DOE Joint Genome Institute

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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    The genome of the common fiber vase or Thelephora terrestris was among those used in the study. (Francis Martin)
    From Competition to Cooperation
    By comparing 135 fungal sequenced genomes, researchers were able to carry out a broader analysis than had ever been done before to look at how saprotrophs have transitioned to the symbiotic lifestyle.

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    Miscanthus grasses. (Roy Kaltschmidt/Berkeley Lab)
    A Grass Model to Help Improve Giant Miscanthus
    The reference genome for M. sinensis, and the associated genomic tools, allows Miscanthus to both inform and benefit from breeding programs of related candidate bioenergy feedstock crops such as sugarcane and sorghum.

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    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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    Scanning electron micrographs of diverse diatoms. (Credits: Diana Sarno, Marina Montresor, Nicole Poulsen, Gerhard Dieckmann)
    Learn About the Approved 2021 Large-Scale CSP Proposals
    A total of 27 proposals have been approved through JGI's annual Community Science Program (CSP) call. For the first time, 63 percent of the accepted proposals come from researchers who have not previously been a principal investigator on an approved JGI proposal.

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    MiddleGaylor Michael Beman UC Merced
    How to Successfully Apply for a CSP Proposal
    Reach out to JGI staff for feedback before submitting a proposal. Be sure to describe in detail what you will do with the data.

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    Click on the image or go here to watch the video "Enriching target populations for genomic analyses using HCR-FISH" from the journal Microbiome describing the research.
    How to Target a Microbial Needle within a Community Haystack
    Enabled by the JGI’s Emerging Technologies Opportunity Program, researchers have developed, tested and deployed a pipeline to first target cells from communities of uncultivated microbes, and then efficiently retrieve and characterize their genomes.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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    The Brachypodium distachyon-B. stacei-B. hybridum polyploid model complex. (Illustrations credits: Juan Luis Castillo)
    The More the Merrier: Making the Case for Plant Pan-genomes
    Crop breeders have harnessed polyploidy to increase fruit and flower size, and confer stress tolerance traits. Using a Brachypodium model system, researchers have sought to learn the origins, evolution and development of plant polyploids. The work recently appeared in Nature Communications.

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Our Science
Home › Our Science › Product Offerings

Product Offerings

The JGI has diverse capabilities in DNA and RNA sequencing, sample and library preparation, DNA synthesis and pathway engineering, and mass spectrometry based metabolomics.  Below is a table of standard sequencing and synthesis products, including a description of the product and deliverables as well as target cycle times from sample receipt to completion of standard analysis.  (Note: raw data is provided for all products below.  In addition, JGI will submit raw sequence data to SRA once the standard analysis is complete.)

For custom requests not on these lists, or to discuss experimental design for a proposal, we encourage you to contact the relevant program leads to discuss available options.

Scientific Program Product Brief Description Deliverables FY20 target cycle time (median), days* FY20 target cycle time (75th %), days*
DNA Synthesis Constructs <5kb in size Single gene or multiple small genes assembled to less than 5kb in length, cloned into vector of choice Glycerol stock of sequence verified clone 80 80
DNA Synthesis Constructs 5-10kb in size Single gene or multiple small genes assembled totaling 5-10kb in length, cloned into vector of choice Glycerol stock of sequence verified clone 100 100
DNA Synthesis Constructs >10kb in size Gene clusters or pathways totaling more than 10kb in length assembled together, cloned into vector of choice Glycerol stock of sequence verified clone 160 160
DNA Synthesis Combinatorial libraries Multiple genes synthesized and cloned into a vector of choice in various combinations Glycerol stock of sequence verified clones if low number of variants, or pool of variants with sample sequencing to predict the number of successful variants made 200 200
DNA Synthesis Complex libraries Multiple variants of sgRNA or a small coding gene assembled together in various combinations and cloned into a vector of choice; up to 210,000 variants can be made Pool of variant libraries; sample sequencing to determine coverage of variants 200 200
Fungal Minimal Draft Lower coverage whole genome shotgun sequencing Assembly, annotation (Mycocosm) 300 475
Fungal Resequencing SNP and short indel calls, rearrangement detection, population analysis Text file of SNPs (incl location in genome, coding/vs non, syn vs non-syn aa change etc) and structural rearrangements, alignment files 215 300
Fungal Standard Draft Whole genome shotgun sequencing. Exact scope items and quality of  finished product depend on genome.  Selected genomes will be improved based on feasibility and scientific merit Assembly, annotation (Mycocosm) 300 475
Fungal Transcriptome RNA for expression profiling and genome annotation (single organism) For annotation: de novo assembly.  For counting: text file of gene counts (mapped against reference transcriptome or de novo assembly), alignment files 215 270
Metabolomics Polar metabolite analysis Relative abundance profiling of polar (e.g. amino acids, nucleosides, etc) metabolites using normal phase chromatography coupled to tandem mass spectrometry (detailed description) Metabolite annotation based on chemical standards or computational approaches. Relative abundance of identified metabolites and unidentified features in spectra. based on experimental design based on experimental design
Metabolomics Non-polar metabolite analysis Relative abundance profiling of non-polar (e.g. secondary metabolites, lipids, etc) metabolites using reverse phase chromatography coupled to tandem mass spectrometry (detailed description) Metabolite annotation based on chemical standards or computational approaches. Relative abundance of identified metabolites and unidentified features in spectra. based on experimental design based on experimental design
Metagenome Metatranscriptome Environmental transcript sequence from prokaryotes and/or eukaryotes Assembly, annotation (IMG/M), mapping to metagenome if applicable 175 215
Metagenome Cell Enrichments
Obtained by physical separation of a biologically relevant unit from a microbial community, such as a microcolony, microbial aggregate, or a specific subset of free-living cells. Due to the low biomass of cell enrichments, the extracted DNA may be amplified using whole-genome amplification prior to sequencing. Assembly, annotation (IMG/M) 240 430
Metagenome Minimal Draft Lower-coverage assembly & annotation of environmental DNA (note the JGI is no longer supporting iTag sequencing) Assembly, annotation (IMG/M), binning 200 220
Metagenome Standard Draft Assembly & annotation of environmental DNA.  Selected metagenomes will be improved based on feasibility and scientific merit.  (Note the JGI is no longer supporting iTag sequencing) Assembly, annotation (IMG/M), binning 200 220
Microbial Improved Draft, Isolate High Quality Draft assembly computationally analyzed and improved.  Semi-manual. Assembly, annotation (IMG), methylation analysis 260 380
Microbial Minimal Draft, Isolate Lowest quality microbial draft product, many unordered contigs. Assembly, annotation (IMG) 240 430
Microbial Minimal Draft, Single Cell Lowest quality microbial draft product, many unordered contigs. Assembly, annotation (IMG) 240 430
Microbial Single Particle Sort Draft assembly of whole genome amplified sorted cell(s)/particle(s) Assembly, annotation (IMG/M) 240 430
Microbial Resequencing SNP and short indel calls, rearrangement detection, population analysis. Text file of SNPs (incl location in genome, coding/vs non, syn vs non-syn aa change etc) and structural rearrangements, alignment files 150 180
Microbial Transcriptome RNA for expression profiling (single organism). For counting: text file of gene counts (mapped against reference transcriptome), alignment files 150 180
Microbial Transcriptome – smRNA smRNA sequencing (size range: 30-200 bp) mapping to reference genome, identifying known miRNAs and predicting novel miRNAs (miRDeep2 software). 150 180
Plant Standard Draft Whole genome shotgun sequencing.  Sequencing generated for initial evaluation varies depending on genome characteristics, availability of external resources and project goals.  Selected genomes will be improved based on feasibility and scientific merit. Assembly, annotation (Phytozome) depends on genome depends on genome
Algal Standard Draft Whole genome shotgun sequencing.  Sequencing generated for initial evaluation varies depending on genome characteristics, availability of external resources and project goals.  Selected genomes will be improved based on feasibility and scientific merit. Assembly, annotation (Phycocosm) depends on genome depends on genome
Plant and Algal Resequencing SNP and short indel calls, rearrangement detection, population analysis. Text file of SNPs (incl location in genome, coding/vs non, syn vs non-syn aa change etc) and structural rearrangements, alignment files 95 140
Plant and Algal Transcriptome RNA for expression profiling and genome annotation (single organism). For annotation: de novo assembly.  For counting: text file of gene counts (mapped against reference transcriptome or de novo assembly), alignment files 210 280
Plant and Algal Bisulphite-seq Used for genome-wide analysis of DNA methylation patterns. Genome-wide methylation calls and summary statistics of fraction of genome methylated in different sequence contexts
Plant, Algal, and Fungal ChIP-seq Used for genome-wide analysis of in vivo binding sites for DNA associated proteins to assess their role in temporal and spatial patterns of gene expression and chromatin remodeling. protein binding sites
Plant, Algal, and Fungal Transcriptome – smRNA smRNA sequencing (size range: up to 35 bp ) mapping to reference genome, identifying known miRNAs and predicting novel miRNAs (miRDeep2 software). 175 225

* FY20 actual cycle times may be affected by JGI’s move to its new facility in FY20 Q1.  If your project will be delayed by the move, your project manager will contact you with more information.

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