DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Science Programs
    • Science Highlights
    • Scientists
    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

    More

    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

    More

    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
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    A panoramic view of a lake reflecting a granite mountain.
    Genome Insider: Methane Makers in Yosemite’s Lakes
    Meet researchers who sampled the microbial communities living in the mountaintop lakes of the Sierra Nevada mountains to see how climate change affects freshwater ecosystems, and how those ecosystems work.

    Listen

    A light green shrub with spiny leaves, up close.
    Genome Insider: A Shrubbier Version of Rubber
    Hear from the consortium working on understanding the guayule plant's genome, which could lead to an improved natural rubber plant.

    Listen

    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    iPHoP image (Simon Roux)
    iPHoP: A Matchmaker for Phages and their Hosts
    Building on existing virus-host prediction approaches, a new tool combines and evaluates multiple predictions to reliably match viruses with their archaea and bacteria hosts.

    More

    Abstract image of gold lights and squares against a black backdrop
    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

    More

    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
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.
    Supercharging SIP in the Fungal Hyphosphere
    Applying high-throughput stable isotope probing to the study of a particular fungi, researchers identified novel interactions between bacteria and the fungi.

    More

    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

    More

    croppe image of the JGI helix sculpture
    Tips for a Winning Community Science Program Proposal
    In the Genome Insider podcast, tips to successfully avail of the JGI's proposal calls, many through the Community Science Program.

    Listen

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

    More

    image from gif that shows where in the globe JGI fungal collaborators are located.
    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

    More

    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

    More

Our Science
Home › Science Highlights › Eucalyptus grandis Genome 2.0—Community Resource

November 26, 2014

Eucalyptus grandis Genome 2.0—Community Resource

Genetic maps improve the reference genome assembly of the candidate bioenergy feedstock

The Science:

A team of French researchers developed an array that allowed them to produce high-resolution genetic maps of two eucalyptus species that they then compared to the reference genome of eucalyptus produced by a team including DOE JGI researchers.

eucalyptus plantation courtesy of the University of Pretoria

In a report published earlier this year, the eucalyptus genome was found to have more than 36,000 genes. Bioenergy researchers are interested in the genes involved in the production of plant cell wall material. (Image courtesy of the University of Pretoria.)

The Impact:

The genetic maps have allowed DOE JGI researchers to improve the reference genome assembly of eucalyptus, available on the plant portal Phytozome.

Summary

Cartographers create maps that show people where to find buildings, cities, or even whole countries, and how these landmarks are situated in relation to each other. For geneticists, a genetic map performs a similar task, linking a gene to a particular trait or condition. These maps also help researchers figure out what chromosome the gene is on, where in the chromosome this gene resides, and can help suggest a gene’s function(s).

In a study that appeared online November 10, 2014 in New Phytologist, a team that included Jeremy Schmutz, Plant Program Head at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, reported the development of two genetic maps that improve the genome assembly of eucalyptus. Grown on 40 million acres in 100 countries, the DOE considers fast-growing and oil-rich eucalyptus a candidate biomass energy crop and sequenced its genome under the DOE JGI Community Science Program. Schmutz was also part of the team that first described the Eucalyptus grandis genome of a Brazilian tree (BRASUZ1) in a Nature paper published this past June.

In this study, French researchers conducted whole-genome resequencing of two eucalyptus species, E. urophylla and E. grandis. Using the DNA sequence variants or SNPs found in the E. grandis genome sequence published by the DOE JGI-led team back in June, the researchers then designed a high-quality SNP DNA-based genotyping array that allowed them to link genes to chromosomes.

“In our study the use of two independent and highly collinear genetic maps enabled cross-validation in the comparison between the genetic maps and the reference genome sequence,” the team reported. In comparing their findings to the BRASUZ1 reference genome, they found 41 potential false joins on two chromosomes, and were able to localize a few million bases of sequence to another seven chromosomes. These findings ultimately helped improve the E. grandis genome assembly available on the DOE JGI plant portal Phytozome, which, in turn, will improve the usefulness of the eucalyptus sequence for bioenergy studies.

Contact

Jeremy Schmutz
DOE Joint Genome Institute Plant Program Head
HudsonAlpha Institute for Biotechnology
jschmutz@husdonalpha.org

Funding

  • U.S. Department of Energy Office of Science
  • FEDER
  • ERANET Plant KBBE

Publication

  • Bartholomé J et al. High-resolution genetic maps of Eucalyptus improve Eucalyptus grandis genome assembly. New Phytol. 2014 Nov 10. doi: 10.1111/nph.13150. [Epub ahead of print]

Related Links

  • http://jgi.doe.gov/just-food-koalas-eucalyptus-global-tree-fuel-fiber/
  • http://bit.ly/Phytozome-Eucalyptus
  • http://bit.ly/eucalyptusTuskan

Share this:

  • Click to share on Facebook (Opens in new window)
  • Click to share on LinkedIn (Opens in new window)
  • Click to share on Pinterest (Opens in new window)
  • Click to share on Twitter (Opens in new window)
  • Click to print (Opens in new window)

Filed Under: Science Highlights

More topics:

  • COVID-19 Status
  • News
  • Science Highlights
  • Blog
  • Webinars
  • CSP Plans
  • Featured Profiles

Related Content:

You can move, but you can’t hide

Illustration of a magnifying glass identifying viruses and plasmids.

iPHoP: A Matchmaker for Phages and their Hosts

iPHoP image (Simon Roux)

Supercharging SIP in the Fungal Hyphosphere

Green plant matter grows from the top, with the area just beneath the surface also visible as soil, root systems and a fuzzy white substance surrounding them.

New Research Sheds Light on Diversity in the Deep Sea

A photo taken in the deep sea. Black clouds billow out of hydrothermal vents.

Sequencing Sphagnum Leads to Discovery of Sex Chromosomes

A photo of two sphagnum species: S. divinum (red) and S. angustifolium (green)]

Busting the Unbreakable Lignin

Pictured is a micrograph of Neocallimastix californiae.
  • Careers
  • Contact Us
  • Events
  • User Meeting
  • MGM Workshops
  • Internal
  • Disclaimer
  • Credits
  • Policies
  • Emergency Info
  • Accessibility / Section 508 Statement
  • Flickr
  • LinkedIn
  • RSS
  • Twitter
  • YouTube
Lawrence Berkeley National Lab Biosciences Area
A project of the US Department of Energy, Office of Science

JGI is a DOE Office of Science User Facility managed by Lawrence Berkeley National Laboratory

© 1997-2023 The Regents of the University of California