DOE JGI releases soybean genome assembly to enable worldwide bioenergy research
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. The genetic information will enable crop improvements and the design of a plant that performs according to specific predetermined tasks for energy production.
The announcement of what it calls 'this monumental project' was made by Eddy Rubin, DOE JGI Director, during his keynote remarks Jan. 15 at the Plant and Animal Genome XVI Conference in San Diego,CA. The preliminary data can be accessed here.
The soybean genome project was initiated through the DOE JGI Community Sequencing Program (CSP), an international scientific program bringing together leading genetic researchers and bio-engineers. The soybean project was conducted by a consortium led by DOE JGI’s Dan Rokhsar, Stanford’s Jeremy Schmutz, Gary Stacey of the University of Missouri-Columbia, Randy Shoemaker of Iowa State University, and Scott Jackson of Purdue University, with support from the U.S. Department of Agriculture and the National Science Foundation.
The large-scale shotgun DNA sequencing project began in the middle of 2006 and will be completed in 2008. A total of about 13 million shotgun reads have been produced and deposited in the National Center for Biotechnology Information (NCBI) Trace Archive in accordance with the consortium’s commitment to early access and consistent with the Fort Lauderdale genome data release policy.
The current assembly (representing 7.23x coverage), gene, set, and browser are collectively referred to as "Glyma0". Glyma0 is a preliminary release, based on a partial dataset. This is expected to be replaced with an improved, chromosome-scale "Glyma1" version by the end of 2008. Early users of this data are encouraged to track their favorite genes by saving local copies of the DNA sequences of these loci, and not by identifier or sequence coordinate, as these will change in future versions.
DOE JGI’s interest in sequencing the soybean stems from its role as a principal source of biodiesel, a renewable, alternative fuel which, it says, has the highest energy content of any alternative fuel.
Detailed knowledge of the soybean genetic code will enable crop improvements for more effective application of this plant for clean bioenergy generation. Knowing which genes control specific traits, researchers are able to change the type, quantity, and/or location of oil produced by the crop:
energy :: sustainability :: biomass :: bioenergy :: biofuels :: ethanol :: biodiesel :: soybean :: genome :: biotechnology :: Joint Genome Institute ::
Through utilization of the sequence information generated by DOE JGI, it may be possible to develop a customized biomass production platform for combining oil seed production for biodiesel with enhanced vegetative growth for ethanol conversion--doubling the energy output of the crop. In 2004, over 3.1 billion bushels of soybeans were grown on nearly 75 million acres in the US, with an estimated annual value exceeding $17 billio--second only to corn, and about twice that of wheat.
Several other individuals, projects, grants, and agencies have made this monumental project possible. These included the four major projects: Public Expressed Sequence Tags (ESTs), SoyMap (which includes BAC libraries, modern physical mapping, and clone-based sequencing), and the Genetic Map with funding from USDA, NSF, United Soybean Board (USB), and the North Central Soybean Research Program (NCSRP).
The Public EST Project, supported by USB and NCSRP, was led by Lila Vodkin of the University of Illinois at Urbana-Champaign; Randy Shoemaker of the USDA-ARS, Ames, Iowa; and P. Steven Keim of Northern Arizona University.
The original physical map development, funded by USB, was conducted by Jan Dvorak, from the University of California, Davis, along with the Washington University Genome Center in St. Louis, Missouri, and David Grant, USDA-ARS, Ames, Iowa.
The NSF SoyMap team, comprising principal investigator Scott Jackson, Gary Stacey and Henry Nguyen, Jeff Doyle of Cornell University, William Beavis of the National Center for Genome Resources (NCGR) in Santa Fe, New Mexico, and Iowa State, Gregory May (NCGR), Will Nelson and Rod Wing of the University of Arizona, with Randy Shoemaker, anchored the map and conducted quality control.
The team devoted to genetic mapping and physical map anchoring, yielding several thousand sequence-based markers, included USDA-Agricultural Research Service (ARS) investigators, including Perry Cregan and Dave Hyten of Beltsville, Maryland, Randy Shoemaker, David Grant, and Steven Cannon of Ames, Iowa, along with James Specht of the University of Nebraska, Lincoln.
The annotation of the soybean genome was carried out by a team of researchers from the DOE JGI and the University of California Berkeley’s Center for Integrative Genomics, with support from the DOE, USDA, NSF, and the Gordon and Betty Moore Foundation.
The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories -- Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest -- along with the Stanford Human Genome Center to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI’s Walnut Creek, CA, Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.
The JGI has sequenced a variety of bioenergy crops, and for the first time ever published the entire genome of a tree, namely the poplar, seen as a biomass crop. It is working on genetic research into many other plants and organisms, including sorghum, eucalyptus, cassava, foxtail millet, and a whole range of microorganisms, algae, fungi and other biological organisms that can be harnessed for the production of biofuels and bioenergy.
References:
DOE JGI: DOE JGI Releases Soybean Genome Assembly To Enable Worldwide Bioenergy Research Efforts - January 17, 2008.
Phytozome.net: Glycine max genome.
Biopact: Joint Genome Institute announces 2008 genome sequencing targets with focus on bioenergy and carbon cycle - June 12, 2007
Biopact: Super-fermenting fungus genome sequenced, to be harnessed for biofuels - Monday, March 05, 2007
Biopact: Moss genome sequenced: shows how aquatic plants adapted to dry land - key to development of drought-tolerant energy crops, cellulosic biofuels - December 14, 2007
Biopact: Scientists sequence and analyse genomes of termite gut microbes to yield novel enzymes for cellulosic biofuel production - November 22, 2007
Biopact: The first tree genome is published: Poplar holds promise as renewable bioenergy resource - September 14, 2006
Article continues
The announcement of what it calls 'this monumental project' was made by Eddy Rubin, DOE JGI Director, during his keynote remarks Jan. 15 at the Plant and Animal Genome XVI Conference in San Diego,CA. The preliminary data can be accessed here.
The soybean genome project was initiated through the DOE JGI Community Sequencing Program (CSP), an international scientific program bringing together leading genetic researchers and bio-engineers. The soybean project was conducted by a consortium led by DOE JGI’s Dan Rokhsar, Stanford’s Jeremy Schmutz, Gary Stacey of the University of Missouri-Columbia, Randy Shoemaker of Iowa State University, and Scott Jackson of Purdue University, with support from the U.S. Department of Agriculture and the National Science Foundation.
The large-scale shotgun DNA sequencing project began in the middle of 2006 and will be completed in 2008. A total of about 13 million shotgun reads have been produced and deposited in the National Center for Biotechnology Information (NCBI) Trace Archive in accordance with the consortium’s commitment to early access and consistent with the Fort Lauderdale genome data release policy.
The current assembly (representing 7.23x coverage), gene, set, and browser are collectively referred to as "Glyma0". Glyma0 is a preliminary release, based on a partial dataset. This is expected to be replaced with an improved, chromosome-scale "Glyma1" version by the end of 2008. Early users of this data are encouraged to track their favorite genes by saving local copies of the DNA sequences of these loci, and not by identifier or sequence coordinate, as these will change in future versions.
DOE JGI’s interest in sequencing the soybean stems from its role as a principal source of biodiesel, a renewable, alternative fuel which, it says, has the highest energy content of any alternative fuel.
Detailed knowledge of the soybean genetic code will enable crop improvements for more effective application of this plant for clean bioenergy generation. Knowing which genes control specific traits, researchers are able to change the type, quantity, and/or location of oil produced by the crop:
energy :: sustainability :: biomass :: bioenergy :: biofuels :: ethanol :: biodiesel :: soybean :: genome :: biotechnology :: Joint Genome Institute ::
Through utilization of the sequence information generated by DOE JGI, it may be possible to develop a customized biomass production platform for combining oil seed production for biodiesel with enhanced vegetative growth for ethanol conversion--doubling the energy output of the crop. In 2004, over 3.1 billion bushels of soybeans were grown on nearly 75 million acres in the US, with an estimated annual value exceeding $17 billio--second only to corn, and about twice that of wheat.
Several other individuals, projects, grants, and agencies have made this monumental project possible. These included the four major projects: Public Expressed Sequence Tags (ESTs), SoyMap (which includes BAC libraries, modern physical mapping, and clone-based sequencing), and the Genetic Map with funding from USDA, NSF, United Soybean Board (USB), and the North Central Soybean Research Program (NCSRP).
The Public EST Project, supported by USB and NCSRP, was led by Lila Vodkin of the University of Illinois at Urbana-Champaign; Randy Shoemaker of the USDA-ARS, Ames, Iowa; and P. Steven Keim of Northern Arizona University.
The original physical map development, funded by USB, was conducted by Jan Dvorak, from the University of California, Davis, along with the Washington University Genome Center in St. Louis, Missouri, and David Grant, USDA-ARS, Ames, Iowa.
The NSF SoyMap team, comprising principal investigator Scott Jackson, Gary Stacey and Henry Nguyen, Jeff Doyle of Cornell University, William Beavis of the National Center for Genome Resources (NCGR) in Santa Fe, New Mexico, and Iowa State, Gregory May (NCGR), Will Nelson and Rod Wing of the University of Arizona, with Randy Shoemaker, anchored the map and conducted quality control.
The team devoted to genetic mapping and physical map anchoring, yielding several thousand sequence-based markers, included USDA-Agricultural Research Service (ARS) investigators, including Perry Cregan and Dave Hyten of Beltsville, Maryland, Randy Shoemaker, David Grant, and Steven Cannon of Ames, Iowa, along with James Specht of the University of Nebraska, Lincoln.
The annotation of the soybean genome was carried out by a team of researchers from the DOE JGI and the University of California Berkeley’s Center for Integrative Genomics, with support from the DOE, USDA, NSF, and the Gordon and Betty Moore Foundation.
The U.S. Department of Energy Joint Genome Institute, supported by the DOE Office of Science, unites the expertise of five national laboratories -- Lawrence Berkeley, Lawrence Livermore, Los Alamos, Oak Ridge, and Pacific Northwest -- along with the Stanford Human Genome Center to advance genomics in support of the DOE missions related to clean energy generation and environmental characterization and cleanup. DOE JGI’s Walnut Creek, CA, Production Genomics Facility provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges.
The JGI has sequenced a variety of bioenergy crops, and for the first time ever published the entire genome of a tree, namely the poplar, seen as a biomass crop. It is working on genetic research into many other plants and organisms, including sorghum, eucalyptus, cassava, foxtail millet, and a whole range of microorganisms, algae, fungi and other biological organisms that can be harnessed for the production of biofuels and bioenergy.
References:
DOE JGI: DOE JGI Releases Soybean Genome Assembly To Enable Worldwide Bioenergy Research Efforts - January 17, 2008.
Phytozome.net: Glycine max genome.
Biopact: Joint Genome Institute announces 2008 genome sequencing targets with focus on bioenergy and carbon cycle - June 12, 2007
Biopact: Super-fermenting fungus genome sequenced, to be harnessed for biofuels - Monday, March 05, 2007
Biopact: Moss genome sequenced: shows how aquatic plants adapted to dry land - key to development of drought-tolerant energy crops, cellulosic biofuels - December 14, 2007
Biopact: Scientists sequence and analyse genomes of termite gut microbes to yield novel enzymes for cellulosic biofuel production - November 22, 2007
Biopact: The first tree genome is published: Poplar holds promise as renewable bioenergy resource - September 14, 2006
Article continues
Friday, January 18, 2008
New method for genetic engineering is simple, inexpensive and portable
In order for this to work, foreign (or synthetic) DNA must be introduced into host cells, which is not exactly a trivial task. Japanese researchers have now developed a method which could represent a true alternative to conventional processes. As described in the journal Angewandte Chemie, the cells are “bombarded” with water droplets produced and accelerated by electrospray.
There are several methods to transfer DNA into a host cell. In the simplest case the foreign DNA forces its way into the cell through a cell membrane that has been made porous, through treatment with electrical current or UV lasers, for example. Viruses and liposomes can be used as genetic transporters and the genetic material can be injected or shot into the cell with a “particle gun”. These methods all have the disadvantage of either severely damaging delicate cells or of being markedly expensive and complicated.
A team at the Saitama University led by Takafumi Sakai, in cooperation with Kazuto Ikemoto (Mitsubishi Gas Chemical Company), has now developed a methodology that could provide an alternative: They “bombard” the cells with tiny electrically charged water droplets. The droplets tear tiny holes in the cell membranes, through which external DNA molecules can enter. After about one minute, the holes have closed back up and even delicate cells survive the procedure undamaged:
energy :: sustainability :: biomass :: bioenergy :: biofuels :: DNA :: genetic engineering :: biotechnology :: cells :: bacteria :: bioconversion ::
This method is based on a technique called electrospray, which has long been used with success, particularly in mass spectrometry. In this process, the tip of an extremely fine steel capillary is put under a high voltage. A highly charged drop of water exits the capillary and is atomized into many micro- or nanoscopic droplets. These charged microdroplets are strongly accelerated in an electrical field—toward the plate holding the cell culture.
The advantage of this new method: It is suitable for a large variety of cell types — mammalian cell cultures and bacteria, as well as living tissue, as was demonstrated with bird embryos. No cytotoxic reagents that could damage the cells are needed; only pure water or a cell-tolerated saline solution are used. An entire plate of cell cultures can be “sprayed” bit by bit, or a specific point on some tissue can be targeted. The equipment needed is simple, inexpensive, and portable.
References:
Yusuke Okubo, et. al. "DNA Introduction into Living Cells by Water Droplet Impact with an Electrospray Process", Angewandte Chemie, Published Online: 18 Jan 2008, DOI: 10.1002/anie.200704429
Wiley InterScience: Cells Get Sprayed: Water droplets produced by electrospray render cells permeable to external DNA - January 18, 2008.
Article continues
posted by Biopact team at 6:15 PM 1 comments links to this post