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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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    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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Home › Archives for Leila Hornick
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September 15, 2010

HudsonAlpha involved in cacao genome project

Excerpted from EurekAlert!: “Mockaitis, a biochemist-turned-genomicist, joined the project in early 2009, and quickly set to work with her collaborators to tackle the challenge of sequencing and accurately pasting together the approximately 400 million base pairs of the tree’s genome. Mockaitis’ Cacao Genome Group partners at the U.S. Department of Agriculture’s Subtropical Horticulture Research Station… [Read More]

September 10, 2010

New clues for understanding a novel cellulolytic process

Fibrobacter succinogenes is an anaerobic bacterium that breaks down plant cell wall biomass in ruminants and converts the cellulose into glucose. Sequenced at the DOE JGI for the Great Lakes Bioenergy Research Center (GLBRC), the 3.8 million base genome was completed and the information submitted to the National Center for Biotechnology Information in late 2009…. [Read More]

September 3, 2010

Bacterial lessons in rare metal recovery

One of the goals of the DOE’s Genomics:GTL Program is understanding how microbes and microbial communities perform the functions that have helped them thrive in a wide variety of environments and which have applications in the DOE mission areas of bioenergy, carbon cycling and biogeochemistry. British scientists applied information gleaned from Desulfovibrio genomes sequenced by… [Read More]

August 30, 2010

Brachypodium genome project on The Warsaw Voice

Brachypodium distachyon, commonly called purple false brome, is a model grass that enables researchers to more easily and thoroughly study temperate cereals, such as wheat, barley, rye and oats. These grasses are one of the most important groups of domesticated plants. The sequencing of the nuclear genome of Brachypodium is a big step towards intensified… [Read More]

August 30, 2010

Sponge genome project on Cosmos magazine

It’s just a blob, with no eyes, no nervous system, no muscle, no gut, no circulatory system, no tissues of any sort really – just cells embedded in a jelly matrix. They’re not even considered true animals. Yet according to the Nature report the sponge genome, which was read by researchers at the University of… [Read More]

August 27, 2010

Standardizing metagenomic classifications

A five-tier metagenome classification system would  enable genomic researchers to better extract and understand data. (Image from Ivanova et al. Env Microbiol. 2010: 12(7):1803-1805.) Studying the genomes of microbial communities, or metagenomics, has been facilitated in the last few years by advances in sequencing technologies. However, as the DOE JGI’s Natalia Ivanova, Susannah Tringe, Dino… [Read More]

August 20, 2010

A bacterium for biohydrogen production

Breaking down organic wastes typically involves microbial communities of bacteria and archaea working in concert with methanogens, which remove the hydrogen generated during the degradation process. The interactions between these syntrophic communities are being studied to understand the roles these microbes play individually and and as whole. In the August 2010 issue of the journal… [Read More]

August 16, 2010

Sponge genome project on Inside Science

According to the new study, which was based on a species of sponge found on the Great Barrier Reef off the coast of Australia, the creature has some 18,000 genes. This is fewer than the number of genes humans possess (currently estimated at about 20,500 genes) — but not far off. A few years ago,… [Read More]

August 13, 2010

Updating Genomics and Bioinformatics Courses for Undergraduates

Responding to the National Research Council of the National Academies’ call to “involve students in working with real data and tolls that reflect the nature of life sciences research in the 21st century,” the DOE JGI’s Education Program, headed by Cheryl Kerfeld, collaborated with faculty members from several universities around the country to develop bioinformatics… [Read More]

August 13, 2010

Syntrophic communities sequencing project on SciGuru

In work published in the advanced online version of the International Society for Microbial Ecology (ISME)’s Journal on August 5, an international team of scientists including DOE JGI researchers report the first metagenome analysis of a microbial community grown in an anaerobic methanogenic (methane producing) bioreactor. The microbial community is syntrophic, i.e., certain organisms live… [Read More]
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