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16S rRNA Gene Amplicon Sequencing Data from Flooded Rice Paddy Mesocosms Treated with Different Silicon-Rich Soil Amendments
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Community standards and future opportunities for synthetic communities in plant–microbiota research
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SIPs with Standards
… show which microbes are handling specific nutrients, or what they're doing with those nutrients, and even how quickly. … catch: SIP labwork and analysis can be very demanding.  The JGI offers SIP analysis to make these experiments accessible … goal is to generate SIP data that can be useful to multiple teams and analyses. This episode, Rex Malmstrom (JGI), and …
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Annotation of metagenome short reads using proxygenes
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Transcriptional control of Clostridium autoethanogenum using CRISPRi
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Promoting the Power of Viral Metagenomics
… summarizing the field of viral metagenomics, authored by JGI researchers Lee Call,  Stephen Nayfach and  Nikos … published in the journal  Annual Review of Biomedical Data Science . The following guest piece was written by Call, … and discuss some of the current challenges faced by those using metagenomics to try to understand the far-reaching …
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Marchantia Pangenome Highlights Adaptive Nature of Plant Lineages
… ancestral and present-day plants The Science In a recent  Nature Genetics paper , researchers focused on the full … involved in adaptations seen in later plant lineages. The team found that some of the adaptation strategies used by … the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at …
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A Pinch of Salt Activates Silent Gene Clusters in Streptomyces
… The Science Soil bacteria in the genus Streptomyces are nature's chemical factories. They hold genetic blueprints for … tracking gene activity and chemical output over time, the team mapped how the bacterium redirects its energy, building … of multiple omics data from various environments — that JGI users can leverage to create a more complete picture of …
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A Complex Confection Decoded: Sugarcane Reference Genome
… for the sugarcane cultivar R570 has been  published in  Nature by an international consortium. With the genetic code … The Impact In providing a reference sugarcane  genome , the JGI provides foundational genetic information that crop … factories for sugar and biomass. Additionally, the team was able to identify a major locus (Bru1) that durable …
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A Plant Root Atlas for Tracking Developmental Trajectories
… A collaborative team led by Geoffrey Schiebinger at the University of … the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science User Facility located at Lawrence Berkeley National … and environmental characterization and cleanup. The JGI provides integrated high-throughput sequencing and …
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Probing the active fraction of soil microbiomes using BONCAT-FACS
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Microbial species delineation using whole genome sequences
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