2024 Progress Report

A record number of primary users — 2,475 — had active proposals with us, along with more than 15,000 secondary users who made use of our data.

• We completed 39,870 projects in FY24
• We generated 871 Terabases of sequence
• We synthesized 9.7 Megabases of DNA
• We processed 13,700 metabolomics samples
• With our users, 247 publications were published
   

Our primary objective is to serve our user community with large-scale advanced genomic capabilities. This year we brought online the latest short-read technology, the Illumina NovaSeq X Plus, and the latest long-read technology, the Pacific Biosciences Revio. They enable increased capacities and faster sequencing, and at the same time help us manage costs. We have also scaled DNA-affinity purification sequencing (DAP-seq),  stable isotope probing (SIP) and omics, and we continue to develop new capabilities in single-cell sequencing, spatial transcriptomics, and cell- and cell-free expression platforms. 

We closed our 2018 Strategic Plan at the end of September, 2023 with over 90% of our two- and five-year milestones completed. Our new Strategic Plan, Innovating Genomics to Serve the Changing Planet, was released in April. It centers our work on four strategic themes: Nutrient Cycling, Functional Diversity, Data and Connectivity and Stewarding Resources. The plan is complemented by two new strategic objectives: Biomolecular Materials and Biosurveillance and Biopreparedness. With this plan as our guide, we’ll continue to enable basic science in support of the bioeconomy, which uses the power of biology to address some of the pressing challenges we face today. 

Ultimately, we’ll enable our users to leverage biological and biochemical functions to meet climate and energy goals, improve food security and sustainability, develop new materials, and manufacture the products and fuels we need. The organisms on our planet encode these functions in their genomes, and the JGI is uniquely positioned to combine sequencing, DNA synthesis and other omics technologies with computational analysis and prediction. Together, and in an integrated fashion, these capabilities will drive genomic innovation to provide the foundational biological understanding that opens up new ways to harness biology. This new plan positions JGI at the forefront of environmental genomics and sets forth a five-year set of milestones to advance our capabilities, user service and workforce development. As of February 2025, we have already completed 37% of the two-year milestones, and 11% of the five-year milestones.

Highlights arising from scientific collaborations with our users over the last year include: 

• A decade of work led by an international consortium culminated in a reference for the complex sugarcane genome sequence.
• The JGI partnered with synchrotron user facilities to define the structure and function of a unique cyanobacterial protein and understand its role in photosynthesis.
• In collaboration with Berkeley Lab Computing Sciences and NERSC, JGI researchers more than doubled the number of known protein families by using AI clustering algorithms to identify billions of protein sequences in metagenomes. 

We continue to engage with our user community through project initiation and progress calls, outreach activities and hosting visiting scientists at all stages of their careers. Our staff have organized, chaired sessions, presented and attended meetings around the world to showcase the JGI’s science and what we enable for our users. We returned to Walnut Creek to host the 15th Annual Genomics of Energy and Environment Meeting, which attracted 276 in-person attendees with a rich agenda across our scientific programs, as well as workshops that gave participants hands-on experience with the data processing and analysis workflows that we offer. We welcomed interns and visiting scientists from around the world — and from our two internship programs with University of California, Merced and Alabama Agriculture and Mechanical University — to spend time with us learning new skills and contributing to scientific projects. 

At the end of 2024, the DOE held a Triennial Science and Operations review of the JGI. This provided not only the chance to speak to our accomplishments of the last three years but to discuss the future activities of the JGI. Whilst we await the guidance from this review, I can say that a key area for the JGI’s evolution is in how we manage our data and how we can make this more accessible to our users. We will integrate data across the JGI and with other BER resources to allow for re-use and interoperability, and as foundation for Artificial Intelligence applications. The growth of AI has been remarkable and this is a huge opportunity for the JGI to lead genomic innovation for AI through “meta-AI-omics”!