Insights into an Eukaryotic Alga that Lives by the Sea

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.

Principal Investigator

Jeremy Schmutz
DOE Joint Genome Institute
[email protected]

Co-Principal Investigator

Susan Brawley
University of Maine
[email protected]

Related Links

BER Program Manager

Ramana Madupu

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


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.


Brawley, S., 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. 2017. “Insights into the Red Algae from the Genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta),” Proceedings of the National Academy of Sciences. DOI:10.1073/pnas.1703088114.