DOE Joint Genome Institute
DOE Mission Areas
Bioenergy Research Centers
Mapping Heat Resistance in Yeasts
In a proof-of-concept study, researchers demonstrated that a new genetic mapping strategy called RH-Seq can identify genes that promote heat resistance in the yeast Saccharomyces cerevisiae, allowing this species to grow better than its closest relative S. paradoxus at high temperatures.
First Monoploid Reference Sequence of Sugarcane
For the highly polyploid sugarcane, an international team of researchers has successfully assembled a first monoploid reference sequence using a targeted approach that focused on the gene rich part of the genome by harnessing information from a sequenced related species – sorghum.
Defining a Pan-Genome for Antarctic Archaea
Some Antarctic lakes have salinities 10 times that of seawater. By collecting and sequencing dominant haloarchaeal sequences from six hypersaline lakes, researchers focused on understanding the genomic variation in haloarchaea across East Antarctica.
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Approved User Proposals
Methane Flux in the Amazon
Wetlands are the single largest global source of atmospheric methane. This project aims to integrate microbial and tree genetic characteristics to measure and understand methane emissions at the heart of the Amazon rainforest.
Infections and Host-Pathogen Interactions of Chlorella
The non-photosynthetic, predatory cyanobacterium Vampirovibrio chlorellavorus is a globally important obligate pathogen of Chlorella species/strains, which are of interest as biofuel feedstocks.
Insights into Functional Diversity in Neurospora
This proposal investigates the genetic bases of fungal thermophily, biomass-degradation, and fungal-bacterial interactions in Sordariales, an order of biomass-degrading fungi frequently encountered in compost and encompassing one of the few groups of thermophilic fungi.
Data & Tools
DAS Tool for Genome Reconstruction from Metagenomes
Through the JGI’s Emerging Technologies Opportunity Program (ETOP), researchers have developed and improved upon a tool that combines existing DNA sequence binning algorithms, allowing them to reconstruct more near-complete genomes from soil metagenomes compared to other methods. The work was published in Nature Microbiology.
New Software Tools Streamline DNA Sequence Design-and-Build Process
Researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI) have developed a suite of build-optimization software tools (BOOST) to streamline the design-build transition in synthetic biology engineering workflows.
DOE JGI Database of DNA viruses and retroviruses debuts on IMG platform
In a series of four articles published in the Database issue of the Nucleic Acids Research journal, DOE JGI researchers report on the latest updates to several publicly accessible databases and computational tools that benefit the global community of microbial researchers.
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Calls for User Proposals
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Preparing for a Sequence Data Deluge
The approved CSP 2019 proposals leverage new capabilities and higher throughput in DNA sequencing, synthesis and metabolomics. Additionally, just over half of the accepted proposals come from primary investigators who have never led any previously accepted JGI proposal.
Innovative Technology Improves Our Understanding of Bacterial Cell Signaling
Cyclic di-GMP (Guanine Monophosphate) is found in nearly all types of bacteria and interacts with cell signaling networks that control many basic cellular functions. To better understand the dynamics of this molecule, researchers developed the first chemiluminescent biosensors for measuring cyclic di-GMP in bacteria through work enabled by the JGI’s Community Science Program (CSP).
Freedom and Flexibility: Thinking Outside the Cell
The latest proposal approved through the JGI’s Emerging Technologies Opportunity Program (ETOP) aims to develop an optimized cell-free platform that will enable researchers to speed up the “build” and “test” portion of the design-build-test-analyze cycle in synthetic biology.
News & Publications
Expanding Fungal Diversity, One Cell at a Time
In Nature Microbiology, a team led by JGI researchers has developed a pipeline to generate genomes from single cells of uncultivated fungi. The approach was tested on several uncultivated fungal species representing early diverging fungi.
Evolutionary Changes in the Genetic Code of Yeasts
In nuclear genomes, a genetic code change where the amino acid assignment of a sense codon is swapped for a different amino acid is very rare. In a Nature Communications that built on a 2016 JGI PNAS study, researchers looked at the genomes of 52 yeast species, including seven newly sequenced and observed all three CUG codon reassignments: CUG-Ser, CUG-Ala, and CUG-Leu.
Celebrating the JGI-UC Merced Genomics Internship Program
Originally conceived as a graduate student summer research experience at the JGI, the Genomics Internship Program expanded to include UC Merced undergraduate students through the California Alliance for Minority Participation (CAMP) program. Since 2014, more than 20 UC Merced students have contributed to the research of 13 JGI scientists.
November 12, 2013