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PRIMER Summer 2009 Volume 6 Issue 1

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PRIMER Summer 2009 Volume 6 Issue 1 the PRIMER Summer 2009 Volume 6 Issue 1 also in this issue Bugs, Big & Small, from On Sequencing, Finishing and Notes from the 4th Annual JGI Inside & Out, Join Sources of Analysis in Santa Fe . 2 User Meeting . 6-7 Supporting Life in Great Salt Improving Crops and Green Genes to Fill CSP Lake . 3 Feedstocks . 8 Brown-rot for Biofuels . 4 A Shortcut called ChIP-seq 9 2010 Pipeline Sequencing with a Algae as a climate change More than 70 projects were could be used to remove heavy Single Cell . 5 sensor . 10 selected for the 2010 Com- metal contaminants from fresh- munity Sequencing Program water streams. (CSP) portfolio. They involve “The information we generate organisms from regions as far from these projects promises north as the Arctic and south to improve the clean, renew- to New Zealand. They include able energy pathways being proposals to study microbial developed now as well as lend contaminants in alcohol that researchers more insight into could impact biofuel production, the global carbon cycle, options microbial communities in the for bioremediation, and biogeo- guts of insects from an area chemical processes,” said DOE geography scholar Jared JGI Director Eddy Rubin. “In processes that support life on cow, termite and Amazonian Diamond once described as translating DNA sequence data the planet, or imperil it.” stinkbird, Mike Taylor from “the nearest approach to life into biology, we generate valu- Following along the lines of New Zealand’s University of on another planet” and a able science that improves our previous CSP-approved meta- Auckland proposed sequencing novel bacterial isolate that understanding of the complex genomic projects involving the microbial communities inside cont. on page 11 Moving Microbial Genomics Forward BY MASSIE SANTOS BALLON why two-thirds of the nearly In an article published in genomic data, still remain to To get an idea of how many 5,000 genome projects report- the July issue of the journal be defined and codified. Due microbes there are on Earth, ed in the Genomes OnLine Nature Biotechnology, Kyrpides to biases in the selection of imagine taking just the small- Database involve microbes. reflects on the role of microbial genomes for study, vast realms est type of microbe, the virus- Another factor is the myriad studies in the genomics revo- of biodiversity remain unex- es that infect other microbes, potential applications of micro- lution of the past decade, and plored. Data release policies and lining them all up in the bial research for targeted drug considers the factors that have very early on led to what he row. How far do you think that development, bioenergy, biore- hindered the advancement of terms “a violation of a long- line would reach? From San mediation, agriculture, and the field. Although nearly standing precept in all scientif- Francisco to Paris? To the other human endeavors. But 1,000 microbial genomes have ic fields” when reviewers of moon? To the sun? The far more could be done with been sequenced over the past submitted publications answer: A thousand times the microbial genomics, according 15 years, he noted that the couldn’t access the underlying distance across the Milky Way. to DOE JGI Genome Biology data obtained has been com- genomic data. Microbes are not only head Nikos Kyrpides, if promised by the lack of a com- Kyrpides offers numerous exceedingly numerous, but researchers would embrace mon language and standard- suggestions to meet these also extremely diverse, encom- the world of possibilities that ized procedures. Such stan- and other challenges that face passing most of Earth’s total extend beyond such human- dards, required for the genomics research in the biodiversity. This is one reason centric studies. exchange and integration of decade ahead. For example, cont. on page 11 2 / the PRIMER Summer 2009 Vol. 6, Issue 1 Seeking Sequencing Standards in Santa Fe BY MASSIE SANTOS BALLON “Data generation is becoming cheaper, something produced in a lab other than a One thing became clear fairly quickly at easier and faster,” he said, ”and this is only large sequencing center such as DOE JGI, the 4th Sequencing, Finishing, Analysis in getting worse.” Based on the current output, which typically generates what he called a the Future Meeting held in Santa Fe, NM Chain predicted that by 2012, there might be “high quality draft,” which has little or no from May 27-29, 2009: the name game 12,000 incomplete genome sequences being manual review. genome researchers play needs new rules. made available to researchers who might In an “improved high quality draft,” the Speaking immediately after the opening not recognize that the datasets may lack data has been reviewed both by people and keynote, Patrick Chain, head of Microbial the information they’re interested in using. machines to some extent so most of the Interactions program at DOE JGI, noted that Chain said another part of the problem genetic data is assembled correctly, but there have traditionally been only two cate- is that as new sequencing technologies some errors may still be present. An gories for sequenced genomes — “draft,” become the machines of choice, they need “annotation grade” sequence would present where the genetic data of an organism has to be evaluated so that researchers under- all the information in various gene regions been collected but not completely organized, stand that the information that comes out as accurately as possible, and the term or “finished,” in which the genetic code has of one company’s instrument may not be “non-contiguous finished” would apply to been correctly put together and can be read the same as the information provided by genomes that are practically finished except like a published book from beginning to end. other equipment. The tags applied to the for “recalcitrant regions” that are proving He then proposed adding four other labels data may also vary based on the sequenc- problematic. Such quirks, Chain said, so that researchers can determine the ing technology used. would be included in the comments when quality of the genomes they’re accessing. All of these changes, Chain said, have the genome sequence is made available. Unfortunately, Chain said, pitching the led to the Consortium’s proposal of four It’s worth wondering after all this what a idea on behalf of the International Genome genome quality categories, as well as some genome sequence has to do to be labeled Sequencing Standards Consortium, the suggested changes to the definitions of the “finished.” To achieve this pinnacle, Chain advent of new sequencing technologies traditional terms, none of which are pegged said, the sequence would have no more has increased the number of genomes to a particular sequencing technology. A than one error in every 100,000 base pairs. being sequenced every year. standard draft, for example, might be Chain noted that one of the hardest parts of coming up with categories of sequence status had been getting every- one in the consortium to agree on the news terms and definitions. “I can barely get agreement in my own group on some of these issues so this was really a fantastic achievement,” he said. He concluded by noting that the Consortium plans to submit their proposal for publication at a later date, and intends to publicize the stan- dards on the websites of the various insti- tutions affiliated with the group. A number of other speakers referenced the need for a standardized terminology that could describe a genome sequence and its various components in their talks over the three days of the conference. Among them was Deanna Church from the Meeting organizers (left to right): Michael Fitzgerald, Broad Institute; Patrick Chain, DOE National Center of Biotechnology Information, JGI; Bob Fulton, Washington University in St. Louis; Donna Muzny, Baylor College of who referred to the need for standard Medicine; Johar Ali, Ontario Institute for Cancer Research; Chris Detter, DOE JGI; Alla Lapidus, DOE JGI terms during her talk when she mentioned cont. on page 9 the PRIMER / 3 Summer 2009 Vol. 6, Issue 1 Salt Lake’s Briny Waters May Harbor Biological Treasures Photo by Charles Uibel, GreatSaltLakePhotos.com BY MADOLYN BOWMAN ROGERS mercury and other heavy metals, and high to provide a baseline picture of microbial In one of the 2009 Community volatile sulfur concentrations that give the diversity. Researchers will combine the Sequencing Projects, the DOE JGI are lake a distinctive rotten-eggs stink. DNA data with measurements of microbial partnering with a consortium of researchers Despite these compounds, the lake sup- metabolites and environmental conditions to sequence the genomes of microbial ports five million migrating birds each year such as salinity and oxygen to paint a communities in Utah’s Great Salt Lake. and is home to brine shrimp and several complete picture of the lake’s ecology. Researchers believe the lake’s harsh envi- kinds of algae including diatoms, as well “We’ve done a lot of diversity assess- ronment harbors a wealth of undiscovered as an untapped diversity of microbial life. ment of the lake in the last two years, biodiversity that may provide new solu- Because the microbes can survive in and we’re not even approaching the limit tions for carbon sequestration and biore- such an extreme environment, Weimer of microbial diversity,” Weimer said. “The mediation, and might even give clues to believes they may contain unique proteins services that the DOE JGI will provide are news the nature of life on other planets. that enable them to chemically fix sulfur going to eclipse anything that we could do “We believe we’re going to find new and carbon and to detoxify pollutants.
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