DOE Joint Genome Institute

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2022 Progress Report

The Integrative Genomics Building (IGB) seen above is home to the DOE Joint Genome Institute (JGI). Researchers from the DOE Systems Biology Knowledgebase (KBase), the National Microbiome Data Collaborative (NMDC), and Berkeley Lab Biosciences Area are also co-located in the IGB.

Vision

The vision of the U.S. Department of Energy (DOE) Joint Genome Institute (JGI), a DOE Office of Science user facility at Lawrence Berkeley National Laboratory (Berkeley Lab), is to become the leading integrative genome science user facility enabling researchers to solve the world’s evolving energy and environmental challenges.

Juying Yan, JGI Principal Research Associate, operates the Sample Access Manager (SAM) from Hamilton Storage, which stores samples in plates and tubes at -80°C.

Mission

The mission of the JGI is to provide the global research community with access to the most advanced integrative genome science capabilities in support of the DOE’s research mission.

Director’s Perspective

Nigel Mouncey, Director, DOE Joint Genome Institute

 

In honor of the JGI’s 25th anniversary, we spent 2022 revisiting a number of notable achievements that showcase our collaborations and capabilities to enable great science that will help solve energy and environmental challenges. Click here to learn more.

Honors & Awards

In 2022, several researchers and staff supporting the JGI user community were recognized by multiple organizations.

Science Highlights

Below are briefs on some of the top research to come out of the JGI in 2022.

Danielle Goudeau, JGI Senior Scientific Engineering Associate, works at the Zeiss PALM LMD microscope, a laser microdissection scope, which targets tissues from plants that are selected under the microscope before a laser cuts the sample and catapults them into collection tubes.

 

February 2022 cover of the Development Cell journal A  Plant Root Atlas for Tracking Developmental Trajectories

Researchers have developed an atlas that maps gene expression patterns in the Arabidopsis root from single root cell profiles.

 : Documented occurrences of different switchgrass cytotypes (4X in blue and 8X in orange) throughout the United States. One of the early interests in exploring 8X switchgrass was because the noticeable occurrence of 8X in 4X distribution gaps. (Joseph Napier) Calculating the Costs of Multiple Switchgrass Gene Copies

In a guest piece on a recent PNAS article, researchers describe the costs associated with switchgrass adaptations to expand its habitat range.
A green fern against a black backdrop Model Fern Reveals Insight into DNA Thievery in Ferns

The Open Green Genome Initiative hit a major milestone when Ceratopteris richardii became its first genome sequence to yield a published manuscript. 

 41 fungal isolates representative of the A. thaliana root mycobiome Fungal Friends or Foes in Plant Roots

Fungi colonizing Arabidopsis thaliana roots have gene families that help determine if these fungi act as friends or foes.
A photograph of the forest floor, covered in pine needles, with burned trees in the background. Understanding Wildfire Recovery, Starting in Soil

A metagenomic look at the soil microbes present a year after a wildfire.

 Photograph of a stream of diatoms beneath Arctic sea ice. Polar Phytoplankton Need Zinc to Cope with the Cold

Antarctic waters harbor higher levels of the nutrient zinc, and phytoplankton have evolved to rely on it.
Collage capturing a diverse set of bacteria and functions that can be better understood using DAP-seq. (Eduardo de Ugarte/Berkeley Lab) Enlarging Windows into Understanding Gene Functions

In a Nature Methods article, JGI researchers developed two approaches that build upon DAP-seq technology.

 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

In Cell, a computational pipeline combed through public metatranscriptome datasets, uncovering a five-fold increase of RNA virus diversity.
Open book with circular representations of microbial genomes above, all against a green background A New Actinobacterial Chapter in the Genomic Encyclopedia of Bacteria and Archaea

The latest chapter of the GEBA compendium includes new Actino genome sequences and an analysis of more than 80,000 BGCs.

 screencap from Amundson and Wilkins subsurface microbiome video Digging into Microbial Ecosystems Deep Underground

Microbiome researchers at Colorado State University are studying microbial ecosystems deep underground.
Filaments of Ca. Thiomargarita magnifica attached to leaf debris are visible to the naked eye on a Petri dish. (Massie S. Ballon) Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts

In Science, researchers describe the features of a giant filamentous bacterium composed of a single cell.

 One of the pools at Dewar Creek hot springs in British Columbia, Canada. (Allyson Brady) The Power of One, Amplified

Researchers showed that large-scale single cell genomics can add significant value when used in complementarity with metagenomic sequencing.
This data image shows the monthly average sea surface temperature for May 2015. Between 2013 and 2016, a large mass of unusually warm ocean water--nicknamed the blob--dominated the North Pacific, indicated here by red, pink, and yellow colors signifying temperatures as much as three degrees Celsius (five degrees Fahrenheit) higher than average. Data are from the NASA Multi-scale Ultra-high Resolution Sea Surface Temperature (MUR SST) Analysis product. (Courtesy NASA Physical Oceanography Distributed Active Archive Center) When “The Blob” Made It Hotter Under the Water

With genomic samples, researchers developed a preliminary model of how marine microbial communities are affected by warming events.

 Boeuf and colleagues collected samples of SAR324 microbial communities from this research vessel, the Kilo Moana. (School of Ocean And Earth Science And Technology at University of Hawaii at Manoa) Marine Microbe Contains Multitudes

A deep dive into microbial genomics reveals one bacterial species is made of four ecologically distinct groups with different lifestyles.
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

Using RIViT-seq technology, researchers were able to identify the target genes of transcription factors in Streptomyces coelicolor.

 A graphic flowchart showing how CRAGE and CRISPR work together Extracting the Secrets of Secondary Metabolites

Microbial secondary metabolites may now be easier to characterize following a JGI proof-of-concept study in which researchers paired CRAGE and CRISPR technologies.

Impact: By the Numbers

Matthew Hamilton, JGI Senior Research Associate, operates the Automated Resource Enabling Synthesis (ARES) platform, which integrates a Hamilton Vantage Liquid Handling System 2.0m platform via a PAA KX-2 robotic arm with off-deck components.

Spending Profile FY2022: Genomic Technologies (34.2%); Science Programs & Analysis (33.2%); Data Science & Informatics (15.1%); Management (7.9%); Project Management Office (4.1%); Computer Infrastructure & Support Team (@ NERSC) 3.2%; Operations (2.2%); Emerging Technologies Opportunity Program (.1%)

Users on the Map: 2,243; North America (1,610); United States (1,518); South America (27); Europe (446); Africa (13); Asia (80); Australia & New Zealand (67). Academic (1,631), Industry (37), DOE — national labs only (196), Government (220), Other (159), Total Users (2,243)

North America 1,610 Denmark 16 Slovenia 2 Malaysia 1
United States 1,518 Estonia 2 Spain 40 Singapore 3
Canada 85 Finland 13 Sweden 17 SouthKorea 6
Mexico 7 France  55 Switzerland 12 Taiwan 4
Germany 89 Turkey 1
South America 27 Greece 4 United Kingdom 59 Australia & New Zealand 67
Argentina 1 Hungary 11 Australia 52
Brazil 20 Iceland 1 Africa 13 New Zealand 15
Chile 1 Ireland 4 Morocco 1
Colombia 1 Italy 24 South Africa 12
Uruguay 4 Netherlands 29
Norway 18 Asia 80
Europe 446 Poland 2 China 21
Austria 10 Portugal 7 India 10
Belgium 16 Russian Federation 5 Israel 11
Czech Republic 7 Serbia 2 Japan 24

Users on the U.S. Map: 1,518. Motion graphic shows CA (333 users); WA, AZ, CO, TX, MN, WI, MI, IL, MO, TN, NC, GA, FL, NY and MS (30-75 users); OR, MT, UT, NM, NE, IA, OH, AL, VA, MD, DE PA, NJ, CT and NH (11-29 users); an AL, NV, ID, WY, ND, SD, KS, OK, LA, MS, SC, KY, WV, RI, VT and ME (1-10 users).

 

Cumulative Number of Projects Completed

Cumulative Number of Scientific Publications

Sequence Output

(in billions of bases or GB)

The JGI supports short- and long-read sequencers, where a read refers to a sequence of DNA bases. Short-read sequencers produce billions of paired-end 150 basepair reads used for quantification, such as in gene expression analysis. Long-read sequencers currently average 60,000–70,000 bp reads and are used for de novo genome assembly. Combined short-read and long-read totals per year give JGI’s annual sequence output. The total sequence output in 2022 was 658,195 GB.

Sequencing Productivity

Billions of Base Pairs

User Letters of Intent/Proposals Submitted & Approved

Computational Infrastructure

JGI Archive and Metadata Organizer (JAMO)

12.819 million file records

JAMO Archived Data Footprint

13.937 Petabytes (PB)

Data Downloads in FY22

Genome Portal: 3.702 million files
Data Portal: 0.429 million files

Users of JGI Tools & Data

The Genome Portal provides unified access to all JGI genomic databases and analytical tools. Users can search, download and explore data sets available for all JGI sequencing projects including their status, assemblies, and annotations of sequenced genomes. The Data Portal allows JGI users to more easily access public data sets through a common set of metadata across files submitted by each scientific program. FY2022 improvements to the Data Portal include improved data parity and new bulk download capabilities. The Genome Portal will be retired once the Data Portal reaches data- and feature-parity with its predecessor.

Photography and cinemagraphs by Thor Swift, Berkeley Lab. Design by Creative Services, IT Division, Berkeley Lab.