Joint Genome Institute

The JGI is celebrating our 30th anniv! Over the next 15 months, we'll trace pivotal breakthroughs, as well as the researchers and staff who made them possible.🖥️🧬 Learn more: https://jgi.doe.gov/user-science/science-stories/jgi-celebrates-30-years-user-science @berkeleylab.lbl.gov @biosci.lbl.gov

In the next several years, the JGIi will develop exciting new projects, opening new ways our users can drive innovation for biomanufacturing and biotechnology. Learn more: https://jointgeno.me/stratplanrelease

From our FY26 joint CMM call: Setsuko Wakao is screening algae that naturally hyperaccumulate critical minerals — aiming to uncover the genetic basis of metal response and building on algae-based metal bioremediation research. Full Portfolio: https://jointgeno.me/CMMFY26 @berkeleylab.lbl.gov

This work is the first from my new-ish postdoc @jgi.doe.gov @berkeleylab.lbl.gov! I’ve learnt lots since I started (almost a year ago) especially about RNA + euk viruses (thanks @urineri.bsky.social). Very grateful to my PI @simrouxvirus.bsky.social who has been absolutely awesome to work with! 🙌

From our FY26 Functional Genomics call: After severe wildfire, fungi may help ponderosa pine seedlings recover by mobilizing nutrients and critical minerals. Claire Willing will study how Rhizopogon olivaceotinctus “switches on” after heat. More: https://jointgeno.me/FGFY26

Congrats to all! 🖥️🧬 @greensi.bsky.social

Efforts outlined in the JGI's new strategic plan directly align with the Genesis Mission — a DOE initiative to link AI, computing, automated experiments and national research facilities like the JGI into one connected system for discovery. Full release: https://jointgeno.me/stratplanrelease

From our FY26 joint CMM call: @Olena Vatamaniuk is developing plant-based methods to recover copper from low-quality soils and waste streams. Learning how plants absorb, transport and store copper lays the groundwork for “phytomining.” Full Portfolio: https://jointgeno.me/CMMFY26

DYK microbes can help extract #CriticalMinerals? Engineered yeast from the @jgi.doe.gov and @molecularfoundry.lbl.gov grab & store elements like mini collection units. We’re studying how the organisms could pull valuable but dilute elements from mining wastewater. https://bit.ly/4ytNkpe

New and evolving user programs will combine genomics with AI, automated experimentation and complementary capabilities across DOE user facilities — giving researchers integrated approaches hard to assemble in a single lab. More in our new strategic plan: jointgeno.me/stratplanrelease

Grateful to receive support from the DOE Joint Genome Institute through the FY26 Community Science Program Functional Genomics Call! Looking forward to investigate the regulatory mechanisms underlying host adaptation and infection in Botrytis cinerea. @jgi.doe.gov

From our FY26 Functional Genomics call: Duckweed is a bioenergy feedstock candidate, but the microbes shaping its growth remain unclear. Jiaqi Tan will pair plant and microbial gene activity to reveal what drives productivity. More: https://jointgeno.me/FGFY26

From our FY26 joint CMM call: Ning Sun wants to know how bacteria capture and separate rare earth elements. The team especially wants to learn how these microscopic systems distinguish "light" from "heavy" rare earth elements. Full Portfolio: https://jointgeno.me/CMMFY26 @berkeleylab.lbl.gov

From our FY26 Functional Genomics call: Gray mold fungus Botrytis cinerea threatens bioenergy crops. Ritu Singh will map genetic switches driving infection, filling a gap in plant pathogen research. https://jointgeno.me/FGFY26 @ritu2806.bsky.social @annajomu.bsky.social @spicybotrytis.bsky.social

Joint us! This year's meeting will feature keynotes from computational biologist Curtis Huttenhower of Harvard T. H. Chan School of Public Health & plant biologist C.J. Tsai of @universityofga.bsky.social More info: jointgeno.me/JGI2027 Sign up for updates: jointgeno.me/newsletter

From our FY26 joint CMM call: Viktoria Steck is investigating a new link between manganese and phosphorus metabolism in ocean microbes, and how this relationship controls the resource distributions of this critical mineral. Full Portfolio: https://jointgeno.me/CMMFY26

From our FY26 Functional Genomics call: Extreme-environment archaea have unique metabolic abilities, but their gene-control networks are unclear. Amy K. Schmid will use DAP-seq to map transcription factor–DNA interactions. More: https://jointgeno.me/FGFY26

Recently published in @science.org : With high-quality genomes, researchers shed light on pathways to starch and lignin — important starting materials for a wide variety of bioproducts. @jleebensmack.bsky.social @biosci.lbl.gov

From our FY26 joint CMM call: John Sedbrook is studying how Brassicaceae plants take up and accumulate metals, and aims to apply that knowledge to optimize the ability of these species to extract nickel from nickel-rich soils. Full Portfolio: https://jointgeno.me/CMMFY26

The JGI is scaling generation of high-quality, AI-ready data via automation. The S2S transformation will expand sequencing capacity through automated sample processing and data delivery—ensuring consistent, standardized datasets suitable for large-scale analysis. More: jointgeno.me/stratplanrelease

From our FY26 Functional Genomics call: Ocean fungi produce enzymes that break down hard-to-degrade polymers. Xuefeng (Nick) Peng will use biodesign and multi-omics to test new GH7 enzymes and map how they convert polymers into useful sugars. More: https://jointgeno.me/FGFY26

From our FY26 joint CMM call: Chris Rinke will explore microbes as an alternative method for extracting rare earth elements. Uncovering the microbial processes involved could help lay a foundation for future biological extraction methods. Full Portfolio: https://jointgeno.me/CMMFY26

New research decodes how a single stress signal transforms bacterial metabolism, offering engineers precise targets for designing better microbial factories. 🖥️ 🧬 More: https://jgi.doe.gov/user-science/science-stories/pinch-salt-activates-silent-gene-clusters-streptomyces

From our FY26 Functional Genomics call: Microbes can boost energy efficiency through electron transfer bifurcation. Anne-Frances Miller will ID bifurcation-capable electron transfer flavoproteins by testing selected ETFs using gene synthesis @ukresearch.bsky.social More: https://jointgeno.me/FGFY26

The NMDC will be merging its core, high-performing functionalities directly into DOE-BRIDGE. We extend our deepest gratitude to our core team, advisors, ambassadors and champions, DOE BER, and the community 🦠 🌎 Thank you for seven incredible years of collaboration! microbiomedata.org/faqs

📣 JGI Releases New Strategic Plan: As AI and advanced computing change what's possible in biology, the JGI is entering a new chapter. "AI-Driven Genomics to Accelerate Biological Discovery" charts a course for the future. Learn more: jointgeno.me/stratplanrelease @biosci.lbl.gov

From our FY26 joint CMM call: Claire Remacle is investigating how two key proteins — an enzyme and a copper carrier — work together in photosynthetic organisms. Full Portfolio: https://jointgeno.me/CMMFY26

We provide genomic capabilities, large-scale data & professional expertise to researchers advancing energy & infrastructure security. 🧬Opportunities: https://jgi.doe.gov/work-with-us/proposals 🧬Resources: https://jgi.doe.gov/work-with-us/offerings-capabilities 🧬Mission: https://jgi.doe.gov/mission

From our FY26 Functional Genomics call: Noncanonical cofactors can cut biomanufacturing costs but need engineered enzymes. Han Li will redesign MDR and formate dehydrogenase enzymes to work in reaction cascades with these cofactors. @UCIEngineering More: jointgeno.me/FGFY26

A team of researchers conducted extensive recoding of the E. coli genome, in a way that frees up space to add new genetic features and enhancements while keeping the engineered cells working properly. @geochurch.bsky.social @akosnyerges.bsky.social

From our FY26 joint CMM call: Serpentine rhizobia have evolved nickel resistance. @stephaniesimone.bsky.social studies nano-scale mechanisms of nickel absorption, movement and storage — contributing to critical mineral bio-recovery efforts. @wsupress.bsky.social More: https://jointgeno.me/CMMFY26

From our FY26 Functional Genomics call: Many high-value chemicals can be made by microbes, but finding the right enzymes is a bottleneck. Seung Hwan (Allen) Lee will screen for thiolase variants that help build better pathways to nylon precursors. Full portfolio: jointgeno.me/FGFY26

Really excited to host Dr Jonelle Basso this afternoon to talk about #phages and plant-host interactions! @jgi.doe.gov @berkeleylab.lbl.gov @sfstatebio.bsky.social

Tomorrow is the LAST DAY for early-bird rates to our VEGA symposium in Berkeley, CA this November. 🖥️ 🧬 🦠 See below for keynote speakers; More information at jointgeno.me/VEGA

From our FY26 joint CMM call: Sergey Nuzhdin and student Leah Ferger will study how genetic differences in giant kelp affect cell-wall binding of rare earth elements, informing bio-inspired strategies for critical mineral recovery. @USCDornsife Full Portfolio: https://jointgeno.me/CMMFY26

In a recent episode of Genome Insider, @jotlovell.bsky.social discussed why a single reference genome for Sorghum proved insufficient, and the value of a pangenome to represent the crop's full genetic diversity: https://jgi.doe.gov/user-science/podcasts/spectrum-sorghum 🖥️ 🧬 🌱

From our FY26 Functional Genomics call: Speciality chemicals like non-standard amino acids could be made more efficiently in microbes with hardier enzymes. @kunjapur.bsky.social will use biodesign to make pathway enzymes more thermostable. Full portfolio: https://jointgeno.me/FGFY26

The Primer goes out every other month and includes updates on user research, upcoming events, proposal recipients and other opportunities. Stay in touch! Sign up at jointgeno.me/newsletter

From our FY26 joint CMM call: @merchant-lab.bsky.social will study ab protein's role in zinc assimilation, then modify it to bind other critical metals in algal cells & test how well it removes them from the growth medium. Full portfolio: https://jointgeno.me/CMMFY26 @ucberkeleyofficial.bsky.social

Thanks @jgi.doe.gov for the opportunity!

Perspective: Pangenomes are Only as Powerful as their Annotation Method Are researchers wasting resources following false trails — due to variations in interpretative methods? 🖥️🧬 🌱 @tomasbruna.bsky.social Full story below⬇️

"The Mobilome in the Mire" DNA sleuths 🕵️‍♀️ @scbagby.bsky.social and 🕵️‍♂️ @simrouxvirus.bsky.social tracked a whole zoo of mobile genetic elements in thawing permafrost ❄️💧 for 8 years. Another Genome Insider podcast from @jgi.doe.gov 🎙️: jgi.doe.gov/user-science...

From our FY26 Functional Genomics call: Bacteriophages reshape plant-associated bacteria by reprogramming gene expression. @michhulin.bsky.social will use DAP-seq to map phage transcription factor binding in Pseudomonas and link it to plant traits. Full portfolio: https://jointgeno.me/FGFY26

🚨 DEADLINE SEPT. 8: First time PIs have until Tuesday to submit proposals for our New Investigator call. Details here: jointgeno.me/CSPnewPI https://bsky.app/profile/jgi.doe.gov/post/3msy2sihm3r2e

From our FY26 joint CMM call: Cecilia Martinez-Gomez aims to figure out the chemical makeup of rare earth elements in M. extorquens AM1 at the subcellular level and connect those properties to specific genetic disruptions. Full portfolio: https://jointgeno.me/CMMFY26 @ucberkeleyofficial.bsky.social

A Lake Mendota time series found invasive zooplankton prompted giant viruses to increase replication rates while maintaining protective DNA mechanisms—suggesting viral-like capability + bacterial-like stability More: https://jgi.doe.gov/user-science/science-stories/broader-sense-evolution-over-time

Nadia is part of our 2026 New Investigator cohort — we are currently accepting projects for 2027! The deadline is Sept. 8 for proposals from PIs who have never led a project with the JGI. More info: jointgeno.me/CSPnewPI

From our FY26 Functional Genomics call: Soil fungi make natural products shaped by life stage and neighboring microbes. Andreas Guerrero will use multiomics to map genes and metabolites behind natural-product production in understudied Mucoromycota fungi. Full portfolio: https://jointgeno.me/FGFY26

A Global Catalog of Microbial Symbionts 🌍🦠🧬🫨 New resource from @jgi.doe.gov, led by @astrogenomics.bsky.social and @fmschu.bsky.social with contributions by @emileyeloe-fadrosh.bsky.social @miferg.bsky.social and many more 🔓 www.nature.com/articles/s41... @biosci.lbl.gov @berkeleylab.lbl.gov

Congrats to #BioBSE researchers Aindrila Mukhopadhyay and co-PI Aparajitha Srinivasan on their funded FY27 FICUS Research proposal! The will study dynamic stress adaptation in a microbe, which could boost #biomanufacturing. www.emsl.pnnl.gov/news/ten-pro... @berkeleylab.lbl.gov @jgi.doe.gov