DOE Joint Genome Institute

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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    A panoramic view of a lake reflecting a granite mountain.
    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

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    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

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    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    iPHoP image (Simon Roux)
    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

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    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    croppe image of the JGI helix sculpture
    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    image from gif that shows where in the globe JGI fungal collaborators are located.
    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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News & Publications
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February 4, 2020

JGI Scientists Pen Genome Watch Articles

For the May 2019 Genome Watch article by Tanja Woyke. (Credit: Philip Patenall/Springer Nature Limited)JGI researchers are sharing their expertise in environmental genomics by writing for the column Genome Watch in Nature Reviews Microbiology. In 2018. Tanja Woyke, who leads the Microbial Program at the JGI, received a message from Andrea Du Toit, senior editor for Nature Reviews Microbiology, with an unusual opportunity: would JGI researchers consider regularly writing for the magazine’s column Genome Watch? [Read More]

December 23, 2019

Expanding Virophage Diversity

Virophage discovery pipeline. (A) MCP amino acid sequences from reference isolated genomes and published metagenomic contigs were queried against the IMG/VR database with stringent e value cutoffs. All homologous sequences detected were then clustered together to build four independent MCP profiles. (B) The resulting four MCP models were used to recruit additional homologous sequences from the entire IMG/M system. All new sequences were clustered, and models were built creating a final set of 15 unique MCP HMMs. (C) These 15 unique MCP HMMs were then used to search two different databases for homologous sequences: the IMG/M system and a custom assembled human gut database containing 3771 samples from NCBI’s Sequence Read Archive (SRA). (D) The resulting set of 28,294 non-redundant (NR) sequences with stringent e value cutoffs was filtered by size and e by the presence of the four core virophage genes (high-quality genomes; HQ virophages). Finally, completeness of novel metagenomic virophage genomes wsa predicted based on circularity or presence of inverted terminal repeats (ITR). (Figure from Paez-Espino et al. Microbiome (2019) 7:157 https://doi.org/10.1186/s40168-019-0768-5)Virophages are small viruses with double-stranded DNA genomes that co-infect eukaryotic cells along with giant viruses. Almost all known virophage genomes share only four genes in common: major and minor capsid proteins (MCP and mCP, respectively), ATPase involved in DNA packaging, and PRO, a cysteine protease involved in capsid maturation. Recently reported in Microbiome, researchers… [Read More]

December 23, 2019

Honey Bee Gut Microbiota Divvy Up Dinner

Honey bees metabolize pollen with the help of their gut microbiota. (Photo by Jason Leung on Unsplash )Scientists have wondered exactly how the honey bee gut microbial community carries out its helpful metabolism: who’s responsible for what biochemical processes? [Read More]

December 10, 2019

10 From JGI on the 2019 Highly Cited Researchers List

2019 JGI Highly Cited ResearchersClarivate Analytics, formerly the IP & Science arm of Thomson Reuters, has released their 2019 list of Highly Cited Researchers, which includes 10 affiliated with the JGI . The 2019 list focused on Highly Cited Papers, defined in the Methodology section as “those that rank in the top 1% by citations for papers published and… [Read More]

December 2, 2019

Mindfully Moving JGI

jgi mindfully movingJGI is in the process of shifting its operations from Walnut Creek to the heart of the Berkeley Lab campus. By Friday, October 18, the production sequencing labs in Building 100 were silent. Twenty years after the JGI united the genomics expertise of three national labs in one long building at Walnut Creek, after countless… [Read More]

October 3, 2019

Triggering Morel Fruiting

Morel by Hao TanA collaborative team led by Hao Tan from the Sichuan Academy of Agricultural Sciences in China and involving Francis Martin from the Institut National de la Recherche Agronomique (INRA) in France and Igor Grigoriev from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility, reported on just… [Read More]

September 30, 2019

A Step Toward Controlling Soybean Rust

Scanning electron microscopy picture of a soybean leaf infected by the rust fungus Phakopsora pachyrhizi. The leaf and the fungus were artificially painted in green and in orange, respectively. The section shows invading infection hyphae of the fungus inside the leaf mesophyll, whereas the spores are visible below the leaf breaking through the lower epidermis (U. Steffens, Bayer Crop Science)The United States is the world’s leading soybean producer, and soybeans are used to produce biodiesel. The fungus Phakopsora pachyrhizi causes Asian Soybean Rust (ASR) and is the major pathogen of soybean. Left uncontrolled, soybean rust could reduce crop yields by as much as 90 percent. As part of the DOE Joint Genome Institute’s 2016… [Read More]

September 20, 2019

Meet a JGI Postdoc: Ping-Hung Hsieh

NPAW 2019 JGI postdoc Ping-Hung HsiehFrom September 16-20, 2019, we introduce you to some of the postdocs at the JGI in honor of National Postdoc Appreciation Week, which recognizes the contributions of these early career researchers. Through a series of hard-hitting questions, we find out what drives each one.   What are you working on? My postdoc research in the Synthetic… [Read More]

September 18, 2019

Meet a JGI Postdoc: Ritesh Mewalal

NPAW 2019 JGI postdoc Ritesh MewalalFrom September 16-20, 2019, we introduce you to some of the postdocs at the JGI in honor of National Postdoc Appreciation Week, which recognizes the contributions of these early career researchers. Through a series of hard-hitting questions, we find out what drives each one.   What are you working on? Beneficial plant-microbe interactions alter valuable… [Read More]

September 17, 2019

Meet a JGI Postdoc: Kyle Hartman

NPAW 2019 JGI postdoc Kyle HartmanFrom September 16-20, 2019, we introduce you to some of the postdocs at the JGI in honor of National Postdoc Appreciation Week, which recognizes the contributions of these early career researchers. Through a series of hard-hitting questions, we find out what drives each one.   What are you working on? I am a member of the… [Read More]
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