U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights
Genomic Science Program

Insights into an Eukaryotic Alga that Lives by the Sea
Published: August 01, 2017
Posted: September 01, 2017

Porphyra umbilicalis (laver) attains high biomass despite the high levels of stress in its habitat in the upper intertidal zone of the North Atlantic, as shown here at low tide at Sand Beach, Acadia National Park, Maine. [Image courtesy of Susan Brawley]

The genome of Porphyra umbilicalis reveals the mechanisms by which it thrives in the intertidal zone at the edge of the ocean.

The Science
Researchers have sequenced and analyzed the genome of Porphyra umbilicalis, a red alga that is thought to represent one of the oldest forms of marine life and the origin for diatoms and other photosynthetic microorganisms. The team found strong cytoskeletal limitations in Porphyra and most other red algae with sequenced genomes, offering a possible explanation for why red algae tend to be small compared to other multicellular eukaryotes.  A 50-member team led by University of Maine, Carnegie Institution for Science, and East Carolina University used the Community Science Program of the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, to carry out the study.

The Impact
Though red algae are one of the oldest multicellular lineages, only a few have had their genomes sequenced. Porphyra umbilicalis is found in the ocean’s intertidal zone, and is subject to constantly changing environmental conditions including temperature, light, and desiccation levels. Analyzing the alga’s genome lends insights into its stress-tolerance mechanisms and how that impacts its ability to fix carbon. Also, since diatoms and other photosynthesizing microorganisms evolved from red algae, red algae metabolism has a significant impact on the planet’s carbon cycle.

The intertidal zone is the area between land and sea that is sometimes concealed by high tide or revealed by low tide. As this ecosystem is in constant flux, the organisms that inhabit the area have adapted to thrive under a range of constantly changing environmental conditions. Porphyra and other genera of bangiophyte red algae thrive in the intertidal zones of the northern and southern hemispheres. Their lineage is ancient, and the oldest taxonomically resolved fossil of a multicellular eukaryote, 1.2 billion years old, was also a bangiophyte.

As reported in the Proceedings of the National Academy of Sciences, the DOE JGI sequenced, assembled and annotated the genome of the red alga Porphyra umbilicalis to better understand how it harvests light and nutrients, and how warming oceans might impact its ability to fix carbon. The team led by University of Maine researchers found that the red alga has previously unrecognized means of tolerating its physically stressful intertidal habitat. For example, Porphyra umbilicalis has multiple strategies to protect cells from being damaged by high light levels, including expanded families of proteins that protect the photosynthetic apparatus from high light and unusual genomic arrangements of the genes that synthesize the mycosporine-like amino acids that protect against ultraviolet light. They also found that the alga has a significantly reduced cytoskeleton and lacks many motors other organisms rely on for intracellular transport. This may explain why red algae, compared to many other multicellular eukaryotes, are smaller and less structurally complex and how they can survive, in the closing words of the publication, in “in the pounding waves, baking sun, and drying winds of the high intertidal zone”

The green algae and red algae are both groups of plants that carry out photosynthesis using light-harnessing organelles called chloroplasts, which evolved from cyanobacteria that were engulfed by the ancestral eukaryotic algae. Later, other environmentally important algae such as diatoms, dinoflagellates and haptophytes evolved when other non-photosynthetic eukaryotes captured red algae and integrated the red algal chloroplast and red algal nuclear genes into their genomes. These processes greatly diversified the organisms capable of conducting photosynthesis, and the red algal imprint on global productivity, aquatic food webs, and oxygen production is significant.

PM Contact
Daniel Drell, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
U.S. Department of Energy

PI Contact
Jeremy Schmutz
Plant Program Head
DOE Joint Genome Institute

Susan Brawley
School of Marine Sciences
University of Maine

Work was conducted by the U.S. Department of Energy (DOE) Joint Genome Institute, a DOE Office of Science user facility (contract number DE-AC02-05CH11231). This work was also supported by the National Science Foundation, National Oceanic and Atmospheric Administration, German Research Foundation, French National Research Agency, US Department of Agriculture/National Institute of Food and Agriculture, Biotechnology and Biological Sciences Research Council and European Union FP7 e Curie Photo. COMM, Connecticut Sea Grant College Program, NOAA National Marine Aquaculture Initiative, National Institutes of Health, UK Natural Environment Research Council IOF Pump-priming + scheme, The Great Barrier Reef Foundation, Australian Research Council, and a University of Queensland Early Career Researcher grant.

S. Brawley, N. Blouin, E. Ficko-Blean, G. Wheeler, M. Lohr, H. Goodson, J. Jenkins, C. Blaby-Haas, K. Helliwell, C. Chan, T. Marriage, D. Bhattacharya, A. Klein, Y. Badis, J. Brodie, Y. Cao, J. Collén, S. Dittami, C. Gachon, B. Green, S. Karpowicz, J. Kim, U. Kudahl, S. Lin, G. Michel, M. Mittag, B. Olson, J. Pangilinan, Y. Peng, H. Qiu, S. Shu, J. Singer, A. Smith, B. Sprecher, V. Wagner, W. Wang, Z.Y. Wang, J. Yan, C. Yarish, S. Zäuner-Riek, Y. Zhuang, Y. Zou, E. Lindquist, J. Grimwood, K. Barry, D. Rokhsar, J. Schmutz, J. Stiller, A. Grossman, and S. Prochnik “Insights into the red algae from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta).” Proc Natl Acad. Sci. 2017. [DOI: 10.1073/pnas.1703088114] (Reference link)

Related Links
University of Maine News Release: “Sequencing reveals how Porphyra thrives in a tough environment
Carnegie Institution of Science News Release: “What makes red algae so different and why should we care?
Scottish Association for Marine Science News Release: “Scientists unlock secrets of red alga immunity
DOE JGI CSP 2008: Why Sequence Porphyra umbilicalis?
Porphyra umbilicalis on DOE JGI Genome Portal
2012 DOE JGI Science Highlight: “Algal Lipid Pathways Linked to Those in Plants and Fungi
Brawley Lab at the University of Maine
2012 DOE JGI News Release: “Tiny Algae Shed Light on Photosynthesis as a Dynamic Property

Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: DOE Joint Genome Institute (JGI)


BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

Recent GSP Highlights

Jul 12, 2018
Microbial Types May Prove Key to Gas Releases from Thawing Permafrost
Scientists discover key types of microbes that degrade organic matter and release carbon dioxide an [more...]

May 28, 2018
New Method Helps Predict Metabolite Concentrations, Rate Constants, and Enzyme Regulation Within Cells
Researchers use Neurospora crassa, a reliable model organism, to demonstrate new method. [more...]

Apr 16, 2018
Under Drought Conditions, Monoderm Bacteria Help Sorghum Continue Growing
Researchers discover how certain bacteria may safeguard plant growth during a drought, making way [more...]

Jan 18, 2018
Engineering Yeast Tolerance to a Promising Biomass Deconstruction Solvent
Chemical genomic-guided engineering of gamma-valerolactone-tolerant yeast. The Science [more...]

Nov 16, 2017
Aerobic Wetlands Emit High Levels of Methane
Genomic analysis reveals a novel methanogenic microbial species that is a significant contributor to [more...]