On Wednesday, February 27, duringa shining interval between rain showers,the JGI dedicated a newly renovated18,000 square-foot building at itsProduction Genomics Facility (PGF) inWalnut Creek. The ceremony entailed aribbon-cutting by the latest robot to beintroduced into the industrial-scale DNAsequencing line at the PGF, the newBenchCel Microplate Handling System,adapted for the occasion by JGI techni-cians George Mercado and Don Miller.

The new addition to the campus hasenabled the JGI to consolidate approxi-

mately 80 administrative and informaticsstaff and includes a new research labo-ratory, bringing the total footprint of thefacilities to 80,000 square feet.

The building to be dedicated is partof a new five-year lease extensionbetween the University of CaliforniaRegents and its landlord, Hall EquitiesGroup, ensuring the JGI’s long-termpresence in the community of WalnutCreek, situated halfway between its par-ent facilities, Lawrence Berkeley andLawrence Livermore NationalLaboratories.

PRIMERthe

JGI Expands Campus, DedicatesBuilding Under New Lease Extension

Spring 2008 Volume 5 Issue 1

From the left, JGI’s Operations Manager, RayTurner; JGI Director Eddy Rubin; Congress-woman Ellen Tauscher’s Field RepresentativeErik Ridley; and Walnut Creek City Councilmember Susan McNulty Rainey, all of whomspoke at the dedication.

JGI PGF now 80,000 SQF

“Here's a DNA molecule you can see with-out a microscope!” said helix sculptor JeffBrees.

Plants gained their ancestral toeholdon dry land with considerable help fromtheir fungal friends. Now, millennia later,that partnership is being exploited as astrategy to bolster biomass productionfor next-generation biofuels. The geneticmechanism of this kind of symbiosis,which contributes to the delicate ecolog-ical balance in healthy forests, also pro-vides insights into plant health that mayenable more efficient carbon sequestra-tion and enhanced phytoremediation—using plants to clean up environmentalcontaminants. These prospects stemfrom the genome analysis of the symbi-otic fungus Laccaria bicolor, generated byJGI and collaborators from INRA, theNational Institute for Agricultural Researchin Nancy, France, and published March6 in the journal Nature (452, 88–92,

DOI: 10.1038/nature06556). This inter-national team effort also involved contri-butions from 16 institutions, includingOak Ridge National Laboratory; GhentUniversity, Belgium; Lund University,Sweden; Göttingen University, Germany;CNRS-Aix-Marseille University, France;Nancy University, France; and theUniversity of Alabama, Huntsville.

Trees’ ability to generate largeamounts of biomass or store carbon isunderpinned by their interactions withsoil microbes known as mycorrhizal fungi,which excel at procuring necessary, butscarce, nutrients such as phosphateand nitrogen. When Laccaria bicolorestablishes a partnership with plantroots, a mycorrhizal root is created. Thefungus within the root is protected fromcompetition with other soil microbes

Mechanisms of Plant-Fungi SymbiosisCharacterized by JGI, Collaborators

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Messages from nearly a half-billionyears ago, conveyed via the inventory ofgenes sequenced from a present-daymoss, provide clues about the earliestcolonization of dry land by plants. TheJGI was among the leaders of an inter-national effort uniting more than 40institutions to complete the first genomesequencing project of a nonvascularland plant, the moss Physcomitrellapatens. The team’s insights into thecode that enabled this seminal emer-gence and dominance of land by plantsare published in the January 4 editionof the journal Science (Vol. 319, No.5859, pp. 64–69 DOI: 10.1126/sci-ence.1150646).

The moss genome project, originallyproposed by Brent Mishler of the Universityof California, Berkeley, and Ralph Quatranoof Washington University in St. Louis(WUSTL), was enabled through the JGI’sCommunity Sequencing Program (CSP).Other project leaders include DOE JGI’sJeffrey Boore, David Cove, and AndrewCuming of the University of Leeds(United Kingdom), Mitsuyasu Hasebeand Tomoaki Nishiyama of the NationalInstitute for Basic Biology (Japan), andRalf Reski of the University of Freiburg(Germany) with his associate StefanRensing, the paper’s first author.

“Physcomitrella is to flowering plantswhat the fruit fly is to humans; that is,in the same way that the fly and mousehave informed animal biology, the genomeof this moss will advance our explorationof plant genes and their functions andutility,” said Eddy Rubin, DOE JGI Director.“Traits such as those that allow plantsto survive and thrive on dry land will beuseful in the selection and optimizationof crops that may be domesticated forbiomass-to-biofuels strategies.”

Physcomitrella, with a genome ofjust under 500 million nucleotides andpossessing nearly 36,000 genes (about

50 percent more than are thought to bein the human genome), is the firstbryophyte to be sequenced. Bryophytesare nonvascular land plants that lackspecialized tissues (phloem or xylem)for circulating fluids. Rather, they pos-sess specialized tissues for internaltransport. They neither flower nor pro-duce seeds, but reproduce via spores.

“The availability of the Physcomitrellagenome is expected to create importantnew opportunities for understanding themolecular mechanisms involved in plantcell wall synthesis and assembly,” saidChris Somerville, Director of the EnergyBiosciences Institute (EBI), the partner-ship between Lawrence Berkeley NationalLaboratory, UC Berkeley, the Universityof Illinois at Urbana-Champaign, and theglobal energy company BP. “The easewith which genes can be experimentallymodified in Physcomitrella will facilitatea wide range of studies of the cell wall,the principal component of terrestrialbiomass. Additionally, the moss has fewercell types than higher plants and has amuch more rapid lifecycle, which also

greatly facilitates experimental studies ofcell walls. Thus, the completion of thegenome is an important step forward infacilitating basic research concerningthe development of cellulosic biofuels.”

“There is a clear connection withthis work and the intensifying interestin the global carbon cycle,” saidMishler, a UC Berkeley professor in theDepartment of Integrative Biology andDirector of the University and JepsonHerbaria. “The moss system is provingquite useful for studies of photosynthe-sis, among many other processes.”

For more on Physcomitrella, see:http://www.jgi.doe.gov/News/news_12_13_07.html

JGI DELIVERS FIRST MOSS GENOME

and gains preferential access to carbo-hydrates within the plant. Thus, themutualistic relationship is established.

Laccaria bicolor occurs frequently inthe birch, fir, and pine forests of NorthAmerica and is a common symbiont ofPopulus trichocarpa, the poplar treewhose genome was determined by theJGI in 2006. The analysis of the 65-mil-lion-base Laccaria genome, the largestfungal genome sequenced to date,yielded 20,000 predicted protein-encod-ing genes, almost as many as in thehuman genome. In sifting through thesedata, researchers have discovered many

unexpected features, including an arse-nal of small secreted proteins (SSPs),several of which are only expressed intissues associated with symbiosis. Themost prominent SSP accumulates in theextending hyphae, the tips of the fungusthat colonize the roots of the host plant.

Francis Martin, the Nature study’slead author, said that the genomeexploration led the team to the discov-ery that Laccaria lacks the enzymesinvolved in degradation of the carbohy-drate polymers of plant cell walls butmaintains the ability to degrade non-plant cell walls—which may account for

Laccariacont. from page 1

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A rolling stone gathers no Physcomitrellapatens.

Spring 2008 Vol. 5, Issue 1

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Revisiting the site of the JGI’s 2007Ergo Cup victory, a team of eightSequencing Department and LBNLEngineering Division staff participatedin the Institute for Industrial Engineers’(IIE) 11th Applied ErgonomicsConference in Orlando, Florida, heldMarch 10–13. Once again, the JGI waschosen as one of the finalists to com-pete for the Ergo Cup Award, recogniz-ing excellence in ergonomic engineeringdesign and teamwork solutions. Suchcompanies as GM, Boeing, Toyota andother industry giants from all over theworld displayed their ergonomic inter-ventions at the conference, where a

panel of judges and the conferenceattendees can learn about the processand the company.

This year, the JGI had entries in twocategories: the Team-Driven WorkplaceSolutions and Engineering andErgonomist-Driven Workplace Solutions.In the Team-Driven category, the “BaseOff” project is a small hand tool thatreduces the ergonomic risk to lab work-ers in separating the lids from thebases that hold the sample plates usedin ABI 3730 sequencers. The “It’s APeeling” project for the Engineering &Ergonomist Driven category is an auto-mated plate-peeling machine designed

in-house by Mark West and CharlieReiter in the Engineering Division, withthe assistance of the JGIInstrumentation Group. The instrumentautomates a high-risk manual task onthe production line, peeling heat sealsoff sample plates.

Conference participants includedChristine Naca, Simon Roberts, MartinPollard, Gerald Ilog, Megan Kennedy,Michael Pintor, and Bridget Swift, allfrom the JGI’s Sequencing Department,and Mark West from LBNL Engineering.

“Although the JGI did not win anErgo Cup this year, it was a valuablelearning experience and an opportunity

Applied Ergonomics

From left to right: Michael Pintor, ChristineNaca, Bridget Swift, and Simon Roberts

”Base Off” “It’s A Peeling”

A preliminary assembly and annota-tion of the soybean genome, Glycinemax, has been made available to thegreater scientific community by the JGI,to enable bioenergy research.

The announcement was made byEddy Rubin, JGI Director, during hiskeynote remarks January 15 at thePlant and Animal Genome XVI

Conference in San Diego. The prelimi-nary data can be accessed athttp://www.phytozome.net/soybean.

The soybean genome project wasinitiated through the DOE JGI CommunitySequencing Program (CSP) by a consor-tium led by the DOE JGI’s Dan Rokhsar,Stanford University’s Jeremy Schmutz,Gary Stacey of the University of

Missouri-Columbia, Randy Shoemaker ofIowa State University, and ScottJackson of Purdue University, with sup-port from the U.S. Department ofAgriculture and the National ScienceFoundation.

The current assembly (representing7.23x coverage), gene, set, and browserare collectively referred to as “Glyma0.”

JGI Releases Soybean Genome Assembly To Enable WorldwideBioenergy Research Efforts

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CSO 14773

CONTACT THE PRIMER / David Gilbert, Editor / degilbert@lbl.gov / (925) 296-5643

May 28–30, 2008Santa Fe, New Mexico

“Finishing in the Future” is a meeting dedicated to bringing together expertsin the field of genomic finishing—including representatives from the industriesthat serve this specialized scientific community. The meeting focuses on lab-oratory methods and computational tools used to help sequence, assemble,and finish genomes, including new sequencing technologies. Talks include anentire day devoted to the expanding field of metagenomics.

KEYNOTE SPEAKERS

Sydney Brenner, 2002 Nobel Prize Winner for Medicine, Founder of theMolecular Sciences Institute, and Senior Distinguished Fellow of the Crick-Jacobs Center, Salk Institute

Bruce Birren, Director of the Microbial Sequencing Center and Co-Director ofthe Genome Sequencing and Analysis Program, Broad Institute

Deanna Church, Coordinator for the Mouse and Human Genome Resourcesand Trace Archive, National Center for Biotechnology Information (NCBI)

Registration is limited to 120; please register soon if you plan to attend.To register, submit an abstract, or obtain more information as it becomesavailable please visit our Web site, http://www.lanl.gov/finishinginthefuture/

No registration fee is required.If you have any questions, or would like further information, please contact

Chris Detter at (505) 667-1326 or cdetter@lanl.gov.

FINISHING IN THE FUTURE

to share the JGI approaches to applyingergonomics to real-world situations,”said Simon Roberts, JGI InstrumentationSupervisor. “We had a very enthusiasticresponse from the hundreds of confer-ence attendees that visited our twobooths,” added Marty Pollard,Instrumentation Group Leader.

“It was great to see that JGI’semployee-empowered ergonomics pro-gram is on the forefront and runs asstrong as many other well-known andsuccessful companies,” said industrialengineer Christine Naca, the JGI’sProduction Ergonomics Lead.

Glyma0 is a preliminary release, basedon a partial dataset. This is expected tobe replaced with an improved, chromo-some-scale “Glyma1” version by theend of 2008. Early users of this dataare encouraged to track their favoritegenes by saving local copies of the DNAsequences of these loci, and not byidentifier or sequence coordinate, asthese will change in future versions.

The DOE JGI’s interest in sequencingthe soybean stems from its role as aprincipal source of biodiesel, a renew-able, alternative fuel with the highestenergy content of any alternative fuel.

Ergonomics Soybean

Laccaria’s protective capacity. Theseobservations point towards the dual lifeof mycorrhizal fungi like Laccaria, andits ability to grow in soil fending offpathogens and using decaying organicmatter while serving as a custodian ofliving plant roots.

The JGI Laccaria effort was led byGenome Annotation Group Leader IgorGrigoriev. In his remarks to the JGI All-Hands gathering on February 27,Grigoriev echoed an analogy coined by

his collaborator Francis Martin.“Laccaria is like Janus, the mythologicalcaretaker of gates, doors and hallways;beginnings and endings. Janus, with histwo faces looking in opposite direc-tions, is ever-aware of opportunity.”

Other JGI authors include AndreaAerts, Erika Lindquist, Asaf Salamov,Harris Shapiro, Peter Brokstein, ChrisDetter (Los Alamos National Laboratory),the DOE JGI Production GenomicsFacility sequencing team led by SusanLucas, and partners at the StanfordHuman Genome Center, Jane Grimwoodand Jeremy Schmutz, and Jerry Tuskanat ORNL. For more of the Laccaria story,see: http://www.jgi.doe.gov/News/news_3_5_08.html

Laccariacont. from page 2

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