DOE Joint Genome Institute

  • COVID-19
  • About Us
  • Contact Us
  • Our Science
    • DOE Mission Areas
    • Bioenergy Research Centers
    • Science Programs
    • Science Highlights
    • Scientists
    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

    (PXFuel)
    Designer DNA: JGI Helps Users Blaze New Biosynthetic Pathways
    In a special issue of the journal Synthetic Biology, JGI scientific users share how they’ve worked with the JGI DNA Synthesis Science Program and what they’ve discovered through their collaborations.

    More

    A genetic element that generates targeted mutations, called diversity-generating retroelements (DGRs), are found in viruses, as well as bacteria and archaea. Most DGRs found in viruses appear to be in their tail fibers. These tail fibers – signified in the cartoon by the blue virus’ downward pointing ‘arms’— allow the virus to attach to one cell type (red), but not the other (purple). DGRs mutate these ‘arms,’ giving the virus opportunities to switch to different prey, like the purple cell. (Courtesy of Blair Paul)
    A Natural Mechanism Can Turbocharge Viral Evolution
    A team has discovered that diversity generating retroelements (DGRs) are not only widespread, but also surprisingly active. In viruses, DGRs appear to generate diversity quickly, allowing these viruses to target new microbial prey.

    More

  • Our Projects
    • Search JGI Projects
    • DOE Metrics/Statistics
    • Approved User Proposals
    • Legacy Projects
    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

    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
    Researchers tracked the impact of a large-scale heatwave event in the ocean known as “The Blob” as part of an approved proposal through the Community Science Program.

    More

    A plantation of poplar trees. (David Gilbert)
    Genome Insider podcast: THE Bioenergy Tree
    The US Department of Energy’s favorite tree is poplar. In this episode, hear from ORNL scientists who have uncovered remarkable genetic secrets that bring us closer to making poplar an economical and sustainable source of energy and materials.

    More

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

    With a common set of "baseline metadata," JGI users can more easily access public data sets. (Steve Wilson)
    A User-Centered Approach to Accessing JGI Data
    Reflecting a structural shift in data access, the JGI Data Portal offers a way for users to more easily access public data sets through a common set of metadata.

    More

    Phytozome portal collage
    A More Intuitive Phytozome Interface
    Phytozome v13 now hosts upwards of 250 plant genomes and provides users with the genome browsers, gene pages, search, BLAST and BioMart data warehouse interfaces they have come to rely on, with a more intuitive interface.

    More

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

    Yeast strains engineered for the biochemical conversion of glucose to value-added products are limited in chemical output due to growth and viability constraints. Cell extracts provide an alternative format for chemical synthesis in the absence of cell growth by isolating the soluble components of lysed cells. By separating the production of enzymes (during growth) and the biochemical production process (in cell-free reactions), this framework enables biosynthesis of diverse chemical products at volumetric productivities greater than the source strains. (Blake Rasor)
    Boosting Small Molecule Production in Super “Soup”
    Researchers supported through the Emerging Technologies Opportunity Program describe a two-pronged approach that starts with engineered yeast cells but then moves out of the cell structure into a cell-free system.

    More

    These bright green spots are fluorescently labelled bacteria from soil collected from the surface of plant roots. For reference, the scale bar at bottom right is 10 micrometers long. (Rhona Stuart)
    A Powerful Technique to Study Microbes, Now Easier
    In JGI's Genome Insider podcast: LLNL biologist Jennifer Pett-Ridge collaborated with JGI scientists through the Emerging Technologies Opportunity Program to semi-automate experiments that measure microbial activity in soil.

    More

  • News & Publications
    • News
    • Blog
    • Podcasts
    • Webinars
    • Publications
    • Newsletter
    • Logos and Templates
    • Photos
    A view of the mangroves from which the giant bacteria were sampled in Guadeloupe. (Hugo Bret)
    Giant Bacteria Found in Guadeloupe Mangroves Challenge Traditional Concepts
    Harnessing JGI and Berkeley Lab resources, researchers characterized a giant - 5,000 times bigger than most bacteria - filamentous bacterium discovered in the Caribbean mangroves.

    More

    In their approved proposal, Frederick Colwell of Oregon State University and colleagues are interested in the microbial communities that live on Alaska’s glacially dominated Copper River Delta. They’re looking at how the microbes in these high latitude wetlands, such as the Copper River Delta wetland pond shown here, cycle carbon. (Courtesy of Rick Colwell)
    Monitoring Inter-Organism Interactions Within Ecosystems
    Many of the proposals approved through JGI's annual Community Science Program call focus on harnessing genomics to developing sustainable resources for biofuels and bioproducts.

    More

    Coloring the water, the algae Phaeocystis blooms off the side of the sampling vessel, Polarstern, in the temperate region of the North Atlantic. (Katrin Schmidt)
    Climate Change Threatens Base of Polar Oceans’ Bountiful Food Webs
    As warm-adapted microbes edge polewards, they’d oust resident tiny algae. It's a trend that threatens to destabilize the delicate marine food web and change the oceans as we know them.

    More

News & Publications
Home › News Releases › Liverwort Genes and Land Plant Evolution

October 5, 2017

Liverwort Genes and Land Plant Evolution

Genome analysis of early plant lineage sheds light on how plants learned to thrive on land.

A Marchantia polymorpha thallus in the vegetative form. Cup-shaped structures on the surface are gemma cups (cupules), reproductive organs producing asexual propagules (gemmae). (Photograph by Shohei Yamaoka, Kyoto University)

A Marchantia polymorpha thallus in the vegetative form. Cup-shaped structures on the surface are gemma cups (cupules), reproductive organs producing asexual propagules (gemmae). (Shohei Yamaoka, Kyoto University)

Though it’s found around the world, it’s easy to overlook the common liverwort – the plant can fit in the palm of one’s hand and appears to be comprised of flat, overlapping leaves. Despite their unprepossessing appearance, these plants without roots or vascular tissues for nutrient transport are living links to the transition from the algae that found its way out of the ocean to the established multitude of land plants.

As reported in the October 5, 2017 issue of Cell, an international team including researchers at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, analyzed the genome sequence of the common liverwort (Marchantia polymorpha) to identify genes and gene families that were deemed crucial to plant evolution and have been conserved over millions of years and across plant lineages. The work was led by researchers at Monash University in Australia, and at Kyoto University and Kindai University in Japan.

“Early plants like the liverwort are what set the world up for land plants. Without them, we wouldn’t have plants more than two feet from the ocean and freshwater,” said DOE JGI Plant Program head Jeremy Schmutz. “In going back to liverworts, we find genes shared with grasses that are candidate genes for crops for biofuel generation. Land plants began with same parts present in Marchantia today so the changes are all due to factors such as evolution, polyploidy, gene exchange and rounds of selection. We want to know what genes do and we do this by translating function across genomes using conserved sequences. Smaller genomes with less complexity – such as those in a basal or early plant model like liverwort – give us the ability to identify ancestral genes for a gene or gene family. We identify gene function in a plant and determine how this gene works, and then we identify other genes by understanding the evolutionary history of gene or gene family across the history of plants.”

Importance of Plant Cell Walls

Video depicts growth of female thalli of Marchantia polymorpha. Pictures were taken for 58 days, 1 picture/hour, starting from a two-week-old thallus. The whole sequence was compressed to 57 sec. After 24 days, far-red light was added, which appears as 'jumping' at the tips of thalli. Female sexual organs (archegoniophores) grow upward after irradiation of far-red light. (Video produced by K.T. Yamato & directed by T. Kohchi, Kyoto University)

Click here or on the above image to watch a video depicting growth of female thalli of Marchantia polymorpha. Pictures were taken for 58 days, 1 picture/hour, starting from a two-week-old thallus. The whole sequence was compressed to 57 sec. After 24 days, far-red light was added, which appears as ‘jumping’ at the tips of thalli. Female sexual organs (archegoniophores) grow upward after irradiation of far-red light. (Video produced by K.T. Yamato & directed by T. Kohchi, Kyoto University)

The liverwort’s genome sequencing and annotation was done through the DOE JGI’s Community Science Program, and allows for genomic comparisons with other early plant lineages sequenced and analyzed by the DOE JGI: the spikemoss Selaginella moellendorffi and the moss Physcomitrella patens. One of the most important biochemical pathways concerns production of the hormone auxin, which is critical for regulating plant growth and development. The team identified a minimal but complete pathway for auxin biosynthesis in the liverwort. Another finding suggests that the genes encoding enzymes producing “sunscreen” that allowed early plants to tolerate ultraviolet light may have been transferred from ancient soil microbes.

One of the team’s most important findings concern plant cell wall development. The variety of genes encoding enzymes for plant cell wall development found in Marchantia emphasizes the importance of plant cell walls for the transition to land plants. The team identified early lignin biosynthesis genes similar to those in Physcomitrella. While they identified genes involved in plasmodesmata formation (plasmodesmata are membrane channels involved in nutrient and signal molecule transfers) a pathway that is involved in cell division, they also found that liverworts retain the vestiges of cell division pathways predating land plant-specific pathway.

Dealing with Drought and Dessication

A copy of the first obviously identifiable printed image of Marchantia polymorpha, from the 1542 book De historia stirpium commentarii insignes by Leonhart Fuchs, with images drawn by Albrecht Meyer. (Image in public domain and provided by John L. Bowman)

A copy of the first obviously identifiable printed image of Marchantia polymorpha, from the 1542 book De historia stirpium commentarii insignes by Leonhart Fuchs, with images drawn by Albrecht Meyer. (Image in public domain and provided by John L. Bowman)

Another important finding involves water retention and distribution. Early plants had to develop strategies for dealing with drought and desiccation, and many of these same strategies are still employed by modern plants. Abscisic acid is a plant stress hormone that regulates when a plant goes dormant when water is in short supply. The team found homologous genes for abscisic acid biosynthesis, and were also able to identify when specific receptors became critical to land plant families.

Schmutz pointed out that through the Community Science Program, the DOE JGI’s exploration of plant evolutionary history is expanding, leading to the development of a comparative genomics framework, including those from early plant lineages like the liverwort, that benefits the plant research community at large. “The more we accumulate this information in early plant lineages, the easier it is to transfer plant function across plant phylogeny and compare plant families to see the radiation of these genes. We’ll be focusing quite a bit more on the basal lineages of plants to get at the evolutionary history and position of genes. If we can understand the origin of these genes then we can understand historical function. Having multiple species allows us to do more and show more than what we can with just one genome.”

By learning the original functions of genes, elucidated from the genomes of earlier, simpler, plants and cells, scientists can more easily solve for the functions of related genes seen in more complex plants that may help address DOE missions in bioenergy and environmental processes.

The Marchantia polymorpha v3.1 genome data are publically available at Phytozome, the DOE JGI’s plant comparative genomics portal which provides users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as selected genomes and datasets that have been sequenced elsewhere.

Collaborators on this project included researchers at: HudsonAlpha Institute for Biotechnology; Kobe University (Japan); National Institute of Genetics (Japan); Gregor Mendel Institute (Austria); Nara Institute of Science and Technology (Japan); University of Osnabruck (Germany); Universidad Veracruzana, INBIOTECA (Mexico); University of Cambridge (United Kingdom); CINVESTAV-IPN (Mexico); University of Oxford (United Kingdom); University of Tennessee-Knoxville; Uppsala University (Sweden); Vienna Biocenter Core Facilities (Austria); Institut de Recherche pour le Developpement (France) and, University of Zurich (Switzerland).

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:

Introducing New Members of the JGI User Executive Committee

incoming 2023 UEC members

JGI Contributes Nine to 2022 Highly Cited Researchers List

Nine headshots, one for each researcher, laid out beside a purple ribbon reading, "Home to Highly Cited Researchers 2022 Clarivate"

JGI announces first round of 2023 New Investigator awardees

Digital ID card with 10 headshots reads: Congratulations to our 2023 New Investigator recipients!

JGI at 25: Following Fungi that Pry Apart Plant Polymers

A brown goat with white horns looks at green hay

Exploring Possibilities: 2022 JGI-UC Merced Interns

2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)

JGI at 25: Using team science to build communities around data

  • 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