View source for Joint Genome Institute

{{Short description|Research facility in California, US}}
{{multiple issues|
{{COI|date=December 2019}}
{{Primary sources|date=February 2023}}
}}

[[File:Glowing ALS-IGB XBD201906-00793012.jpg|thumb|The Integrative Genomics Building (IGB) at Lawrence Berkeley National Laboratory (Berkeley Lab), the home of the DOE Joint Genome Institute and the DOE Systems Biology Knowledgebase (KBase). The Advanced Light Source (ALS) is above in the background.]]

The '''Joint Genome Institute''' ('''JGI''') is a scientific user facility for integrative genomic science at [[Lawrence Berkeley National Laboratory]].<ref>{{ cite web | url=https://biosciences.lbl.gov/area-organization/jgi/| title = DOE Joint Genome Institute | website = Berkeley Lab |access-date=February 20, 2023 }}</ref> The mission of the JGI is to advance genomics research in support of the [[United States Department of Energy]]'s (DOE) missions of energy and the environment. It is one of three national scientific user facilities supported by the Office of Biological and Environmental Research (BER) within the Department of Energy's Office of Research.<ref>{{cite web|title=BER User Facilities|url=https://science.osti.gov/User-Facilities/User-Facilities-at-a-Glance/BER|website=US Department of Energy Office of Science |date=9 December 2014 | access-date=February 20, 2023}}</ref> These BER facilities are part of a more extensive network of 28 national scientific user facilities that operate at the DOE national laboratories.<ref>{{cite web | url= https://science.osti.gov/User-Facilities | title = User Facilities | website = US Department of Energy Office of Science | date = 29 September 2020 | access-date = February 14, 2023 }}</ref><ref>{{cite web | url=https://science.osti.gov/User-Facilities/User-Facilities-at-a-Glance | title = User Facilities at a Glance | website = US Department of Energy Office of Science | date = 3 May 2022 | access-date=February 14, 2023}}</ref>

The JGI advances genomics research by providing the research community with access to the latest generation of genome sequencing and analysis capabilities. It employs a staff of 250 scientists, technicians, and other personnel to support the research of the 2,180 scientific users who make use of it for their research each year.<ref>{{cite web |url=https://science.osti.gov/ber/Facilities/User-Facilities/JGI | title=Joint Genome Institute | website = U.S. Department of Energy Office of Science | date=29 April 2022 | access-date=February 20, 2023}}</ref> The facility sequenced 658&nbsp;trillion total bases in FY 2022, and this output is now doubling about every two years.<ref>{{cite web |url=https://jgi.doe.gov/our-projects/statistics/ | title= DOE metrics/statistics | website = Joint Genome Institute | access-date=February 20, 2023 }}</ref>

== Research at JGI ==
Research at JGI is organized into seven programs:<ref>{{cite web |url=https://jgi.doe.gov/our-science/ | title = Our Science | website = Joint Genome Institute | access-date = February 20, 2023 }}</ref>
{{bulleted list | '''Plant Program''' The Plant Program focuses on the fundamental biology of photosynthesis and characterizing the role of terrestrial plants in carbon sequestration and the development of plant feedstocks for biofuels.| '''Fungal & Algal Program''' The Fungal & Algal Program scale-up the sequencing and analysis of genomes to explore the diversity of fungi and algae that play a critical role in bioenergy and environmental research.| '''Metagenome Program'''The Metagenome Program leverages high-throughput sequencing to uncover the principles governing microbial community functions and interactions that impact ecosystem processes. | '''Microbial Program'''The Microbial Program exploits expertise and emerging technologies in sequencing, annotation and analysis, to deliver high quality and high throughput sequence-based science. | '''DNA Synthesis Science Program''' The DNA Synthesis Science Program is focused on the identification and refactoring of biological pathways with potential application in DOE mission-relevant areas.| '''Metabolics Program'''The Metabolomics Program provides functional annotation of genomes and improved understanding of the role of small molecules in diverse biological systems. | '''Secondary Metabolites''' The Secondary Metabolites Group identifies and pursues opportunities associated with secondary metabolite discovery and characterization.}}

The JGI provides users with access, at no cost, to high-throughput genomic and specialized capabilities and data analysis.<ref>{{cite web |url=https://jgi.doe.gov/user-programs/ | title=User Programs | website = Joint Genome Institute | access-date = February 20, 2023 }}</ref> Researchers submit proposals to one of the seven JGI user programs, and all proposals are reviewed for scientific merit and relevance to the DOE research mission. If the proposal is approved, the JGI provides the users a number of standard sequencing, synthesis, and metabolomics products.

== Collaborations ==

The JGI collaborates extensively with the [[Environmental Molecular Sciences Laboratory]] at [[Pacific Northwest National Laboratory]] (PNNL). The two facilities jointly manage the ''Facilities Integrating Collaborations for User Science'' (FICUS) program, designed for researchers who require the capabilities of both user facilities to perform their research. The JGI also performs extensive sequencing on behalf of the 
four DOE Bioenergy Research Centers.<ref>{{cite web | url=https://jgi.doe.gov/our-science/doe-bioenergy-research-centers/ | title=DOE Bioenergy Research Centers | website = Joint Genome Institute | access-date=February 20, 2023 }}</ref><ref>{{cite web |url=https://genomicscience.energy.gov/bioenergy-research-centers/ | title=Bioenergy Research Centers | website = U.S. Department of Energy | access-date=February 20, 2023}}
</ref>

==Leadership==
The Director of JGI since 2017 is Nigel Mouncey.<ref>{{cite web | url=https://jgi.doe.gov/about-us/organization/strategic-management/ | title = Strategic Management | website = Joint Genome Institute | access-date = February 20, 2023}}</ref> Mouncey also serves as the President of the Society for Industrial Microbiology and Biotechnology (SIMB)<ref>{{cite web |url=https://www.simbhq.org/about-simb/board-committee-members/ | title=Board Committee Members | website = Society for Industrial Microbiology and Biotechnology }}</ref>

==History==
The '''Joint Genome Institute''' ('''JGI''') was created in 1997 to unite the expertise and resources in [[genome]] mapping, [[DNA sequencing]], technology development, and information sciences pioneered at the DOE genome centers at [[Lawrence Berkeley National Laboratory]] (Berkeley Lab), [[Lawrence Livermore National Laboratory]] (LLNL) and [[Los Alamos National Laboratory]] (LANL).In 1999, the [[University of California]], which manages the three national labs for the DOE, leased laboratory and office space in a light industrial park in [[Walnut Creek, California]] to consolidate genome research activities. Led by biotechnology industry veteran Nigel Mouncey, who assumed the position of Director in March 2017, the DOE JGI receives its funding from the Office of Biological and Environmental Research in DOE's Office of Science.

Originally established to work on the [[Human Genome Project]]—the JGI generated the complete sequences of Chromosomes 5, 16 and 19—the JGI has since shifted its focus to the non-human components of the biosphere, particularly those relevant to the DOE's science mission. Since 2004, the JGI has been a user facility that advances genomics research in a broad range of disciplines where DNA sequence information is likely to drive scientific discoveries.<ref>{{cite web |title=History |url=https://jgi.doe.gov/about-us/history/ |website=Joint Genome Institute |access-date=30 August 2022}}</ref>

In February 2004, the JGI launched the Community Sequencing Program (CSP), known as the Community Science Program, which provides the scientific community at large with access to high-throughput, high-quality sequencing, DNA synthesis, metabolomics and analysis capabilities. The projects involve many important multicellular organisms, microbes and communities of microbes called [[metagenome]]s (or microbiomes) related to the DOE mission areas of [[bioenergy]], understanding global cycles such as the [[carbon cycle]], and [[biogeochemistry]] and are chosen primarily based on scientific merit as determined by outside review.<ref>{{cite web |title=CSP Overview |url=https://jgi.doe.gov/user-programs/program-info/csp-overview/ |website=Joint Genome Institute}}</ref>

==Genome sequencing milestones==

In 2006, the JGI published the genome of the first tree sequenced—the cottonwood ([[Populus|''Populus trichocarpa'']]). 
<ref>{{cite web |url=https://jgi.doe.gov/2006-2016-poplar-genome-10-anniversary/| title= The Poplar Genome at 10 | website = Joint Genome Institute| date= 15 September 2016 }}</ref> 
In partnership with other federal institutions and universities, the JGI has also published the genome sequences of sorghum, a candidate feedstock for biofuels and biomanufacturing.<ref>{{cite web | url=https://jgi.doe.gov/jgi-at-25-studying-sorghums-survival-skills/ | title= Studying Sorghums Survival Skills | website = Joint Genome Institute | date= 24 June 2022 | access-date=February 20, 2023}}</ref>

==Data management systems==

The JGI also supports programs dedicated to functional and evolutionary genomics related to the organisms and environments being sequenced and the development of computational and bioinformatic tools for data management and mining. These genome and metagenome/microbiome analysis systems include Genome Portal, Phytozome, IMG and the Genomes OnLine Database.

The [[Integrated Microbial Genomes System]] (IMG), which provides a framework for comparative analysis of primarily microbial genomes, though the system also supports eukaryotic genomes and environmental samples. Its goal is to facilitate the visualization and exploration of genomes from a functional and evolutionary perspective.

==References==
{{Reflist}}

==External links==
* {{official|http://www.jgi.doe.gov}}
* [https://gold.jgi.doe.gov/ Genomes OnLine Database]

{{U.S. National Labs}}

{{authority control}}

[[Category:Government agencies established in 1997]]
[[Category:United States Department of Energy national laboratories]]
[[Category:University of California]]
[[Category:Genetics or genomics research institutions]]
[[Category:Research institutes in the San Francisco Bay Area]]
[[Category:Research institutes in California]]