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Coral reefs are diverse and vibrant underwater ecosystems that are crucial to the health of our planet, providing habitat for a staggering 35% of all marine species. Unfortunately, the world's coral reefs face numerous anthropogenic threats, including ocean acidification and rising seawater temperatures due to climate change. Such challenges have already increased the rate of coral bleaching, a life-threatening process that results from a breakdown in the mutually beneficial relationship between corals and their symbiotic algae (i.e. dinoflagellates in the genus Symbiodinium). It is therefore imperative that key targets and approaches for coral reef conservation be identified and implemented swiftly. In a new Perspective article published in Genome Biology and Evolution, Chuya Shinzato from the University of Tokyo and Yuki Yoshioka from the Okinawa Institute of Science and Technology highlight the importance of genomic analyses of reef-building corals (Shinzato and Yoshioka 2024). “Coral reef conservation is one of the most pressing environmental issues of our time,” note Shinzato and Yoshioka, and analysis of coral genomes is critical for helping to direct conservation efforts to better preserve these keystone species.
Stony corals, or scleractinian corals, produce the calcium carbonate skeletons that serve as the foundational structure for coral reefs. As summarized by Shinzato and Yoshioka, forty species of reef-building corals have been sequenced since the first coral genome was published in 2011. While nine of the 37 families of scleractinian corals are represented, nearly half of the sequenced species derive from a single genus, Acropora. Encompassing around 140 species, Acropora is the most diverse scleractinian genus, and the high growth rates of these species make them key contributors to reef growth (Fig. 1). Nevertheless, Shinzato and Yoshioka note that a wealth of coral diversity has not yet been studied intensively, making this a key area of need for additional coral genomic research.
Scleractinian corals like Acropora digitifera, pictured here, serve as the foundations of coral reefs. Credit: Chuya Shinzato.
According to Shinzato and Yoshioka, the genomic resources that are available have provided several surprising insights that not only deepen our understanding of coral biology but also pave the way for effective conservation strategies. For example, genes that may allow corals to influence their own local climate in the face of climate change have been identified in Acropora genomes. The protein dimethlysulfoniopropionate (DMSP) lyase breaks down DMSP and releases dimethyl sulfide, a volatile compound that has been shown to activate cloud formation and reduce solar radiation and ocean temperatures. Studies have revealed expansions in the DSMP lyase-like (DL-L) gene family in Acropora during past warm geological periods, and it now represents the most diverse gene family in the Acropora genome. This mechanism for atmosphere–ocean feedback may have helped Acropora survive past warming periods and represents an intriguing area for future research as corals attempt to adapt to warmer climates.
Another surprise described in the article was the identification of scleractinian genes encoding photo-protective compounds that protect corals from the sun's harmful ultraviolet (UV) radiation. These compounds were originally thought to be provided by the dinoflagellate algae that reside within corals, but genes encoding UV-protective proteins have now been found in the Acropora genome, indicating that corals may not depend solely on symbiotic algae for these compounds. This may become more relevant to conservation efforts as changes in cloud cover affect coral exposure to UV radiation, particularly if coral bleaching continues to become more prevalent among reefs.
One of the most important parameters for directing coral conservation efforts is understanding coral genetic diversity and the connectivity among different coral populations. Population genomic studies of Acropora species off the coast of the Ryukyu Islands and Okinawa, Japan have revealed surprisingly complex population structures, suggesting the existence of hidden barriers to larval dispersal and gene flow, despite the fact that these corals are broadcast spawners. Such studies are critical for preserving coral diversity and understanding dispersal following reef seeding efforts.
While the results of coral genomic studies have so far provided numerous avenues for future research, there are several hurdles to translating these findings into effective conservation strategies. According to study author Chuya Shinzato, “The most likely obstacle to research in this field is that the speed of climate change may be too fast for research to keep up.” In addition, “because coral reefs are so diverse, their impacts may also be diverse, making it extremely difficult to understand the full picture of how climate change affects coral reefs,” explains Shinzato. “Open questions include how effective genome analysis will actually be in the conservation and restoration of coral reefs, and how much genomic information on coral and symbiotic algae is needed.”
Despite these challenges, Shinzato and Yoshioka have issued a call to action to support the expansion of coral genomic resources. Such efforts are crucial not only for gaining insight into the natural history of corals but also for crafting effective conservation plans that will enable the preservation of coral reefs for generations to come.
Want to learn more? Check out these recent articles on coral genomics also published in Genome Biology and Evolution: “The First Genome of the Cold-Water Octocoral, the Pink Sea Fan, Eunicella verrucosa” (Macleod et al. 2023) adds to the limited genomic resources available for temperate, shallow-water octocoral species and represents a key step in investigating the genomic and transcriptomic responses of these corals to climate change.
“Ploidy Variation and Its Implications for Reproduction and Population Dynamics in Two Sympatric Hawaiian Coral Species” (Stephens et al. 2023) highlights the differences in reproductive behavior and genome biology between coral species and how these contribute to coral resilience and persistence.
“Comparative Genome and Evolution Analyses of an Endangered Stony Coral Species Dendrophyllia cribrosa Near Dokdo Islands in the East Sea” (Kim et al. 2022) investigates how a stony coral species that lacks photosynthetic symbionts evolved alternative mechanisms to acquire cellular energy.
