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
    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

    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

    More

    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

    More

  • Data & Tools
    • IMG
    • Data Portal
    • MycoCosm
    • PhycoCosm
    • Phytozome
    • GOLD
    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

    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

    More

  • User Programs
    • Calls for Proposals
    • Special Initiatives & Programs
    • Product Offerings
    • User Support
    • Policies
    • Submit a Proposal
    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

    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

    More

    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

    Read more

  • 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

    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

News & Publications
Home › News Releases › Seagrass Genome Sequence Lends Insights to Salt Tolerance

January 27, 2016

Seagrass Genome Sequence Lends Insights to Salt Tolerance

First marine flowering plant genome provides clues on how crops could adapt to saline environments.

eelgrass in Finland by Christoffer Bostrom

Zostera marina meadow in the Archipelago Sea off Finland, from which the sequenced sample was taken. (Christoffer Bostrom)

To mitigate carbon emissions in the atmosphere, researchers have turned to sinks–reservoirs that accumulate and store carbon such as tropical rainforests, but also including a variety of terrestrial plants as well as oceans. However, another lesser known but very large carbon sink is located along the earth’s soft-sediment shorelines.

Coastal seagrass ecosystems cover some 200,000 square kilometers. They account for an estimated 15 percent of carbon fixed in global ocean, and also impact sulfur and nitrogen cycles. Additionally, they act as nurseries for young fish and other organisms, protect the coastline from erosion, and help maintain water clarity.

First marine angiosperm genome

Published January 27, 2016 in the journal Nature, a European team including researchers from the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, sequenced a seagrass genome: that of the eelgrass Zostera marina, taken from the Archipelago Sea off Finland. Despite the name, eelgrasses aren’t true grasses but rather completely submerged marine flowering plants, or angiosperms, and members of an ancient monocot family. To better understand the adaptations the plant made in returning to a saltwater environment, the team compared the eelgrass genome to its freshwater relative, Greater duckweed (Spirodela polyrhiza). The duckweed genome was also sequenced and analyzed by the DOE JGI.

Zostera marina 021816 Nature cover

The February 18, 2016 issue of Nature featured the seagrass as its cover image.

Found throughout the northern hemisphere, Zostera marina is the first marine flowering plant to be fully sequenced, work done through the DOE JGI’s Community Science Program. As a foundational species in the coastal marine ecosystem, researchers are interested in understanding how the plant—and by extension other plants in the ecosystem—adapts to climate change.

In adapting to an underwater lifestyle, eelgrass gained genes that allowed it to live in saltwater but lost genes involved in traits associated with land-based plants. The team was interested in identifying the pathways that underwent major modifications upon Zostera marina’s return to the sea.

Study lead author Jeanine Olsen of the University of Groningen in the Netherlands called this “arguably the most extreme adaptation a terrestrial (and even a freshwater) species can undergo.” Following what she describes as the “use it, lose it, or change it” scenario, eelgrass has modified its cell walls—which are uniquely more seaweed-like—and genes associated with light-sensing, plant defense and signaling, pollination system and regulation of internal water balance. Zostera marina has lost genes related to UV protection and the production of various volatiles including terpenes—hydrocarbons that have applications such as serving as an alternative source of advanced fuels.

Comparing freshwater and saltwater plant genomes

Jeanine Olsen

Jeanine Olsen appears in a short video regarding the importance of studying Zostera marina and seagrass meadows – watch it here. (courtesy of J. Olsen)

The team compared the eelgrass genome to duckweed, one of the simplest flowering plants and Zostera marina’s closest sequenced relative. They noted differences in genes related to cell wall structure due to adaptations to freshwater or terrestrial conditions. For example, plants such as duckweed have seemingly lost genes that help plants retain water in the cell wall, while eelgrass has regained these genes to better deal with osmotic stress at low tide.

“They have re-engineered themselves,” said Olsen of the changes affecting the eelgrass cell walls. “Although this has been known biochemically for many years, the underlying pathway that produces these sulfated polysaccharides for the cell wall matrix, in combination with the expansion of low methylated pectins (zosterin), are now unravelled and their strong negatively charged nature is hypothesized to help protect the cells from osmotic stress. Crop breeders may benefit from lessons on how salt tolerance has evolved in these plants.”

With Zostera marina meadows stretching from Alaska to Baja California, and from the White Sea to southern Portugal, Olsen noted that these ecosystems afford researchers “a natural experiment to investigate rapid adaptation to warmer or colder waters, as well as to salinity tolerance, ocean acidification and light.”

Learning more about eco-evolutionary interactions is also relevant to the development of genomics-based, early-warning indicators that may foreshadow seagrass ecosystem collapse. Jeremy Schmutz, head of the DOE JGI’s Plant Program, emphasized that while eelgrasses are key players in coastal marine ecosystem functions and considered the “lungs of the sea,” they are also endangered. “There are estimates that nearly a third of the eelgrass meadows worldwide have been destroyed by runoff into the ocean,” he said, “reducing their potential capabilities as carbon sinks. Thus, studying the adaptive capacity of eelgrass is urgent to assist conservation efforts.”

eelgrass in Norway by Frithjof Moy

Eelgrass in a Norwegian fjord that has the same morphotype as the Finnish eelgrass. (Frithjof Moy)

The latest release of the DOE JGI Plant Portal Phytozome includes the Zostera marina genome and is available at http://phytozome.jgi.doe.gov/.

Aside from Olsen at the University of Groningen, collaborators on this project included researchers at: Ghent University (Belgium); GEOMAR Helmholtz Centre for Ocean Research-Kiel (Germany); University of Kiel (Germany); Stazione Zoologica Anton Dohrn (Italy); Sorbonne Université (France); University of Udine (Italy); INRA (France); Westfälische Wilhelms-University of Münster (Germany); University of Gothenburg (Sweden); Åbo Akademi University (Finland); HudsonAlpha Institute for Biotechnology; Nord University (Norway); University of Delaware; University of Algarve (Portugal); King Abdullah University of Science and Technology (Saudi Arabia); and, University of Pretoria (South Africa).

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)

The U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility at Lawrence Berkeley National Laboratory, is committed to advancing genomics in support of DOE missions related to clean energy generation and environmental characterization and cleanup. JGI provides integrated high-throughput sequencing and computational analysis that enable systems-based scientific approaches to these challenges. Follow @jgi on Twitter.

DOE’s Office of Science is the largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit science.energy.gov.

Filed Under: News Releases

More topics:

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

Related Content:

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.

Tracing the Evolution of Shiitake Mushrooms

A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.

JGI announces final round of 2022 Functional Genomics awardees

Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!

Introducing New Members of the JGI User Executive Committee

incoming 2023 UEC members
  • 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