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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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    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
Home › Blog
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June 1, 2009

“DOE JGI releases expanded version of Phytozome.net”

Phytozome provides a central “hub” for web access to a rapidly growing number of plant genomes, and includes tools for visualization of plant genomes and associated annotations, sequence analysis, and bulk, as well as targeted, plant data retrieval. The gene families available in Phytozome, defined at several evolutionarily significant epochs, provide a framework for the… [Read More]

June 1, 2009

“Integrated microbial genomes expert review goes primetime”

Scientists at the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the Biological Data Management and Technology Center (BDMTC) at Lawrence Berkeley National Laboratory have launched the Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system. IMG ER supports and enhances the review and revision of annotations for both publicly available… [Read More]

June 1, 2009

“Hands-on research inspires freshman biology students”

At the beginning of her first quarter at UC Santa Cruz, freshman biology student Kimberly Davis collected some soil from the forest floor near Thimann Labs. She then isolated a bacterial virus from the soil, took pictures of it with an electron microscope, extracted the virus’s DNA, sent it off for sequencing by the national… [Read More]

June 1, 2009

“HHMI Seeks Schools to Join Science Education Revolution”

The purified DNA from one virus was sent by each school to the Joint Genome Institute-Los Alamos National Laboratory in New Mexico for sequencing. That resulting data allowed students to spend the second term using bioinformatics tools to analyze and annotate the DNA sequence and identify genes. Students compared their DNA sequence to that characterized… [Read More]

June 1, 2009

“DOE JGI releases expanded version of Phytozome.net”

An enhanced version of Phytozome.net, a web portal for comparative plant genomics geared to advance biofuel, food, feed, and fiber research, has been released by the U.S. Department of Energy (DOE) Joint Genome Institute (JGI). The rest of the story appears here. [Read More]

April 16, 2009

‘Algae leading the way to photosynthesis’

Scientists have decoded genomes of two strains of green algae, highlighting genes that allow them to capture carbon emissions and maintain the oceans’ chemical balance, a study said on Thursday. The strains’ productivity as a significant source of marine food and their ability to capture carbon means the algae can influence the carbon flux and… [Read More]

April 16, 2009

Genes from tiny marine algae opens new avenues of research

By sequencing the DNA of two tiny marine algae, a team of scientists has opened up a myriad of possibilities for new research in algal physiology, plant biology, and marine ecology. The project was led by Alexandra Worden at the Monterey Bay Aquarium Research Institute (MBARI) and the Joint Genome Institute (JGI). The genome analyses… [Read More]

April 16, 2009

UI biologist studies ocean plant cell adaptation in climate change

How will plant cells that live in the oceans and serve as the basic food supply for many of the world’s sea creatures react to climate change? A University of Iowa biologist and faculty member in the Roy J. Carver Center for Comparative Genomics and his colleagues came one step closer to answering that question… [Read More]

April 16, 2009

Unraveling the Mysteries in Sorghum’s ‘Simple’ Genome

Mapping out a genetic blueprint involves determining several short sections that would make up a gene, and sequencing those in bulk. Then, scientists take all of those pieces and put them together like a puzzle—a difficult puzzle, according to Dan Rokhsar, the computational biology leader at the U.S. DOE Joint Genome Institute in Walnut Creek,… [Read More]
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