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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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    A light green shrub with spiny leaves, up close.
    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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    Abstract image of gold lights and squares against a black backdrop
    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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November 7, 2013

Why Sequence Catfish?

Catfish are a two-billion-dollar industry in the United States, representing 68% of all U.S. aquaculture production. Catfish have served as model species for comparative immunology, reproductive physiology, and toxicology among ectothermic vertebrates because of their unique characteristics. This project involves sequencing expressed sequence tags (ESTs) for two closely related catfish species. Channel catfish (Ictalurus punctatus)… [Read More]

November 7, 2013

Why Sequence the Hydractinia Allorecognition Gene Complex?

Colonial animals typically display the capacity to discriminate between their own tissues and those of unrelated members of their own species, the recognition event culminating in either fusion or rejection. Such allorecognition systems have long been of interest to geneticists by virtue of the substantial allotypic diversity they display. The sequencing of the Hydractinia symbiolongicarpus… [Read More]

November 7, 2013

Why Sequence Sea Squirt cDNA?

Ascidians are invertebrate chordates, which diverged from the vertebrate lineage near the root of the chordate phylogenetic tree. Their larvae have a tadpole structure that closely resembles lower vertebrate larvae. They are, however, composed of a very small number of cells (2600 for Ciona intestinalis), have a stereotyped development due to invariant cleavage patterns, and… [Read More]

November 7, 2013

Why Sequence Campanulales Chloroplasts?

Something happened in the plant order Campanulales that fundamentally destabilized the chloroplast genome. Chloroplast gene order is highly conserved among virtually all land plants, and foreign DNA is not normally incorporated into the chloroplast genome. In the Campanulales, however, inversions and other genome rearrangements occur exceptionally often, and these are commonly associated with the insertion… [Read More]

November 7, 2013

Why Sequence a Butterfly?

The Lepidoptera (butterflies and moths) comprise more than 150,000 species, many of economic importance (e.g., as pollinators, as agricultural pests, and in silk production), and have characteristic biological properties that distinguish them from all other insects (e.g., females as the heterogametic sex, derived wing color patterns and color vision, and holocentric chromosomes). However, genomic resources… [Read More]

November 7, 2013

Why Sequence a Frog-Killing Fungus?

Batrachochytrium dendrobatidis is a unique fungus responsible for chytridiomycosis, an emerging infectious disease that is responsible for global amphibian declines. First identified in 1998 on frogs originating from Australia and Central America, B. dendrobatidis has now been reported to be killing frogs on every continent except Asia and Antarctica. Despite international collaboration and considerable research… [Read More]

November 7, 2013

Why Sequence Sorghum?

One of the world’s leading grain crops, sorghum is also an important model for tropical grasses of worldwide importance with a collective minimum economic impact of $69 billion U.S. per year. As a model for the tropical grasses, sorghum is a logical complement to Oryza (rice), the first monocot plant to be sequenced. Sorghum is… [Read More]

November 7, 2013

Why Sequence the Monkey Flower?

One of the challenges of 21st-century biology is to determine, at the DNA sequence level, the basis of adaptive evolution in nature. The flowering plant genus Mimulus (monkey flowers) has become a leading model system for studying ecological and evolutionary genetics in nature. JGI will sequence the species Mimulus guttatus. Since Darwin, Mimulus species have… [Read More]

November 7, 2013

Why Sequence Arabidopsis lyrata and Capsella rubella?

Sequencing Arabidopsis lyrata and Capsella rubella, close relatives of Arabidopsis thaliana, will leverage the rich information now available for A. thaliana, arguably the most important reference plant. Arabidopsis lyrata is the closest well-characterized relative in the same genus as A. thaliana, and Capsella is the closest well-characterized genus. Several technologies are currently being used to… [Read More]

November 7, 2013

Why Sequence Sulfur-Oxidizing Bacteria?

Several environmental problems, such as acid rain, biocorrosion, etc., are caused by sulfur compounds, such as sulfur dioxide (SO2) and hydrogen sulfide (H2S). A sustainable process to remove these sulfur compounds is the production of elemental sulfur from H2S-containing gas streams by the use of sulfide-oxidizing bacteria. In this process, H2S is absorbed into the… [Read More]
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