels complete fungus genome

Biobased Digest

Tom Saidak
October 18, 2012   Read more

Biopulping’s Role in Bioenergy

Biomass Magazine
By Luke Geiver
July 03, 2012

Lignin degradation research is hip, and it could cut costs on biomass processing

Something special is happening with a research project focused on two white rot fungi genomes. Led by the U.S. DOE’s Joint Genome Institute, a team of international researchers is collaborating on a project to sequence and analyze the fungi strains to understand how enzymes present in the fungi break down plant biomass. It’s not the research that is special, however, it’s the number of people working on the project, revealing that the continual quest for super enzymes used to break down biomass is not only a strong trend in the field of bioenergy research, it’s a popular area of research to be in.

“The fact that we have such a large group of people involved in this project is a clear demonstration that there’s certainly interest in enzyme discovery,” says Dan Cullen, senior author of the research study and a member of the USDA’s Agricultural Forest Service’s Forest Products Laboratory.

In the study, “Comparative genomics of Ceriporiopsis subvermispora and Phanerochaete chrysosporium provide insight into selective ligninolysis,” Cullen and his huge team analyzed C. subvermispora and P. chrysosporium, finding large differences in the way each breaks down lignin. According to Cullen, few fungi have the capability to degrade lignin in the first place, and even fewer have the ability to selectively remove lignin at such an efficient rate. “C. subvermispora is one exception in its ability to do just that,” he said.

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Miscanthus Map

The Daily Scan
May 23, 2012

Two independent Miscanthus sinensis chromosome maps show that M. sinesis has undergone a number of chromosome duplications and fusions, says ScienceDaily. In the first study, researchers from Ceres present a high-resolution linkage map of M. sinensis that they developed using genotyping by sequencing. As they report in PLoS One, the Ceres researchers found that the diploid M. sinensis has a tetraploid origin and contains two sub-genomes. The second study, from the University of Illinois Urbana-Champagne's Stephen Moose and the DOE Joint Genome Institute's Daniel Rokhsar used RNA-seq and a genotyping array to construct an M. sinensis genotype map that also shows a tetraploid origin. "The genus Miscanthus experienced an ancestral tetraploidy and chromosome fusion prior to its diversification, but after its divergence from the closely related sugarcane clade," researchers led by Moose and Rokhsar write in BMC Genomics.

M. sinensis is an ornamental plant, ScienceDaily notes, but it is closely related to the biofuel crop Miscanthus giganteus. Having a chromosome map is a step toward a Miscanthus genome, and such a genome "will help scientists understand the evolution of grasses and the genetic mechanisms that give them their desirable traits," ScienceDaily adds.

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Foxtail Millet Offers Clues for Assembling the Switchgrass Genome

Science Daily

ScienceDaily (May 14, 2012) — 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. For example, a reference genome might be so distantly related from the one being assembled, it would be akin to comparing a Model-T to a contemporary hybrid car.

For researchers interested in switchgrass, a perennial grass that the U.S. Department of Energy (DOE) is investigating as a prospective biofuels feedstock, assembling the plant genome poses an even more complicated puzzle than usual because it has multiple copies of its chromosomes. The DOE Joint Genome Institute (JGI), in an international partnership that includes the DOE BioEnergy Science Center (BESC) and the DOE Joint BioEnergy Institute (JBEI), two of the three DOE Bioenergy Research Centers, has sequenced plant genomes of related candidate bioenergy crops such as sorghum and the model grass Brachypodium. Both plants have been used as references for switchgrass, however sorghum last shared a common ancestor with switchgrass more than 20 million years ago while Brachypodium last shared a common ancestor with switchgrass more than 50 million years ago. The genome of a much closer switchgrass relative -- foxtail millet (Setaria italica) -- is described in the May 13, 2012 edition of Nature Biotechnology. All three genomes, along with those of other plants sequenced by the DOE JGI are publicly accessible on www.phytozome.net.

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Salt Loving Microbe May Aid Biofuel Production

DomesticFuel.com
Posted by Joanna Schroeder – July 7th, 2011

Researchers from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Joint BioEnergy Institute (JBEI) at DOE’s Lawrence Berkeley National Laboratory are trying to discover salt-loving organisms that may be more efficient in treating biomass and improve sugar yield for biofuel production. The class of solvents known as ionic liquids, are liquid forms of salt that will inactivate enzymes by interfering with the folding of polypeptides—the building-blocks of proteins. These solvents are useful for breaking down biomass; however, they can also hinder the ability of cellulases used to produce sugars after pretreatment.

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Salt-loving microbe provides new enzymes for the production of next-gen biofuels

EurekaAlert.com
Public release date: 30-Jun-2011

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. Existing biomass pretreatment technologies are typically derived from the pulp and paper industry and rely on dilute acids and bases to break down the biomass. The treated biomass product is then exposed to biological catalysts, or enzymes, to liberate the sugars.

A new class of solvents, referred to as ionic liquids, have been reported to be much more efficient in treating the biomass and enhancing the yield of sugars liberated from it. While ionic liquids are useful for breaking down biomass, they can also hinder the ability of the cellulases (usually derived from fungi) used to produce sugars after pretreatment. Ionic liquids are a liquid form of salt that will inactivate enzymes by interfering with the folding of polypeptides—the building-blocks of proteins. To help identify new enzymes that are tolerant of ionic liquids, researchers from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Joint BioEnergy Institute (JBEI) at DOE's Lawrence Berkeley National Laboratory are turning to those found in the complete genome sequences of halophilic (salt-tolerant) organisms.

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Formidable fungal force counters biofuel plant pathogens

EurekaAlert.com
DOE/Joint Genome Institute
May 3, 2011

WALNUT CREEK, Calif.—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. One large fungal group with such enzymes are the rust plant pathogens which cannot survive on their own so they use crops as hosts, leading to reduced yields and potentially hindering efforts to grow biomass for fuel. Factors that could reduce the growth of plant biomass, thus reducing biofuel production, are a target for investigation of the Department of Energy (DOE) Joint Genome Institute (JGI).

Published the week of May 2, 2011 in the early edition of the Proceedings of the National Academy of Sciences, the work of an international team of researchers that included Fungal Genome Program head Igor Grigoriev, as well as several members from the DOE JGI, compared the genomes of two rust fungi to identify the characteristics by which these pathogens can invade their plant hosts and to develop methods of controlling the damage they can cause. The team led by co-first author Sebastien Duplessis of the French national agricultural research institute (INRA) worked on the poplar leaf rust fungus while a team led by co-first author Christina Cuomo of the Broad Institute of MIT and Harvard and Les Szabo from Agricultural Research Service USDA and University of Minnesota worked separately on the wheat and Barley stem rust fungus. The two-genome consortia joined their efforts to compare the genomic features of the two rust pathogens to reveal the role they play in infecting the host plant and acquiring nutrients.

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Scientists Find Potential Enzymes for Biofuel Production in Cow Rumen

Korea IT Times
Tuesday, February 1st, 2011

Cows may hold the key to advancing production of second generation biofuels as scientists from the University of Illinois and Washington State University discover new enzymes in the bovine rumen that effectively breakdown switchgrass, a prime feedstock for bioenergy.

The bovine rumen is the cow's primary grass digestion chamber. This chamber holds a range of organisms such as fungi, bacteria, archaea, protista and viruses which process all food matter that pass through the rumen.

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Obama's 2011 Budget Seeks $69.3M for JGI

GenomeWeb.com
March 26, 2010
By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – Under the White House's proposed budget for 2011, the US Department of Energy expects to receive a total of $322 million next fiscal year for its Biological Systems Science Research (BSSR) efforts, including $69.3 million for the Joint Genome Institute (JGI), an increase of less than one percent over the $69 million JGI received for this year.

Under President Barack Obama's proposed budget for fiscal 2011, the DOE's Office of Science would receive an increase in funding to $5.1 billion from $4.9 billion in 2010, including $220 million for biofuels and biomass research.

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DOE Joint Genome Institute 5th Annual Meeting

Physorg.com
March 18th, 2010

Planned for March 24-26, 2010
Researchers from all over the world will be at the Marriott in Walnut Creek for the U.S. Department of Energy Joint Genome Institute 5th Annual Genomics of Energy and Environment Meeting, which will feature genomics research in the fields of clean energy generation and the environment. Keynote speeches will be delivered by Jay Keasling, CEO of the DOE Joint BioEnergy Institute, Steve Pennell of Ceres Inc. on genomics-based gene selection for energy crop improvement and former National Science Foundation director Rita Colwell of the University of Maryland at College Park and Johns Hopkins University on "solving problems with sequences."

Also presenting at the Meeting are several researchers from the Energy Biosciences Institute, a research and development collaboration between the University of California, Berkeley, the Lawrence Berkeley National Laboratory, the University of Illinois, and BP.

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Opening New Frontiers: First Volume of Microbial Encyclopedia Published

ScienceDaily.com

ScienceDaily (Dec. 24, 2009) — 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."

Two thousand years after Pliny the Elder compiled one of the earliest surviving encyclopedic works, and in the spirit of his goal of providing "light to the obscure," the Department of Energy Joint Genome Institute (DOE JGI) has published the initial "volume" of the Genomic Encyclopedia of Bacteria and Archaea (GEBA). Presenting a provocative glimpse into this uncharted territory, an analysis of the first 56 genomes representing two of the three domains of the tree of life appears in the December 24 edition of the journal Nature.

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