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Chen J, Yu X, Yu K, Chen B, Qin Z, Liao Z, Ma Y, Xu L, Wang Y. Potential adaptation of scleractinian coral Pocillopora damicornis during hypo-salinity stress caused by extreme pre-flood rainfall over south China. ENVIRONMENTAL RESEARCH 2024; 262:119848. [PMID: 39216737 DOI: 10.1016/j.envres.2024.119848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 08/23/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
Global warming intensifies the water cycle, resulting in significant increases in precipitation and river runoff, which brings severe hypo-salinity stress to nearshore coral reefs. Ecological investigations have found that some corals exhibit remarkable adaptability to hypo-salinity stress during mass-bleaching events. However, the exact cause of this phenomenon remains unclear. To elucidate the potential molecular mechanism leading to high tolerance to hypo-salinity stress, Pocillopora damicornis was used as a research object in this study. We compared the differences in transcriptional responses and symbiotic microbiomes between bleaching and unbleaching P. damicornis during hypo-salinity stress caused by extreme pre-flood rainfall over South China in 2022. The results showed that: (1) Under hypo-salinity stress, the coral genes related to immune defense and cellular stress were significantly upregulated in bleaching corals, indicating more severe immune damage and stress, and the Symbiodiniaceae had no significant gene enrichment. Conversely, metabolic genes related to glycolysis/gluconeogenesis were significantly downregulated in unbleaching corals, whereas Symbiodiniaceae genes related to oxidative phosphorylation were significantly upregulated to meet the energy requirements of coral holobiont; (2) C1d was the dominant Symbiodiniaceae subclade in all samples, with no significant difference between the two groups; (3) The symbiotic bacterial community structure was reorganized under hypo-salinity stress. The abundance of opportunistic bacteria increased significantly in bleaching coral, whereas the relative abundance of probiotics was higher in unbleaching coral. This may be due to severe immune damage, making the coral more susceptible to opportunistic infection and bleaching. These results suggest that long-term hypo-salinity acclimation in the Pearl River Estuary enhances the tolerance of some corals to hypo-salinity stress. Corals with higher tolerance may reduce energy consumption by slowing down their metabolism, improve the energy metabolism of Symbiodiniaceae to meet the energy requirements of the coral holobiont, and alter the structure of symbiotic bacterial communities to avoid bleaching.
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Affiliation(s)
- Junling Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China.
| | - Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China; Nanning Normal University, Nanning, China
| | - Yuling Ma
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Lijia Xu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, China.
| | - Yongzhi Wang
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou, China
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Poding LH, Jägers P, Herlitze S, Huhn M. Diversity and function of fluorescent molecules in marine animals. Biol Rev Camb Philos Soc 2024; 99:1391-1410. [PMID: 38468189 DOI: 10.1111/brv.13072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 02/24/2024] [Accepted: 02/29/2024] [Indexed: 03/13/2024]
Abstract
Fluorescence in marine animals has mainly been studied in Cnidaria but is found in many different phyla such as Annelida, Crustacea, Mollusca, and Chordata. While many fluorescent proteins and molecules have been identified, very little information is available about the biological functions of fluorescence. In this review, we focus on describing the occurrence of fluorescence in marine animals and the behavioural and physiological functions of fluorescent molecules based on experimental approaches. These biological functions of fluorescence range from prey and symbiont attraction, photoprotection, photoenhancement, stress mitigation, mimicry, and aposematism to inter- and intraspecific communication. We provide a comprehensive list of marine taxa that utilise fluorescence, including demonstrated effects on behavioural or physiological responses. We describe the numerous known functions of fluorescence in anthozoans and their underlying molecular mechanisms. We also highlight that other marine taxa should be studied regarding the functions of fluorescence. We suggest that an increase in research effort in this field could contribute to understanding the capacity of marine animals to respond to negative effects of climate change, such as rising sea temperatures and increasing intensities of solar irradiation.
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Affiliation(s)
- Lars H Poding
- Department of General Zoology and Neurobiology, Institute of Biology and Biotechnology, Ruhr-University Bochum, Bochum, 44801, Germany
| | - Peter Jägers
- Department of General Zoology and Neurobiology, Institute of Biology and Biotechnology, Ruhr-University Bochum, Bochum, 44801, Germany
| | - Stefan Herlitze
- Department of General Zoology and Neurobiology, Institute of Biology and Biotechnology, Ruhr-University Bochum, Bochum, 44801, Germany
| | - Mareike Huhn
- Department of General Zoology and Neurobiology, Institute of Biology and Biotechnology, Ruhr-University Bochum, Bochum, 44801, Germany
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Shikina S, Yoshioka Y, Chiu YL, Uchida T, Chen E, Cheng YC, Lin TC, Chu YL, Kanda M, Kawamitsu M, Fujie M, Takeuchi T, Zayasu Y, Satoh N, Shinzato C. Genome and tissue-specific transcriptomes of the large-polyp coral, Fimbriaphyllia (Euphyllia) ancora: a recipe for a coral polyp. Commun Biol 2024; 7:899. [PMID: 39048698 PMCID: PMC11269664 DOI: 10.1038/s42003-024-06544-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 07/03/2024] [Indexed: 07/27/2024] Open
Abstract
Coral polyps are composed of four tissues; however, their characteristics are largely unexplored. Here we report biological characteristics of tentacles (Te), mesenterial filaments (Me), body wall (Bo), and mouth with pharynx (MP), using comparative genomic, morpho-histological, and transcriptomic analyses of the large-polyp coral, Fimbriaphyllia ancora. A draft F. ancora genome assembly of 434 Mbp was created. Morpho-histological and transcriptomic characterization of the four tissues showed that they have distinct differences in structure, primary cellular composition, and transcriptional profiles. Tissue-specific, highly expressed genes (HEGs) of Te are related to biological defense, predation, and coral-algal symbiosis. Me expresses multiple digestive enzymes, whereas Bo expresses innate immunity and biomineralization-related molecules. Many receptors for neuropeptides and neurotransmitters are expressed in MP. This dataset and new insights into tissue functions will facilitate a deeper understanding of symbiotic biology, immunology, biomineralization, digestive biology, and neurobiology in corals.
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Affiliation(s)
- Shinya Shikina
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan.
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan.
| | - Yuki Yoshioka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Yi-Ling Chiu
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Taiga Uchida
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Emma Chen
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Yin-Chu Cheng
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Tzu-Chieh Lin
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Yu-Ling Chu
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan
| | - Miyuki Kanda
- DNA Sequencing Center Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Mayumi Kawamitsu
- DNA Sequencing Center Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Manabu Fujie
- DNA Sequencing Center Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Yuna Zayasu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan.
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Rachmilovitz EN, Shaish L, Douek J, Rinkevich B. Population genetics assessment of two pocilloporid coral species from the northern red sea: Implications for urbanized reef sustainability. MARINE ENVIRONMENTAL RESEARCH 2024; 199:106580. [PMID: 38851082 DOI: 10.1016/j.marenvres.2024.106580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 05/30/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
Understanding the genetic makeup of key coral species is vital for effective coral reef management, as heightened genetic diversity directly influences long-term survival and resilience against environmental changes. This study focused on two widespread Indo-Pacific branching corals, Pocillopora damicornis (referred as Pocillopora cf. damicornis (as identified only morphologically) and Seriatopora hystrix, by genotyping 222 and 195 colonies, respectively, from 10 sites in the northern Gulf of Eilat, Red Sea, using six and five microsatellite markers, respectively. Both species exhibited low observed heterozygosity (0.47 for P. cf. damicornis, 0.32 for S. hystrix) and similar expected heterozygosity (0.576 for P. cf. damicornis, 0.578 for S. hystrix). Pocillopora cf. damicornis showed minimal deviations from Hardy-Weinberg equilibrium (HWE) and low but positive F values, indicating high gene flow, while S. hystrix exhibited higher diversion from HWE and positive F values, suggesting isolation by distance and possible non-random mating or genetic drift. As the Gulf of Eilat undergoes rapid urbanization, this study highlights the anthropogenic impacts on the population genetics of key ecosystem engineering species and emphasizes the importance of managing genetics of Marine Protected Areas while implementing active coral reef restoration. The differences in reproductive traits between the two species (S. hystrix being a brooder, while P. cf. damicornis a broadcast spawner), underscore the need for sustainable population genetics management of the coral reefs for the future and resilience of the coral reef ecosystem of the northern Red Sea region.
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Affiliation(s)
- Elad Nehoray Rachmilovitz
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Tel Shikmona, P.O. Box 2336, Haifa, 3102201, Israel; Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Mount Carmel, Haifa, 3498838, Israel.
| | - Lee Shaish
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Tel Shikmona, P.O. Box 2336, Haifa, 3102201, Israel
| | - Jacob Douek
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Tel Shikmona, P.O. Box 2336, Haifa, 3102201, Israel.
| | - Baruch Rinkevich
- Israel Oceanographic and Limnological Research, National Institute of Oceanography, Tel Shikmona, P.O. Box 2336, Haifa, 3102201, Israel.
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Lock C, Gabriel MM, Bentlage B. Transcriptomic signatures across a critical sedimentation threshold in a major reef-building coral. Front Physiol 2024; 15:1303681. [PMID: 38919851 PMCID: PMC11196755 DOI: 10.3389/fphys.2024.1303681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 05/10/2024] [Indexed: 06/27/2024] Open
Abstract
Sedimentation is a major cause of global near-shore coral reef decline. Although the negative impacts of sedimentation on coral reef community composition have been well-documented, the effects of sedimentation on coral metabolism in situ have received comparatively little attention. Using transcriptomics, we identified gene expression patterns changing across a previously defined sedimentation threshold that was deemed critical due to changes in coral cover and community composition. We identified genes, pathways, and molecular processes associated with this transition that may allow corals, such as Porites lobata, to tolerate chronic, severe sedimentation and persist in turbid environments. Alternative energy generation pathways may help P. lobata maintain a persistent stress response to survive when the availability of light and oxygen is diminished. We found evidence for the expression of genes linked to increased environmental sensing and cellular communication that likely allow P. lobata to efficiently respond to sedimentation stress and associated pathogen challenges. Cell damage increases under stress; consequently, we found apoptosis pathways over-represented under severe sedimentation, a likely consequence of damaged cell removal to maintain colony integrity. The results presented here provide a framework for the response of P. lobata to sedimentation stress under field conditions. Testing this framework and its related hypotheses using multi-omics approaches can deepen our understanding of the metabolic plasticity and acclimation potential of corals to sedimentation and their resilience in turbid reef systems.
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Jiang L, Zhang P, Huang LT, Yu XL, Liu CY, Yuan XC, Liu S, Huang H. Life-stage specificity and temporal variations in transcriptomes and DNA methylomes of the reef coral Pocillopora damicornis in response to thermal acclimation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:171098. [PMID: 38387572 DOI: 10.1016/j.scitotenv.2024.171098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 02/03/2024] [Accepted: 02/17/2024] [Indexed: 02/24/2024]
Abstract
Understanding the acclimation capacity of reef corals across generations to thermal stress and its underlying molecular underpinnings could provide insights into their resilience and adaptive responses to future climate change. Here, we acclimated adult brooding coral Pocillopora damicornis to high temperature (32 °C vs. 29 °C) for three weeks and analyzed the changes in phenotypes, transcriptomes and DNA methylomes of adult corals and their brooded larvae. Results showed that although adult corals did not show noticeable bleaching after thermal exposure, they released fewer but larger larvae. Interestingly, larval cohorts from two consecutive lunar days exhibited contrasting physiological resistance to thermal stress, as evidenced by the divergent responses of area-normalized symbiont densities and photochemical efficiency to thermal stress. RNA-seq and whole-genome bisulfite sequencing revealed that adult and larval corals mounted distinct transcriptional and DNA methylation changes in response to thermal stress. Remarkably, larval transcriptomes and DNA methylomes also varied greatly among lunar days and thermal treatments, aligning well with their physiological metrics. Overall, our study shows that changes in transcriptomes and DNA methylomes in response to thermal acclimation can be highly life stage-specific. More importantly, thermally-acclimated adult corals could produce larval offspring with temporally contrasting photochemical performance and thermal resilience, and such variations in larval phenotypes are associated with differential transcriptomes and DNA methylomes, and are likely to increase the likelihood of reproductive success and plasticity of larval propagules under thermal stress.
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Affiliation(s)
- Lei Jiang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou 510301, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya 572000, China; Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
| | - Pan Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou 510301, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya 572000, China; Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin-Tao Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou 510301, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya 572000, China; Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Lei Yu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou 510301, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya 572000, China; Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
| | - Cheng-Yue Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou 510301, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya 572000, China; Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
| | - Xiang-Cheng Yuan
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou 510301, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya 572000, China; Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
| | - Sheng Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou 510301, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya 572000, China; Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China
| | - Hui Huang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology (SCSIO), Chinese Academy of Sciences, Guangzhou 510301, China; CAS-HKUST Sanya Joint Laboratory of Marine Science Research, Key Laboratory of Tropical Marine Biotechnology of Hainan Province, Sanya Institute of Ocean Eco-Environmental Engineering, SCSIO, Sanya 572000, China; Sanya National Marine Ecosystem Research Station, Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya 572000, China.
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Oury N, Magalon H. Investigating the potential roles of intra-colonial genetic variability in Pocillopora corals using genomics. Sci Rep 2024; 14:6437. [PMID: 38499737 PMCID: PMC10948807 DOI: 10.1038/s41598-024-57136-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 03/14/2024] [Indexed: 03/20/2024] Open
Abstract
Intra-colonial genetic variability (IGV), the presence of more than one genotype in a single colony, has been increasingly studied in scleractinians, revealing its high prevalence. Several studies hypothesised that IGV brings benefits, but few have investigated its roles from a genetic perspective. Here, using genomic data (SNPs), we investigated these potential benefits in populations of the coral Pocillopora acuta from Reunion Island (southwestern Indian Ocean). As the detection of IGV depends on sequencing and bioinformatics errors, we first explored the impact of the bioinformatics pipeline on its detection. Then, SNPs and genes variable within colonies were characterised. While most of the tested bioinformatics parameters did not significantly impact the detection of IGV, filtering on genotype depth of coverage strongly improved its detection by reducing genotyping errors. Mosaicism and chimerism, the two processes leading to IGV (the first through somatic mutations, the second through fusion of distinct organisms), were found in 7% and 12% of the colonies, respectively. Both processes led to several intra-colonial allelic differences, but most were non-coding or silent. However, 7% of the differences were non-silent and found in genes involved in a high diversity of biological processes, some of which were directly linked to responses to environmental stresses. IGV, therefore, appears as a source of genetic diversity and genetic plasticity, increasing the adaptive potential of colonies. Such benefits undoubtedly play an important role in the maintenance and the evolution of scleractinian populations and appear crucial for the future of coral reefs in the context of ongoing global changes.
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Affiliation(s)
- Nicolas Oury
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, 97744, St Denis Cedex 09, La Réunion, France.
- Laboratoire Cogitamus, Paris, France.
- KAUST Red Sea Research Center and Marine Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), 23955-6900, Thuwal, Saudi Arabia.
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, 97744, St Denis Cedex 09, La Réunion, France
- Laboratoire Cogitamus, Paris, France
- Laboratoire d'Excellence CORAIL, Perpignan, France
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Wei Y, Chen B, Yu K, Liao Z, Yu X, Qin Z, Bao Z, Xu L, Wang Y. Evolutionary radiation and microbial community dynamics shape the thermal tolerance of Fungiidae in the southern South China Sea. Microbiol Spectr 2024; 12:e0243623. [PMID: 38174936 PMCID: PMC10845974 DOI: 10.1128/spectrum.02436-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Fungiidae have shown increased thermal adaptability in coral reef ecosystems under global warming. This study analyzes the evolutionary divergence and microbial communities of Fungiidae in the Sanjiao Reef of the southern South China Sea and explores the impact of coral evolution radiation and microbial dynamics on the heat tolerance of Fungiidae. The results found that Cycloseris was an ancient branch of Fungiidae, dating back approximately 147.8953 Mya, and Fungiidae differentiated into two ancestral clades (clades I and II) before 107.0312 Ma. Fungiidae exhibited specific symbioses with the Cladocopium C27 sub-clade. Notably, the Cladocopium C1 sub-clade has a high relative abundance in clade I, whereas the heat-tolerant Cladocopium C40 and C3u sub-clades subdominante in clade II. Regarding bacterial communities, Cycloseris costulata, the earliest divergent species, had higher bacterial β-diversity, while the latest divergent species, Lithophyllon scabra, displayed lower bacterial α-diversity and higher community stability. Beneficial bacteria dominante Fungiidae's bacterial community (54%). The co-occurrence network revealed that microbial networks in clade II exhibited lower complexity and greater resilience than those in clade I. Our study highlights that host evolutionary radiation and microbial communities shaped Fungiidae's thermal tolerance. The variability in subdominant Symbiodiniaceae populations may contribute to interspecific differences in thermal tolerance along the evolutionary branches of Fungiidae. The presence of abundant beneficial bacteria may further enhance the thermal ability of the Fungiidae. Furthermore, the later divergent species of Fungiidae have stronger heat tolerance, possibly driven by the increased regulation ability of the host on the bacterial community, greater microbial community stability, and interaction network resistance.IMPORTANCECoral reefs are facing significant threats due to global warming. The heat tolerance of coral holobionts depends on both the coral host and its microbiome. However, the association between coral evolutionary radiation and interspecific differences in microbial communities remains unclear. In this study, we investigated the role of evolutionary radiation and microbial community dynamics in shaping the thermal acclimation potential of Fungiidae in the Sanjiao Reef of the southern South China Sea. The study's results suggest that evolutionary radiation enhances the thermal tolerance of Fungiidae. Fungiidae species that have diverged more recently have exhibited a higher presence of heat-tolerant Symbiodiniaceae taxa, more stable bacterial communities, and a robust and resilient microbial interaction network, improving the thermal adaptability of Fungiidae. In summary, this study provides new insights into the thermal adaptation patterns of corals under global warming conditions.
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Affiliation(s)
- Yuxin Wei
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
- Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou, China
| | - Zhiheng Liao
- Key Laboratory of Environmental Change and Resource Use in Beibu Gulf, Ministry of Education, Nanning Normal University, Nanning, China
| | - Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zeming Bao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Lijia Xu
- South China Institute of Environmental Sciences, MEE, Guangzhou, China
| | - Yongzhi Wang
- South China Institute of Environmental Sciences, MEE, Guangzhou, China
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Yu X, Yu K, Chen B, Liao Z, Liang J, Qin Z, Gao X. Metabolic and immune costs balance during natural acclimation of corals in fluctuating environments. MARINE ENVIRONMENTAL RESEARCH 2024; 193:106284. [PMID: 38048660 DOI: 10.1016/j.marenvres.2023.106284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/06/2023]
Abstract
Epigenetic modifications based on DNA methylation can rapidly improve the potential of corals to adapt to environmental pressures by increasing their phenotypic plasticity, a factor important for scleractinian corals to adapt to future global warming. However, the extent to which corals develop similar adaptive mechanisms and their specific adaptation processes remain unclear. Here, to reveal the regulatory mechanism by which DNA methylation improves thermal tolerance in Pocillopora damicornis under fluctuating environments, we analyzed genome-wide DNA methylation signatures in P. damicornis and compared the differences in the methylation and transcriptional responses of P. damicornis from fluctuating and stable environments using whole-genome bisulfite sequencing and nanopore-based RNA sequencingtranscriptome sequencing. We discovered low methylation levels in P. damicornis (average methylation 4.14%), with CpG accounting for 74.88%, CHH for 13.27%, and CHG for 11.85% of this methylation. However, methylation levels did not change between coral samples from the fluctuating and stable environments. The varied methylation levels in different regions of the gene revealed that the overall methylation level of the gene body was relatively high and showed a bimodal methylation pattern. Methylation occurs primarily in exons rather than introns within the gene body In P. damicornis, there was only a weak correlation between methylation and transcriptional changes at the individual gene level, and the methylation and gene expression levels generally exhibited a bell-shaped relationship, which we speculate may be due to the specificity of cnidarian species. Correlation analysis between methylation levels and the transcriptome revealed that the highest proportion of the top 20 enriched KEGG pathways was related to immunity. Additionally, P. damicornis collected from a high-temperature pool had a lower metabolic rate than those collected from a low-temperature pool. We hypothesize that the dynamic balance of energy-expenditure costs between immunity and metabolism is an important strategy for increasing P. damicornis tolerance. The fluctuating environment of high-temperature pools may increase the heat tolerance in corals by increasing their immunity and thus lowering their metabolism.
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Affiliation(s)
- Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
| | - Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Xu Gao
- Guangxi University of Chinese Medicine, Nanning, Guangxi, China
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10
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Zimmermann B, Montenegro JD, Robb SMC, Fropf WJ, Weilguny L, He S, Chen S, Lovegrove-Walsh J, Hill EM, Chen CY, Ragkousi K, Praher D, Fredman D, Schultz D, Moran Y, Simakov O, Genikhovich G, Gibson MC, Technau U. Topological structures and syntenic conservation in sea anemone genomes. Nat Commun 2023; 14:8270. [PMID: 38092765 PMCID: PMC10719294 DOI: 10.1038/s41467-023-44080-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
There is currently little information about the evolution of gene clusters, genome architectures and karyotypes in early branching animals. Slowly evolving anthozoan cnidarians can be particularly informative about the evolution of these genome features. Here we report chromosome-level genome assemblies of two related anthozoans, the sea anemones Nematostella vectensis and Scolanthus callimorphus. We find a robust set of 15 chromosomes with a clear one-to-one correspondence between the two species. Both genomes show chromosomal conservation, allowing us to reconstruct ancestral cnidarian and metazoan chromosomal blocks, consisting of at least 19 and 16 ancestral linkage groups, respectively. We show that, in contrast to Bilateria, the Hox and NK clusters of investigated cnidarians are largely disintegrated, despite the presence of staggered hox/gbx expression in Nematostella. This loss of microsynteny conservation may be facilitated by shorter distances between cis-regulatory sequences and their cognate transcriptional start sites. We find no clear evidence for topologically associated domains, suggesting fundamental differences in long-range gene regulation compared to vertebrates. These data suggest that large sets of ancestral metazoan genes have been retained in ancestral linkage groups of some extant lineages; yet, higher order gene regulation with associated 3D architecture may have evolved only after the cnidarian-bilaterian split.
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Affiliation(s)
- Bob Zimmermann
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Research platform SinCeReSt, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Juan D Montenegro
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Research platform SinCeReSt, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Sofia M C Robb
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Whitney J Fropf
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Lukas Weilguny
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Shuonan He
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Shiyuan Chen
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Jessica Lovegrove-Walsh
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Eric M Hill
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Cheng-Yi Chen
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
| | - Katerina Ragkousi
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA
- Department of Biology, Amherst College, Amherst, MA, 01002, USA
| | - Daniela Praher
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - David Fredman
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Darrin Schultz
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Yehu Moran
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Oleg Simakov
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
- Research platform SinCeReSt, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Grigory Genikhovich
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria
| | - Matthew C Gibson
- Stowers Institute for Medical Research, Kansas City, MO, 64110, USA.
| | - Ulrich Technau
- Department of Neurosciences and Developmental Biology, Faculty of Life Sciences, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Research platform SinCeReSt, University of Vienna, Djerassiplatz 1, 1030, Vienna, Austria.
- Max Perutz laboratories, University of Vienna, Dr. Bohrgasse 5, 1030, Vienna, Austria.
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11
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Chen B, Yu K, Fu L, Wei Y, Liang J, Liao Z, Qin Z, Yu X, Deng C, Han M, Ma H. The diversity, community dynamics, and interactions of the microbiome in the world's deepest blue hole: insights into extreme environmental response patterns and tolerance of marine microorganisms. Microbiol Spectr 2023; 11:e0053123. [PMID: 37861344 PMCID: PMC10883803 DOI: 10.1128/spectrum.00531-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/08/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE This study comprehensively examined the community dynamics, functional profiles, and interactions of the microbiome in the world's deepest blue hole. The findings revealed a positive correlation between the α-diversities of Symbiodiniaceae and archaea, indicating the potential reliance of Symbiodiniaceae on archaea in an extreme environment resulting from a partial niche overlap. The negative association between the α-diversity and β-diversity of the bacterial community suggested that the change rule of the bacterial community was consistent with the Anna Karenina effects. The core microbiome comprised nine microbial taxa, highlighting their remarkable tolerance and adaptability to sharp environmental gradient variations. Bacteria and archaea played significant roles in carbon, nitrogen, and sulfur cycles, while fungi contributed to carbon metabolism. This study advanced our understanding of the community dynamics, response patterns, and resilience of microorganisms populating the world's deepest blue hole, thereby facilitating further ecological and evolutional exploration of microbiomes in diverse extreme environments.
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Affiliation(s)
- Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Zhuhai, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Zhuhai, China
| | - Liang Fu
- Sansha Track Ocean Coral Reef Conservation Research Institute Co. Ltd. , Qionghai, China
| | - Yuxin Wei
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
- Key Laboratory of Environmental Change and Resource Use in Beibu Gulf, Ministry of Education, Nanning Normal University , Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Chuanqi Deng
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Minwei Han
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University , Nanning, China
| | - Honglin Ma
- Key Laboratory of Environmental Change and Resource Use in Beibu Gulf, Ministry of Education, Nanning Normal University , Nanning, China
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12
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Selwyn JD, Vollmer SV. Whole genome assembly and annotation of the endangered Caribbean coral Acropora cervicornis. G3 (BETHESDA, MD.) 2023; 13:jkad232. [PMID: 37804092 PMCID: PMC10700113 DOI: 10.1093/g3journal/jkad232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/08/2023]
Abstract
Coral species in the genus Acropora are key ecological components of coral reefs worldwide and represent the most diverse genus of scleractinian corals. While key species of Indo-Pacific Acropora have annotated genomes, no annotated genome has been published for either of the two species of Caribbean Acropora. Here we present the first fully annotated genome of the endangered Caribbean staghorn coral, Acropora cervicornis. We assembled and annotated this genome using high-fidelity nanopore long-read sequencing with gene annotations validated with mRNA sequencing. The assembled genome size is 318 Mb, with 28,059 validated genes. Comparative genomic analyses with other Acropora revealed unique features in A. cervicornis, including contractions in immune pathways and expansions in signaling pathways. Phylogenetic analysis confirms previous findings showing that A. cervicornis diverged from Indo-Pacific relatives around 41 million years ago, with the closure of the western Tethys Sea, prior to the primary radiation of Indo-Pacific Acropora. This new A. cervicornis genome enriches our understanding of the speciose Acropora and addresses evolutionary inquiries concerning speciation and hybridization in this diverse clade.
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Affiliation(s)
- Jason D Selwyn
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA 01908, USA
| | - Steven V Vollmer
- Department of Marine and Environmental Sciences, Northeastern University, Nahant, MA 01908, USA
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13
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Li J, Zou Y, Li Q, Zhang J, Bourne DG, Lyu Y, Liu C, Zhang S. A coral-associated actinobacterium mitigates coral bleaching under heat stress. ENVIRONMENTAL MICROBIOME 2023; 18:83. [PMID: 37996910 PMCID: PMC10668361 DOI: 10.1186/s40793-023-00540-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND The positive effects of exposing corals to microorganisms have been reported though how the benefits are conferred are poorly understood. Here, we isolated an actinobacterial strain (SCSIO 13291) from Pocillopora damicornis with capabilities to synthesize antioxidants, vitamins, and antibacterial and antiviral compounds supported with phenotypic and/or genomic evidence. Strain SCSIO 13291 was labeled with 5 (and - 6)-carboxytetramethylrhodamine, succinimidyl ester and the labeled cell suspension directly inoculated onto the coral polyp tissues when nubbins were under thermal stress in a mesocosm experiment. We then visualized the labelled bacterial cells and analyzed the coral physiological, transcriptome and microbiome to elucidate the effect this strain conferred on the coral holobiont under thermal stress. RESULTS Subsequent microscopic observations confirmed the presence of the bacterium attached to the coral polyps. Addition of the SCSIO 13291 strain reduced signs of bleaching in the corals subjected to heat stress. At the same time, alterations in gene expression, which were involved in reactive oxygen species and light damage mitigation, attenuated apoptosis and exocytosis in addition to metabolite utilization, were observed in the coral host and Symbiodiniaceae populations. In addition, the coral associated bacterial community altered with a more stable ecological network for samples inoculated with the bacterial strain. CONCLUSIONS Our results provide insights into the benefits of a putative actinobacterial probiotic strain that mitigate coral bleaching signs. This study suggests that the inoculation of bacteria can potentially directly benefit the coral holobiont through conferring metabolic activities or through indirect mechanisms of suppling additional nutrient sources.
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Affiliation(s)
- Jie Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China.
- Sanya National Marine Ecosystem Research Station, Chinese Academy of Sciences, Sanya, Hainan, China.
| | - Yiyang Zou
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Qiqi Li
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Jian Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - David G Bourne
- College of Science and Engineering, James Cook University, Townsville, QLD, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Yuanjiao Lyu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Cong Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Si Zhang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China
- Sanya National Marine Ecosystem Research Station, Chinese Academy of Sciences, Sanya, Hainan, China
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14
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Yoshioka Y, Chiu YL, Uchida T, Yamashita H, Suzuki G, Shinzato C. Genes possibly related to symbiosis in early life stages of Acropora tenuis inoculated with Symbiodinium microadriaticum. Commun Biol 2023; 6:1027. [PMID: 37853100 PMCID: PMC10584924 DOI: 10.1038/s42003-023-05350-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/12/2023] [Indexed: 10/20/2023] Open
Abstract
Due to the ecological importance of mutualism between reef-building corals and symbiotic algae (Family Symbiodiniaceae), various transcriptomic studies on coral-algal symbiosis have been performed; however, molecular mechanisms, especially genes essential to initiate and maintain these symbioses remain unknown. We investigated transcriptomic responses of Acropora tenuis to inoculation with the native algal symbiont, Symbiodinium microadriaticum, during early life stages, and identified possible symbiosis-related genes. Genes involved in immune regulation, protection against oxidative stress, and metabolic interactions between partners are particularly important for symbiosis during Acropora early life stages. In addition, molecular phylogenetic analysis revealed that some possible symbiosis-related genes originated by gene duplication in the Acropora lineage, suggesting that gene duplication may have been the driving force to establish stable mutualism in Acropora, and that symbiotic molecular mechanisms may vary among coral lineages.
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Affiliation(s)
- Yuki Yoshioka
- Atmosphere and Ocean Research Institute (AORI), The University of Tokyo, Kashiwa, Chiba, Japan.
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.
| | - Yi-Ling Chiu
- Atmosphere and Ocean Research Institute (AORI), The University of Tokyo, Kashiwa, Chiba, Japan
| | - Taiga Uchida
- Atmosphere and Ocean Research Institute (AORI), The University of Tokyo, Kashiwa, Chiba, Japan
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Go Suzuki
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute (AORI), The University of Tokyo, Kashiwa, Chiba, Japan.
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15
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Vollmer SV, Selwyn JD, Despard BA, Roesel CL. Genomic signatures of disease resistance in endangered staghorn corals. Science 2023; 381:1451-1454. [PMID: 37769073 DOI: 10.1126/science.adi3601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/09/2023] [Indexed: 09/30/2023]
Abstract
White band disease (WBD) has caused unprecedented declines in the Caribbean Acropora corals, which are now listed as critically endangered species. Highly disease-resistant Acropora cervicornis genotypes exist, but the genetic underpinnings of disease resistance are not understood. Using transmission experiments, a newly assembled genome, and whole-genome resequencing of 76 A. cervicornis genotypes from Florida and Panama, we identified 10 genomic regions and 73 single-nucleotide polymorphisms that are associated with disease resistance and that include functional protein-coding changes in four genes involved in coral immunity and pathogen detection. Polygenic scores calculated from 10 genomic loci indicate that genetic screens can detect disease resistance in wild and nursery stocks of A. cervicornis across the Caribbean.
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Affiliation(s)
- Steven V Vollmer
- Department of Marine and Environmental Sciences, Northeastern University, 430 Nahant Road, Nahant, MA 01908, USA
| | - Jason D Selwyn
- Department of Marine and Environmental Sciences, Northeastern University, 430 Nahant Road, Nahant, MA 01908, USA
| | - Brecia A Despard
- Department of Marine and Environmental Sciences, Northeastern University, 430 Nahant Road, Nahant, MA 01908, USA
| | - Charles L Roesel
- Department of Marine and Environmental Sciences, Northeastern University, 430 Nahant Road, Nahant, MA 01908, USA
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16
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Veglia AJ, Bistolas KSI, Voolstra CR, Hume BCC, Ruscheweyh HJ, Planes S, Allemand D, Boissin E, Wincker P, Poulain J, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Zoccola D, Correa AMS, Vega Thurber RL. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes. Commun Biol 2023; 6:566. [PMID: 37264063 DOI: 10.1038/s42003-023-04917-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.
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Affiliation(s)
- Alex J Veglia
- BioSciences Department, Rice University, Houston, TX, USA
| | | | | | | | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, F-06230, Villefranche-sur-Mer, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road H91 TK33, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
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17
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Noel B, Denoeud F, Rouan A, Buitrago-López C, Capasso L, Poulain J, Boissin E, Pousse M, Da Silva C, Couloux A, Armstrong E, Carradec Q, Cruaud C, Labadie K, Lê-Hoang J, Tambutté S, Barbe V, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores JM, Forcioli D, Furla P, Galand PE, Lombard F, Pesant S, Reynaud S, Sullivan MB, Sunagawa S, Thomas OP, Troublé R, Thurber RV, Allemand D, Planes S, Gilson E, Zoccola D, Wincker P, Voolstra CR, Aury JM. Pervasive tandem duplications and convergent evolution shape coral genomes. Genome Biol 2023; 24:123. [PMID: 37264421 DOI: 10.1186/s13059-023-02960-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/05/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Over the last decade, several coral genomes have been sequenced allowing a better understanding of these symbiotic organisms threatened by climate change. Scleractinian corals are reef builders and are central to coral reef ecosystems, providing habitat to a great diversity of species. RESULTS In the frame of the Tara Pacific expedition, we assemble two coral genomes, Porites lobata and Pocillopora cf. effusa, with vastly improved contiguity that allows us to study the functional organization of these genomes. We annotate their gene catalog and report a relatively higher gene number than that found in other public coral genome sequences, 43,000 and 32,000 genes, respectively. This finding is explained by a high number of tandemly duplicated genes, accounting for almost a third of the predicted genes. We show that these duplicated genes originate from multiple and distinct duplication events throughout the coral lineage. They contribute to the amplification of gene families, mostly related to the immune system and disease resistance, which we suggest to be functionally linked to coral host resilience. CONCLUSIONS At large, we show the importance of duplicated genes to inform the biology of reef-building corals and provide novel avenues to understand and screen for differences in stress resilience.
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Affiliation(s)
- Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Alice Rouan
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | | | - Laura Capasso
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
- Sorbonne Université, Collège Doctoral, 75005, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Emilie Boissin
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Mélanie Pousse
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Arnaud Couloux
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Eric Armstrong
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Quentin Carradec
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Corinne Cruaud
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Karine Labadie
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
| | - Julie Lê-Hoang
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Sylvie Tambutté
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Valérie Barbe
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Fondation Tara Océan, Base Tara, 8 Rue de Prague, 75 012, Paris, France
| | | | - Guillaume Iwankow
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Sarah Romac
- AD2M, UMR 7144, Sorbonne Université, CNRS, Station Biologique de Roscoff, ECOMAP, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, USA
| | - Chris Bowler
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Institut de Biologie de L'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- AD2M, UMR 7144, Sorbonne Université, CNRS, Station Biologique de Roscoff, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire Des Sciences du Climat Et de L'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, Gif-Sur-Yvette, 91191, France
| | - J Michel Flores
- Department of Earth and Planetary Sciences, Weizmann Institute of Science, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
| | - Pierre E Galand
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls Sur Mer, France
| | - Fabien Lombard
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Institut de La Mer de Villefranche Sur Mer, Sorbonne Université, Laboratoire d'Océanographie de Villefranche, Villefranche-Sur-Mer, 06230, France
- Institut Universitaire de France, Paris, 75231, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH, 43210, USA
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Vladimir-Prelog-Weg 4, CH-8093, Zurich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road H91 TK33, Galway, Ireland
| | - Romain Troublé
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Fondation Tara Océan, Base Tara, 8 Rue de Prague, 75 012, Paris, France
| | - Rebecca Vega Thurber
- Department of Microbiology, Oregon State University, 220 Nash Hall, Corvallis, OR, 97331, USA
| | - Denis Allemand
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Serge Planes
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
- Laboratoire d'Excellence CORAIL, PSL Research University, EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Cedex, Perpignan, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, Inserm, IRCAN, Nice, France
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Department of Human Genetics, CHU Nice, Nice, France
| | - Didier Zoccola
- LIA ROPSE, Laboratoire International Associé, Université Côte d'Azur - Centre Scientifique de Monaco, France
- Centre Scientifique de Monaco, Marine Biology Department, Monaco City, 98000, Monaco
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France
| | | | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, 91057, France.
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, R2022/Tara Oceans GO-SEE, 3 Rue Michel-Ange, 75016, Paris, France.
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18
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Oury N, Noël C, Mona S, Aurelle D, Magalon H. From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals. Mol Phylogenet Evol 2023; 184:107803. [PMID: 37120114 DOI: 10.1016/j.ympev.2023.107803] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/06/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data is available due to the small number of currently available markers and obscures species boundaries. Difficulties in inferring gene trees and morphological incongruences further blur the study and conservation of these organisms. Yet, can genomics alone be used to delimit species? Here, focusing on the coral genus Pocillopora, whose colonies play key roles in Indo-Pacific reef ecosystems but have challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNP) were first used to resolve Pocillopora phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to other lines of evidence based on genetic, morphology, biogeography and symbiont associations. Out of 21 species hypotheses delimited by genomics, 13 were strongly supported by all approaches, while six could represent either undescribed species or nominal species that have been synonymised incorrectly. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine Pocillopora species boundaries, (2) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, (3) the requirement of molecular identification when species identity of colonies is absolutely necessary to interpret results, as morphology can blur species identification in the field, and (4) the need for a taxonomic revision of the genus Pocillopora. These results give new insights into the usefulness of multiple criteria for resolving Pocillopora, and more widely, scleractinian species boundaries, and will ultimately contribute to the taxonomic revision of this genus and the conservation of its species.
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Affiliation(s)
- Nicolas Oury
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, St Denis, La Réunion, France; Laboratoire Cogitamus, Paris, France.
| | - Cyril Noël
- IFREMER - IRSI - Service de Bioinformatique (SeBiMER), Plouzané, France
| | - Stefano Mona
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE-PSL, Université PSL, CNRS, SU, UA, Paris, France; EPHE, PSL Research University, Paris, France; Laboratoire d'Excellence CORAIL, Perpignan, France
| | - Didier Aurelle
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, EPHE-PSL, Université PSL, CNRS, SU, UA, Paris, France; Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO, Marseille, France
| | - Hélène Magalon
- UMR ENTROPIE (Université de La Réunion, IRD, IFREMER, Université de Nouvelle-Calédonie, CNRS), Université de La Réunion, St Denis, La Réunion, France; Laboratoire Cogitamus, Paris, France; Laboratoire d'Excellence CORAIL, Perpignan, France
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19
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Kumar L, Brenner N, Sledzieski S, Olaosebikan M, Roger LM, Lynn-Goin M, Klein-Seetharaman R, Berger B, Putnam H, Yang J, Lewinski NA, Singh R, Daniels NM, Cowen L, Klein-Seetharaman J. Transfer of knowledge from model organisms to evolutionarily distant non-model organisms: The coral Pocillopora damicornis membrane signaling receptome. PLoS One 2023; 18:e0270965. [PMID: 36735673 PMCID: PMC9897584 DOI: 10.1371/journal.pone.0270965] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 06/21/2022] [Indexed: 02/04/2023] Open
Abstract
With the ease of gene sequencing and the technology available to study and manipulate non-model organisms, the extension of the methodological toolbox required to translate our understanding of model organisms to non-model organisms has become an urgent problem. For example, mining of large coral and their symbiont sequence data is a challenge, but also provides an opportunity for understanding functionality and evolution of these and other non-model organisms. Much more information than for any other eukaryotic species is available for humans, especially related to signal transduction and diseases. However, the coral cnidarian host and human have diverged over 700 million years ago and homologies between proteins in the two species are therefore often in the gray zone, or at least often undetectable with traditional BLAST searches. We introduce a two-stage approach to identifying putative coral homologues of human proteins. First, through remote homology detection using Hidden Markov Models, we identify candidate human homologues in the cnidarian genome. However, for many proteins, the human genome alone contains multiple family members with similar or even more divergence in sequence. In the second stage, therefore, we filter the remote homology results based on the functional and structural plausibility of each coral candidate, shortlisting the coral proteins likely to have conserved some of the functions of the human proteins. We demonstrate our approach with a pipeline for mapping membrane receptors in humans to membrane receptors in corals, with specific focus on the stony coral, P. damicornis. More than 1000 human membrane receptors mapped to 335 coral receptors, including 151 G protein coupled receptors (GPCRs). To validate specific sub-families, we chose opsin proteins, representative GPCRs that confer light sensitivity, and Toll-like receptors, representative non-GPCRs, which function in the immune response, and their ability to communicate with microorganisms. Through detailed structure-function analysis of their ligand-binding pockets and downstream signaling cascades, we selected those candidate remote homologues likely to carry out related functions in the corals. This pipeline may prove generally useful for other non-model organisms, such as to support the growing field of synthetic biology.
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Affiliation(s)
- Lokender Kumar
- Department of Chemistry, Colorado School of Mines, Golden, CO, United States of America
| | - Nathanael Brenner
- Department of Chemistry, Colorado School of Mines, Golden, CO, United States of America
| | - Samuel Sledzieski
- MIT Computer Science & Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Monsurat Olaosebikan
- Department of Computer Science, Tufts University, Medford, MA, United States of America
| | - Liza M. Roger
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Matthew Lynn-Goin
- Department of Chemistry, Colorado School of Mines, Golden, CO, United States of America
| | | | - Bonnie Berger
- MIT Computer Science & Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Hollie Putnam
- Department of Biological Sciences, University of Rhode Island, South Kingstown, RI, United States of America
| | - Jinkyu Yang
- Department of Department of Aeronautics & Astronautics, University of Washington, Seattle, WA, United States of America
| | - Nastassja A. Lewinski
- Department of Chemical and Life Science Engineering, Virginia Commonwealth University, Richmond, VA, United States of America
| | - Rohit Singh
- MIT Computer Science & Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - Noah M. Daniels
- Department of Computer Science and Statistics, University of Rhode Island, South Kingstown, RI, United States of America
| | - Lenore Cowen
- Department of Computer Science, Tufts University, Medford, MA, United States of America
| | - Judith Klein-Seetharaman
- Department of Chemistry, Colorado School of Mines, Golden, CO, United States of America
- * E-mail:
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20
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Ashley IA, Kitchen SA, Gorman LM, Grossman AR, Oakley CA, Suggett DJ, Weis VM, Rosset SL, Davy SK. Genomic conservation and putative downstream functionality of the phosphatidylinositol signalling pathway in the cnidarian-dinoflagellate symbiosis. Front Microbiol 2023; 13:1094255. [PMID: 36777026 PMCID: PMC9909359 DOI: 10.3389/fmicb.2022.1094255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/28/2022] [Indexed: 01/28/2023] Open
Abstract
The mutualistic cnidarian-dinoflagellate symbiosis underpins the evolutionary success of stony corals and the persistence of coral reefs. However, a molecular understanding of the signalling events that lead to the successful establishment and maintenance of this symbiosis remains unresolved. For example, the phosphatidylinositol (PI) signalling pathway has been implicated during the establishment of multiple mutualistic and parasitic interactions across the kingdoms of life, yet its role within the cnidarian-dinoflagellate symbiosis remains unexplored. Here, we aimed to confirm the presence and assess the specific enzymatic composition of the PI signalling pathway across cnidaria and dinoflagellates by compiling 21 symbiotic anthozoan (corals and sea anemones) and 28 symbiotic dinoflagellate (Symbiodiniaceae) transcriptomic and genomic datasets and querying genes related to this pathway. Presence or absence of PI-kinase and PI-phosphatase orthologs were also compared between a broad sampling of taxonomically related symbiotic and non-symbiotic species. Across the symbiotic anthozoans analysed, there was a complete and highly conserved PI pathway, analogous to the pathway found in model eukaryotes. The Symbiodiniaceae pathway showed similarities to its sister taxon, the Apicomplexa, with the absence of PI 4-phosphatases. However, conversely to Apicomplexa, there was also an expansion of homologs present in the PI5-phosphatase and PI5-kinase groups, with unique Symbiodiniaceae proteins identified that are unknown from non-symbiotic unicellular organisms. Additionally, we aimed to unravel the putative functionalities of the PI signalling pathway in this symbiosis by analysing phosphoinositide (PIP)-binding proteins. Analysis of phosphoinositide (PIP)-binding proteins showed that, on average, 2.23 and 1.29% of the total assemblies of anthozoan and Symbiodiniaceae, respectively, have the potential to bind to PIPs. Enrichment of Gene Ontology (GO) terms associated with predicted PIP-binding proteins within each taxon revealed a broad range of functions, including compelling links to processes putatively involved in symbiosis regulation. This analysis establishes a baseline for current understanding of the PI pathway across anthozoans and Symbiodiniaceae, and thus a framework to target future research.
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Affiliation(s)
- Immy A. Ashley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Sheila A. Kitchen
- Department of Marine Biology, Texas A&M University at Galveston, Galveston, TX, United States
| | - Lucy M. Gorman
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Arthur R. Grossman
- Department of Plant Biology, The Carnegie Institution, Stanford, CA, United States
| | - Clinton A. Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - David J. Suggett
- Climate Change Cluster, Faculty of Science, University of Technology Sydney, Broadway, NSW, Australia
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Sabrina L. Rosset
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand,*Correspondence: Simon K. Davy,
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21
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Aguilar-Camacho JM, Foreman K, Jaimes-Becerra A, Aharoni R, Gründer S, Moran Y. Functional analysis in a model sea anemone reveals phylogenetic complexity and a role in cnidocyte discharge of DEG/ENaC ion channels. Commun Biol 2023; 6:17. [PMID: 36609696 PMCID: PMC9822975 DOI: 10.1038/s42003-022-04399-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/21/2022] [Indexed: 01/09/2023] Open
Abstract
Ion channels of the DEG/ENaC family share a similar structure but serve strikingly diverse biological functions, such as Na+ reabsorption, mechanosensing, proton-sensing, chemosensing and cell-cell communication via neuropeptides. This functional diversity raises the question of the ancient function of DEG/ENaCs. Using an extensive phylogenetic analysis across many different animal groups, we found a surprising diversity of DEG/ENaCs already in Cnidaria (corals, sea anemones, hydroids and jellyfish). Using a combination of gene expression analysis, electrophysiological and functional studies combined with pharmacological inhibition as well as genetic knockout in the model cnidarian Nematostella vectensis, we reveal an unanticipated role for a proton-sensitive DEG/ENaC in discharge of N. vectensis cnidocytes, the stinging cells typifying all cnidarians. Our study supports the view that DEG/ENaCs are versatile channels that have been co-opted for diverse functions since their early occurrence in animals and that respond to simple and ancient stimuli, such as omnipresent protons.
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Affiliation(s)
- Jose Maria Aguilar-Camacho
- grid.9619.70000 0004 1937 0538Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel ,grid.40803.3f0000 0001 2173 6074Present Address: Department of Biological Sciences, North Carolina State University, Raleigh, NC USA
| | - Katharina Foreman
- grid.1957.a0000 0001 0728 696XInstitute of Physiology, RWTH Aachen University, Aachen, Germany
| | - Adrian Jaimes-Becerra
- grid.9619.70000 0004 1937 0538Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Reuven Aharoni
- grid.9619.70000 0004 1937 0538Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Stefan Gründer
- grid.1957.a0000 0001 0728 696XInstitute of Physiology, RWTH Aachen University, Aachen, Germany
| | - Yehu Moran
- grid.9619.70000 0004 1937 0538Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem, Jerusalem, Israel
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22
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Herrera S, Cordes EE. Genome assembly of the deep-sea coral Lophelia pertusa. GIGABYTE 2023; 2023:gigabyte78. [PMID: 36935863 PMCID: PMC10022433 DOI: 10.46471/gigabyte.78] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/14/2023] [Indexed: 03/17/2023] Open
Abstract
Like their shallow-water counterparts, cold-water corals create reefs that support highly diverse communities, and these structures are subject to numerous anthropogenic threats. Here, we present the genome assembly of Lophelia pertusa from the southeastern coast of the USA, the first one for a deep-sea scleractinian coral species. We generated PacBio continuous long reads data for an initial assembly and proximity ligation data for scaffolding. The assembly was annotated using evidence from transcripts, proteins, and ab initio gene model predictions. This assembly is comparable to high-quality reference genomes from shallow-water scleractinian corals. The assembly comprises 2,858 scaffolds (N50 1.6 Mbp) and has a size of 556.9 Mbp. Approximately 57% of the genome comprises repetitive elements and 34% of coding DNA. We predicted 41,089 genes, including 91.1% of complete metazoan orthologs. This assembly will facilitate investigations into the ecology of this species and the evolution of deep-sea corals.
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Affiliation(s)
- Santiago Herrera
- Department of Biological Sciences, Lehigh University, Bethlehem, PA, USA
- Corresponding author. E-mail:
| | - Erik E. Cordes
- Biology Department, Temple University, Philadelphia, PA, USA
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23
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Ide K, Nishikawa Y, Maruyama T, Tsukada Y, Kogawa M, Takeda H, Ito H, Wagatsuma R, Miyaoka R, Nakano Y, Kinjo K, Ito M, Hosokawa M, Yura K, Suda S, Takeyama H. Targeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral. MICROBIOME 2022; 10:220. [PMID: 36503599 PMCID: PMC9743535 DOI: 10.1186/s40168-022-01395-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 10/13/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Endozoicomonas bacteria symbiosis with various marine organisms is hypothesized as a potential indicator of health in corals. Although many amplicon analyses using 16S rRNA gene have suggested the diversity of Endozoicomonas species, genome analysis has been limited due to contamination of host-derived sequences and difficulties in culture and metagenomic analysis. Therefore, the evolutionary and functional potential of individual Endozoicomonas species symbiotic with the same coral species remains unresolved. RESULTS In this study, we applied a novel single-cell genomics technique using droplet microfluidics to obtain single-cell amplified genomes (SAGs) for uncultured coral-associated Endozoicomonas spp. We obtained seven novel Endozoicomonas genomes and quantitative bacterial composition from Acropora tenuis corals at four sites in Japan. Our quantitative 16S rRNA gene and comparative genomic analysis revealed that these Endozoicomonas spp. belong to different lineages (Clade A and Clade B), with widely varying abundance among individual corals. Furthermore, each Endozoicomonas species possessed various eukaryotic-like genes in clade-specific genes. It was suggested that these eukaryotic-like genes might have a potential ability of different functions in each clade, such as infection of the host coral or suppression of host immune pathways. These Endozoicomonas species may have adopted different host adaptation strategies despite living symbiotically on the same coral. CONCLUSIONS This study suggests that coral-associated Endozoicomonas spp. on the same species of coral have different evolutional strategies and functional potentials in each species and emphasizes the need to analyze the genome of each uncultured strain in future coral-Endozoicomonas relationships studies. Video Abstract.
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Affiliation(s)
- Keigo Ide
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Yohei Nishikawa
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Toru Maruyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Yuko Tsukada
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Masato Kogawa
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
| | - Hiroki Takeda
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Haruka Ito
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Ryota Wagatsuma
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Rimi Miyaoka
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
| | - Yoshikatsu Nakano
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
- Marine Science Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | | | - Michihiro Ito
- Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan
| | - Masahito Hosokawa
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan
| | - Kei Yura
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Shoichiro Suda
- Faculty of Science, University of the Ryukyus, Okinawa, Japan
| | - Haruko Takeyama
- Department of Life Science and Medical Bioscience, Waseda University, Tokyo, Japan.
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
- Research Organization for Nano and Life Innovation, Waseda University, Tokyo, Japan.
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Tokyo, Japan.
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24
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Stephens TG, Lee J, Jeong Y, Yoon HS, Putnam HM, Majerová E, Bhattacharya D. High-quality genome assembles from key Hawaiian coral species. Gigascience 2022; 11:6815755. [PMID: 36352542 PMCID: PMC9646523 DOI: 10.1093/gigascience/giac098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/11/2022] [Accepted: 09/22/2022] [Indexed: 11/11/2022] Open
Abstract
Background Coral reefs house about 25% of marine biodiversity and are critical for the livelihood of many communities by providing food, tourism revenue, and protection from wave surge. These magnificent ecosystems are under existential threat from anthropogenic climate change. Whereas extensive ecological and physiological studies have addressed coral response to environmental stress, high-quality reference genome data are lacking for many of these species. The latter issue hinders efforts to understand the genetic basis of stress resistance and to design informed coral conservation strategies. Results We report genome assemblies from 4 key Hawaiian coral species, Montipora capitata, Pocillopora acuta, Pocillopora meandrina, and Porites compressa. These species, or members of these genera, are distributed worldwide and therefore of broad scientific and ecological importance. For M. capitata, an initial assembly was generated from short-read Illumina and long-read PacBio data, which was then scaffolded into 14 putative chromosomes using Omni-C sequencing. For P. acuta, P. meandrina, and P. compressa, high-quality assemblies were generated using short-read Illumina and long-read PacBio data. The P. acuta assembly is from a triploid individual, making it the first reference genome of a nondiploid coral animal. Conclusions These assemblies are significant improvements over available data and provide invaluable resources for supporting multiomics studies into coral biology, not just in Hawaiʻi but also in other regions, where related species exist. The P. acuta assembly provides a platform for studying polyploidy in corals and its role in genome evolution and stress adaptation in these organisms.
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Affiliation(s)
- Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, NJ 08901, USA
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University , Daegu, Buk-gu 41566, Korea
| | - YuJin Jeong
- Department of Oceanography, Kyungpook National University , Daegu, Buk-gu 41566, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University , Suwon 16419, Korea
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island , Kingston, RI 02881, USA
| | - Eva Majerová
- Hawaiʻi Institute of Marine Biology , Kāneʻohe, HI 96744, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, NJ 08901, USA
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25
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Harman TE, Barshis DJ, Hauff Salas B, Hamsher SE, Strychar KB. Indications of symbiotic state influencing melanin-synthesis immune response in the facultative coral Astrangia poculata. DISEASES OF AQUATIC ORGANISMS 2022; 151:63-74. [PMID: 36173117 DOI: 10.3354/dao03695] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Increased ocean warming is causing detrimental impacts to tropical corals worldwide. Compounding the effects of heat stress, incidences of tropical coral disease have risen concurrently. While tropical coral responses to these impacts are well studied, temperate coral responses remain largely unknown. The present study focused on the immune response of the temperate coral Astrangia poculata to increased temperature and disease. Symbiotic and aposymbiotic A. poculata were collected from Narragansett Bay, Rhode Island (USA) in summer and winter seasons and exposed to control (18°C) versus elevated temperatures (26°C) in the presence of an immune stimulant (i.e. lipopolysaccharide) for a 12 h period. Prophenoloxidase (PPO) and melanin concentrations from the melanin-synthesis pathway were assessed via spectrophotometry to examine immune responses. While PPO measurements were higher on average in symbiotic corals compared with aposymbiotic corals, temperature and season did not significantly affect this metric. Melanin was significantly higher in symbiotic compared to aposymbiotic corals, implying that symbiotic state may be important for melanin-synthesis response. Conversely, melanin as an immune response may be of less importance in aposymbiotic A. poculata due to the potential capacity of other immune responses in this species. In addition, differences in resource allocation to immune investment as a result of symbiosis is plausible given melanin production observed within the present study. However, thermal stressors may reduce the overall influence of symbiosis on melanin production. Future studies should build upon these results to further understand the entirety of innate immunity responses in temperate coral species.
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Affiliation(s)
- Tyler E Harman
- Annis Water Resources Institute, Grand Valley State University, 740 West Shoreline Dr, Muskegon, MI 49441, USA
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26
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Salazar OR, N. Arun P, Cui G, Bay LK, van Oppen MJH, Webster NS, Aranda M. The coral Acropora loripes genome reveals an alternative pathway for cysteine biosynthesis in animals. SCIENCE ADVANCES 2022; 8:eabq0304. [PMID: 36149959 PMCID: PMC9506716 DOI: 10.1126/sciadv.abq0304] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/10/2022] [Indexed: 05/28/2023]
Abstract
The metabolic capabilities of animals have been derived from well-studied model organisms and are generally considered to be well understood. In animals, cysteine is an important amino acid thought to be exclusively synthesized through the transsulfuration pathway. Corals of the genus Acropora have lost cystathionine β-synthase, a key enzyme of the transsulfuration pathway, and it was proposed that Acropora relies on the symbiosis with dinoflagellates of the family Symbiodiniaceae for the acquisition of cysteine. Here, we identify the existence of an alternative pathway for cysteine biosynthesis in animals through the analysis of the genome of the coral Acropora loripes. We demonstrate that these coral proteins are functional and synthesize cysteine in vivo, exhibiting previously unrecognized metabolic capabilities of animals. This pathway is also present in most animals but absent in mammals, arthropods, and nematodes, precisely the groups where most of the animal model organisms belong to, highlighting the risks of generalizing findings from model organisms.
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Affiliation(s)
- Octavio R. Salazar
- Marine Science Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Prasanna N. Arun
- Marine Science Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Guoxin Cui
- Marine Science Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Line K. Bay
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Division of Research and Innovation, James Cook University, Townsville, Australia
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nicole S. Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, University of Queensland, St Lucia, Australia
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Australia
| | - Manuel Aranda
- Marine Science Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
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27
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Full-Length Transcriptome Maps of Reef-Building Coral Illuminate the Molecular Basis of Calcification, Symbiosis, and Circa-Dian Genes. Int J Mol Sci 2022; 23:ijms231911135. [PMID: 36232445 PMCID: PMC9570262 DOI: 10.3390/ijms231911135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/08/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Coral transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Here, we sequence the full-length transcriptomes of four common and frequently dominant reef-building corals using the PacBio Sequel II platform. We obtain information on reported gene functions, structures, and expression profiles. Among them, a comparative analysis of biomineralization-related genes provides insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiont Symbiodiniaceae are also isolated and annotated from the holobiont sequence data. Finally, a phylogenetic analysis of key circadian clock genes among 40 evolutionarily representative species indicates that there are four key members in early metazoans, including cry genes; Clock or Npas2; cyc or Arntl; and tim, while per, as the fifth member, occurs in Bilateria. In summary, this work provides a foundation for further work on the manipulation of skeleton production or symbiosis to promote the survival of these important organisms.
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28
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Species and population genomic differentiation in Pocillopora corals (Cnidaria, Hexacorallia). Genetica 2022; 150:247-262. [PMID: 36083388 DOI: 10.1007/s10709-022-00165-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/01/2022] [Indexed: 11/04/2022]
Abstract
Correctly delimiting species and populations is a prerequisite for studies of connectivity, adaptation and conservation. Genomic data are particularly useful to test species differentiation for organisms with few informative morphological characters or low discrimination of cytoplasmic markers, as in Scleractinians. Here we applied Restriction site Associated DNA sequencing (RAD-sequencing) to the study of species differentiation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia, with the objectives to test species hypotheses, and to study the genetic structure among sampling sites within species. We focused here on coral colonies morphologically similar to P. acuta (damicornis type β). We tested the impact of different filtering strategies on the stability of the results. The main genetic differentiation was observed between samples from Oman and French Polynesia. These samples corresponded to different previously defined primary species hypotheses (PSH), i.e., PSHs 12 and 13 in Oman, and PSH 5 in French Polynesia. In Oman, we did not observe any clear differentiation between the two putative species PSH 12 and 13, nor between sampling sites. In French Polynesia, where a single species hypothesis was studied, there was no differentiation between sites. Our analyses allowed the identification of clonal lineages in Oman and French Polynesia. The impact of clonality on genetic diversity is discussed in light of individual-based simulations.
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29
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Wada N, Hsu MT, Tandon K, Hsiao SSY, Chen HJ, Chen YH, Chiang PW, Yu SP, Lu CY, Chiou YJ, Tu YC, Tian X, Chen BC, Lee DC, Yamashiro H, Bourne DG, Tang SL. High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral Stylophora pistillata. SCIENCE ADVANCES 2022; 8:eabo2431. [PMID: 35857470 PMCID: PMC9258956 DOI: 10.1126/sciadv.abo2431] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/13/2022] [Indexed: 05/29/2023]
Abstract
Bacteria commonly form aggregates in a range of coral species [termed coral-associated microbial aggregates (CAMAs)], although these structures remain poorly characterized despite extensive efforts studying the coral microbiome. Here, we comprehensively characterize CAMAs associated with Stylophora pistillata and quantify their cell abundance. Our analysis reveals that multiple Endozoicomonas phylotypes coexist inside a single CAMA. Nanoscale secondary ion mass spectrometry imaging revealed that the Endozoicomonas cells were enriched with phosphorus, with the elemental compositions of CAMAs different from coral tissues and endosymbiotic Symbiodiniaceae, highlighting a role in sequestering and cycling phosphate between coral holobiont partners. Consensus metagenome-assembled genomes of the two dominant Endozoicomonas phylotypes confirmed their metabolic potential for polyphosphate accumulation along with genomic signatures including type VI secretion systems allowing host association. Our findings provide unprecedented insights into Endozoicomonas-dominated CAMAs and the first direct physiological and genomic linked evidence of their biological role in the coral holobiont.
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Affiliation(s)
- Naohisa Wada
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Ming-Tsung Hsu
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Kshitij Tandon
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Silver Sung-Yun Hsiao
- Institute of Astronomy and Astrophysics, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Hsing-Ju Chen
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Yu-Hsiang Chen
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Pei-Wen Chiang
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Sheng-Ping Yu
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Chih-Ying Lu
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 40227, Taiwan
| | - Yu-Jing Chiou
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Yung-Chi Tu
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Xuejiao Tian
- Research Center for Applied Sciences, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Der-Chuen Lee
- Institute of Earth Sciences, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
| | - Hideyuki Yamashiro
- Sesoko Station, Tropical Biosphere Research Center, University of the Ryukyus, 3422 Sesoko, Motobu, Okinawa 905-0227, Japan
| | - David G. Bourne
- College of Science and Engineering, James Cook University, Townsville, 4811 QLD, Australia
- Australian Institute of Marine Science, Townsville, 4810 QLD, Australia
- AIMS@JCU, Townsville, 4811 QLD, Australia
| | - Sen-Lin Tang
- Biodiversity Research Center, Academia Sinica, No. 128, Section 2, Academia Rd., Nangang, Taipei 11529, Taiwan
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30
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Cowen LJ, Putnam HM. Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience. Annu Rev Biomed Data Sci 2022; 5:205-231. [PMID: 35537462 DOI: 10.1146/annurev-biodatasci-122120-030732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coral reefs are home to over two million species and provide habitat for roughly 25% of all marine animals, but they are being severely threatened by pollution and climate change. A large amount of genomic, transcriptomic, and other omics data is becoming increasingly available from different species of reef-building corals, the unicellular dinoflagellates, and the coral microbiome (bacteria, archaea, viruses, fungi, etc.). Such new data present an opportunity for bioinformatics researchers and computational biologists to contribute to a timely, compelling, and urgent investigation of critical factors that influence reef health and resilience. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Lenore J Cowen
- Department of Computer Science, Tufts University, Medford, Massachusetts, USA;
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA;
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31
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Titus BM, Daly M. Population genomics for symbiotic anthozoans: can reduced representation approaches be used for taxa without reference genomes? Heredity (Edinb) 2022; 128:338-351. [PMID: 35418670 PMCID: PMC9076904 DOI: 10.1038/s41437-022-00531-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 11/08/2022] Open
Abstract
Population genetic studies of symbiotic anthozoans have been historically challenging because their endosymbioses with dinoflagellates have impeded marker development. Genomic approaches like reduced representation sequencing alleviate marker development issues but produce anonymous loci, and without a reference genome, it is unknown which organism is contributing to the observed patterns. Alternative methods such as bait-capture sequencing targeting Ultra-Conserved Elements are now possible but costly. Thus, RADseq remains attractive, but how useful are these methods for symbiotic anthozoan taxa without a reference genome to separate anthozoan from algal sequences? We explore this through a case-study using a double-digest RADseq dataset for the sea anemone Bartholomea annulata. We assembled a holobiont dataset (3854 loci) for 101 individuals, then used a reference genome to create an aposymbiotic dataset (1402 loci). For both datasets, we investigated population structure and used coalescent simulations to estimate demography and population parameters. We demonstrate complete overlap in the spatial patterns of genetic diversity, demographic histories, and population parameter estimates for holobiont and aposymbiotic datasets. We hypothesize that the unique combination of anthozoan biology, diversity of the endosymbionts, and the manner in which assembly programs identify orthologous loci alleviates the need for reference genomes in some circumstances. We explore this hypothesis by assembling an additional 21 datasets using the assembly programs pyRAD and Stacks. We conclude that RADseq methods are more tractable for symbiotic anthozoans without reference genomes than previously realized.
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Affiliation(s)
- Benjamin M Titus
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, USA.
- Dauphin Island Sea Lab, Dauphin Island, AL, USA.
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA.
| | - Marymegan Daly
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, OH, USA
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32
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Levy S, Mass T. The Skeleton and Biomineralization Mechanism as Part of the Innate Immune System of Stony Corals. Front Immunol 2022; 13:850338. [PMID: 35281045 PMCID: PMC8913943 DOI: 10.3389/fimmu.2022.850338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/31/2022] [Indexed: 11/15/2022] Open
Abstract
Stony corals are among the most important calcifiers in the marine ecosystem as they form the coral reefs. Coral reefs have huge ecological importance as they constitute the most diverse marine ecosystem, providing a home to roughly a quarter of all marine species. In recent years, many studies have shed light on the mechanisms underlying the biomineralization processes in corals, as characterizing the calicoblast cell layer and genes involved in the formation of the calcium carbonate skeleton. In addition, considerable advancements have been made in the research field of coral immunity as characterizing genes involved in the immune response to pathogens and stressors, and the revealing of specialized immune cells, including their gene expression profile and phagocytosis capabilities. Yet, these two fields of corals research have never been integrated. Here, we discuss how the coral skeleton plays a role as the first line of defense. We integrate the knowledge from both fields and highlight genes and proteins that are related to biomineralization and might be involved in the innate immune response and help the coral deal with pathogens that penetrate its skeleton. In many organisms, the immune system has been tied to calcification. In humans, immune factors enhance ectopic calcification which causes severe diseases. Further investigation of coral immune genes which are involved in skeleton defense as well as in biomineralization might shed light on our understanding of the correlation and the interaction of both processes as well as reveal novel comprehension of how immune factors enhance calcification.
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Affiliation(s)
- Shani Levy
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel
- *Correspondence: Shani Levy, ; Tali Mass,
| | - Tali Mass
- Department of Marine Biology, Leon H. Charney School of Marine Sciences, University of Haifa, Haifa, Israel
- Morris Kahn Marine Research Station, The Leon H. Charney School of Marine Sciences, University of Haifa, Sdot Yam, Israel
- *Correspondence: Shani Levy, ; Tali Mass,
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33
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Machine-Learning-Based Proteomic Predictive Modeling with Thermally-Challenged Caribbean Reef Corals. DIVERSITY 2022. [DOI: 10.3390/d14010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Coral health is currently diagnosed retroactively; colonies are deemed “stressed” upon succumbing to bleaching or disease. Ideally, health inferences would instead be made on a pre-death timescale that would enable, for instance, environmental mitigation that could promote coral resilience. To this end, diverse Caribbean coral (Orbicella faveolata) genotypes of varying resilience to high temperatures along the Florida Reef Tract were exposed herein to elevated temperatures in the laboratory, and a proteomic analysis was taken with a subset of 20 samples via iTRAQ labeling followed by nano-liquid chromatography + mass spectrometry; 46 host coral and 40 Symbiodiniaceae dinoflagellate proteins passed all stringent quality control criteria, and the partial proteomes of biopsies of (1) healthy controls, (2) sub-lethally stressed samples, and (3) actively bleaching corals differed significantly from one another. The proteomic data were then used to train predictive models of coral colony bleaching susceptibility, and both generalized regression and machine-learning-based neural networks were capable of accurately forecasting the bleaching susceptibility of coral samples based on their protein signatures. Successful future testing of the predictive power of these models in situ could establish the capacity to proactively monitor coral health.
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34
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Traylor-Knowles N, Emery M. Analysis of Spatial Gene Expression at the Cellular Level in Stony Corals. Methods Mol Biol 2022; 2450:359-371. [PMID: 35359318 PMCID: PMC9761507 DOI: 10.1007/978-1-0716-2172-1_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Scleractinians, or stony corals, are colonial animals that possess a high regenerative capacity and a highly diverse innate immune system. As such they present the opportunity to investigate the interconnection between regeneration and immunity in a colonial animal. Understanding the relationship between regeneration and immunity in stony corals is of further interest as it has major implications for coral reef health. One method for understanding the role of innate immunity in scleractinian regeneration is in situ hybridization using RNA probes. Here we describe a protocol for in situ hybridization in adult stony corals using a digoxigenin (DIG)-labeled RNA antisense probe which can be utilized to investigate the spatial expression of immune factors during regeneration.
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Affiliation(s)
- Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA.
| | - Madison Emery
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, USA
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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35
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Shinzato C, Takeuchi T, Yoshioka Y, Tada I, Kanda M, Broussard C, Iguchi A, Kusakabe M, Marin F, Satoh N, Inoue M. Whole-Genome Sequencing Highlights Conservative Genomic Strategies of a Stress-Tolerant, Long-Lived Scleractinian Coral, Porites australiensis Vaughan, 1918. Genome Biol Evol 2021; 13:6456307. [PMID: 34878117 PMCID: PMC8691061 DOI: 10.1093/gbe/evab270] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 12/13/2022] Open
Abstract
Massive corals of the genus Porites, common, keystone reef builders in the Indo-Pacific Ocean, are distinguished by their relative stress tolerance and longevity. In order to identify genetic bases of these attributes, we sequenced the complete genome of a massive coral, Porites australiensis. We developed a genome assembly and gene models of comparable quality to those of other coral genomes. Proteome analysis identified 60 Porites skeletal matrix protein genes, all of which show significant similarities to genes from other corals and even to those from a sea anemone, which has no skeleton. Nonetheless, 30% of its skeletal matrix proteins were unique to Porites and were not present in the skeletons of other corals. Comparative genomic analyses showed that genes widely conserved among other organisms are selectively expanded in Porites. Specifically, comparisons of transcriptomic responses of P. australiensis and Acropora digitifera, a stress-sensitive coral, reveal significant differences in regard to genes that respond to increased water temperature, and some of the genes expanded exclusively in Porites may account for the different thermal tolerances of these corals. Taken together, widely shared genes may have given rise to unique biological characteristics of Porites, massive skeletons and stress tolerance.
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Affiliation(s)
- Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Takeshi Takeuchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Ipputa Tada
- Department of Genetics, SOKENDAI (Graduate University for Advanced Studies), Mishima, Shizuoka, Japan
| | - Miyuki Kanda
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | | | - Akira Iguchi
- Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | | | - Frédéric Marin
- Biogéosciences, Bâtiment des Sciences Gabriel, Université de Bourgogne, Dijon, France
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Mayuri Inoue
- Division of Earth Science, Graduate School of Natural Science and Technology, Okayama University, Japan
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36
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Bollati E, Rosenberg Y, Simon-Blecher N, Tamir R, Levy O, Huang D. Untangling the molecular basis of coral response to sedimentation. Mol Ecol 2021; 31:884-901. [PMID: 34738686 DOI: 10.1111/mec.16263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/23/2022]
Abstract
Urbanized coral reefs are often chronically affected by sedimentation and reduced light levels, yet many species of corals appear to be able to thrive under these highly disturbed conditions. Recently, these marginal ecosystems have gained attention as potential climate change refugia due to the shading effect of suspended sediment, as well as potential reservoirs for stress-tolerant species. However, little research exists on the impact of sedimentation on coral physiology, particularly at the molecular level. Here, we investigated the transcriptomic response to sediment stress in corals of the family Merulinidae from a chronically turbid reef (one genet each of Goniastrea pectinata and Mycedium elephantotus from Singapore) and a clear-water reef (multiple genets of G. pectinata from the Gulf of Aqaba/Eilat). In two ex-situ experiments, we exposed corals to either natural sediment or artificial sediment enriched with organic matter and used whole-transcriptome sequencing (RNA sequencing) to quantify gene expression. Analysis revealed a shared basis for the coral transcriptomic response to sediment stress, which involves the expression of genes broadly related to energy metabolism and immune response. In particular, sediment exposure induced upregulation of anaerobic glycolysis and glyoxylate bypass enzymes, as well as genes involved in hydrogen sulphide metabolism and in pathogen pattern recognition. Our results point towards hypoxia as a probable driver of this transcriptomic response, providing a molecular basis to previous work that identified hypoxia as a primary cause of tissue necrosis in sediment-stressed corals. Potential metabolic and immunity trade-offs of corals living under chronic sedimentation should be considered in future studies on the ecology and conservation of turbid reefs.
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Affiliation(s)
- Elena Bollati
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.,Department of Biology, Marine Biology Section, University of Copenhagen, Helsingør, Denmark
| | - Yaeli Rosenberg
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Noa Simon-Blecher
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Raz Tamir
- School of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Oren Levy
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.,The Interuniversity Institute for Marine Sciences in Eilat, Eilat, Israel
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.,Tropical Marine Science Institute, National University of Singapore, Singapore, Singapore.,Centre for Nature-based Climate Solutions, National University of Singapore, Singapore, Singapore
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37
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Li Y, Liao X, Bi K, Han T, Chen J, Lu J, He C, Lu Z. Micro-CT reconstruction reveals the colony pattern regulations of four dominant reef-building corals. Ecol Evol 2021; 11:16266-16279. [PMID: 34824826 PMCID: PMC8601894 DOI: 10.1002/ece3.8308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 01/23/2023] Open
Abstract
Colonies are the basic geometric building blocks of coral reefs. However, the forming regulations of both colonies and reefs are still not understood adequately. Therefore, in this study, we reconstructed 25 samples using high-resolution micro-computed tomography to investigate coral growth patterns and parameters. Our skeleton and canal reconstructions revealed the characteristics of different coral species, and we further visualized the growth axes and growth rings to understand the coral growth directions. We drew a skeleton grayscale map and calculated the coral skeleton void ratios to ascertain the skeletal diversity, devising a method to quantify coral growth. On the basis of the three-dimensional (3D) reconstructions and growth parameters, we investigated the growth strategies of different coral species. This research increases the breadth of knowledge on how reef-building corals grow their colonies, providing information on reef-forming regulations. The data in this paper contain a large amount of coral growth information, which can be used in further research on reef-forming patterns under different conditions. The method used in this study can also be applied to animals with porous skeletons.
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Affiliation(s)
- Yixin Li
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
| | - Xin Liao
- Guangxi Key Lab of Mangrove Conservation and UtilizationGuangxi Academy of SciencesGuangxi Mangrove Research CenterBeihaiChina
| | - Kun Bi
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
| | - Tingyu Han
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
| | - Junyuan Chen
- Nanjing Institute of Geology and PalaeontologyChinese Academy of SciencesNanjingChina
| | - Jing Lu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of SciencesInstitute of Vertebrate Paleontology and PaleoanthropologyChinese Academy of SciencesBeijingChina
- CAS Center for Excellence in Life and PaleoenvironmentBeijingChina
| | - Chunpeng He
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
| | - Zuhong Lu
- State Key Laboratory of BioelectronicsSchool of Biological Science and Medical EngineeringSoutheast UniversityNanjingChina
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38
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Gault JA, Bentlage B, Huang D, Kerr AM. Lineage-specific variation in the evolutionary stability of coral photosymbiosis. SCIENCE ADVANCES 2021; 7:eabh4243. [PMID: 34550731 PMCID: PMC8457658 DOI: 10.1126/sciadv.abh4243] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
More than half of reef-building corals (Scleractinia) participate in a nutritional symbiosis, known as photosymbiosis, with photosynthetic dinoflagellates that ranges from obligate to facultative dependence. Fitting hidden-rates models allowing among-lineage variation in the rate of trait evolution to supertree and molecular phylogenies of Scleractinia, we reconstruct the history of photosymbiosis within Scleractinia and characterize its evolutionary stability. We find that most lineages of scleractinians are extraordinarily stable for the trait, evincing no instances of loss, but that in some clades photosymbiosis is more labile, thus providing a framework for comparative studies to further our mechanistic understanding of the factors that shape the evolutionary fates of scleractinian photosymbiosis.
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Affiliation(s)
- Jordan A. Gault
- Marine Laboratory, University of Guam, 303 University Dr., Mangilao, GU 96913, USA
| | - Bastian Bentlage
- Marine Laboratory, University of Guam, 303 University Dr., Mangilao, GU 96913, USA
| | - Danwei Huang
- Department of Biological Sciences, Tropical Marine Science Institute, and Centre for Nature-based Climate Solutions, National University of Singapore, Singapore 117558, Singapore
| | - Alexander M. Kerr
- Marine Laboratory, University of Guam, 303 University Dr., Mangilao, GU 96913, USA
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39
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Buitrago-López C, Mariappan KG, Cárdenas A, Gegner HM, Voolstra CR. The Genome of the Cauliflower Coral Pocillopora verrucosa. Genome Biol Evol 2021; 12:1911-1917. [PMID: 32857844 PMCID: PMC7594246 DOI: 10.1093/gbe/evaa184] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 02/06/2023] Open
Abstract
Climate change and ocean warming threaten the persistence of corals worldwide. Genomic resources are critical to study the evolutionary trajectory, adaptive potential, and genetic distinctiveness of coral species. Here, we provide a reference genome of the cauliflower coral Pocillopora verrucosa, a broadly prevalent reef-building coral with important ecological roles in the maintenance of reefs across the Red Sea, the Indian Ocean, and the Pacific Ocean. The genome has an assembly size of 380,505,698 bp with a scaffold N50 of 333,696 bp and a contig N50 of 75,704 bp. The annotation of the assembled genome returned 27,439 gene models of which 89.88% have evidence of transcription from RNA-Seq data and 97.87% show homology to known genes. A high proportion of the genome (41.22%) comprised repetitive elements in comparison to other cnidarian genomes, in particular in relation to the small genome size of P. verrucosa.
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Affiliation(s)
- Carol Buitrago-López
- Red Sea Research Center, Division of Biological BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Kiruthiga G Mariappan
- Red Sea Research Center, Division of Biological BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Anny Cárdenas
- Department of Biology, University of Konstanz, Germany
| | - Hagen M Gegner
- Red Sea Research Center, Division of Biological BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Centre for Organismal Studies (COS), University of Heidelberg, Germany
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological BESE, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Biology, University of Konstanz, Germany
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40
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Snyder GA, Eliachar S, Connelly MT, Talice S, Hadad U, Gershoni-Yahalom O, Browne WE, Palmer CV, Rosental B, Traylor-Knowles N. Functional Characterization of Hexacorallia Phagocytic Cells. Front Immunol 2021; 12:662803. [PMID: 34381444 PMCID: PMC8350327 DOI: 10.3389/fimmu.2021.662803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 06/03/2021] [Indexed: 11/20/2022] Open
Abstract
Phagocytosis is the cellular defense mechanism used to eliminate antigens derived from dysregulated or damaged cells, and microbial pathogens. Phagocytosis is therefore a pillar of innate immunity, whereby foreign particles are engulfed and degraded in lysolitic vesicles. In hexacorallians, phagocytic mechanisms are poorly understood, though putative anthozoan phagocytic cells (amoebocytes) have been identified histologically. We identify and characterize phagocytes from the coral Pocillopora damicornis and the sea anemone Nematostella vectensis. Using fluorescence-activated cell sorting and microscopy, we show that distinct populations of phagocytic cells engulf bacteria, fungal antigens, and beads. In addition to pathogenic antigens, we show that phagocytic cells engulf self, damaged cells. We show that target antigens localize to low pH phagolysosomes, and that degradation is occurring within them. Inhibiting actin filament rearrangement interferes with efficient particle phagocytosis but does not affect small molecule pinocytosis. We also demonstrate that cellular markers for lysolitic vesicles and reactive oxygen species (ROS) correlate with hexacorallian phagocytes. These results establish a foundation for improving our understanding of hexacorallian immune cell biology.
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Affiliation(s)
- Grace A Snyder
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Shir Eliachar
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Michael T Connelly
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
| | - Shani Talice
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Uzi Hadad
- Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Orly Gershoni-Yahalom
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - William E Browne
- Department of Biology, University of Miami, Coral Gables, FL, United States
| | - Caroline V Palmer
- School of Biological and Marine Sciences, University of Plymouth, Plymouth, United Kingdom
| | - Benyamin Rosental
- The Shraga Segal Department of Microbiology, Immunology, and Genetics, Faculty of Health Sciences, Regenerative Medicine and Stem Cell Research Center, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States
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41
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Emery MA, Dimos BA, Mydlarz LD. Cnidarian Pattern Recognition Receptor Repertoires Reflect Both Phylogeny and Life History Traits. Front Immunol 2021; 12:689463. [PMID: 34248980 PMCID: PMC8260672 DOI: 10.3389/fimmu.2021.689463] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022] Open
Abstract
Pattern recognition receptors (PRRs) are evolutionarily ancient and crucial components of innate immunity, recognizing danger-associated molecular patterns (DAMPs) and activating host defenses. Basal non-bilaterian animals such as cnidarians must rely solely on innate immunity to defend themselves from pathogens. By investigating cnidarian PRR repertoires we can gain insight into the evolution of innate immunity in these basal animals. Here we utilize the increasing amount of available genomic resources within Cnidaria to survey the PRR repertoires and downstream immune pathway completeness within 15 cnidarian species spanning two major cnidarian clades, Anthozoa and Medusozoa. Overall, we find that anthozoans possess prototypical PRRs, while medusozoans appear to lack these immune proteins. Additionally, anthozoans consistently had higher numbers of PRRs across all four classes relative to medusozoans, a trend largely driven by expansions in NOD-like receptors and C-type lectins. Symbiotic, sessile, and colonial cnidarians also have expanded PRR repertoires relative to their non-symbiotic, mobile, and solitary counterparts. Interestingly, cnidarians seem to lack key components of mammalian innate immune pathways, though similar to PRR numbers, anthozoans possess more complete immune pathways than medusozoans. Together, our data indicate that anthozoans have greater immune specificity than medusozoans, which we hypothesize to be due to life history traits common within Anthozoa. Overall, this investigation reveals important insights into the evolution of innate immune proteins within these basal animals.
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Affiliation(s)
- Madison A Emery
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
| | - Bradford A Dimos
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
| | - Laura D Mydlarz
- Department of Biology, University of Texas at Arlington, Arlington, TX, United States
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42
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Shinzato C, Khalturin K, Inoue J, Zayasu Y, Kanda M, Kawamitsu M, Yoshioka Y, Yamashita H, Suzuki G, Satoh N. Eighteen Coral Genomes Reveal the Evolutionary Origin of Acropora Strategies to Accommodate Environmental Changes. Mol Biol Evol 2021; 38:16-30. [PMID: 32877528 PMCID: PMC7783167 DOI: 10.1093/molbev/msaa216] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The genus Acropora comprises the most diverse and abundant scleractinian corals (Anthozoa, Cnidaria) in coral reefs, the most diverse marine ecosystems on Earth. However, the genetic basis for the success and wide distribution of Acropora are unknown. Here, we sequenced complete genomes of 15 Acropora species and 3 other acroporid taxa belonging to the genera Montipora and Astreopora to examine genomic novelties that explain their evolutionary success. We successfully obtained reasonable draft genomes of all 18 species. Molecular dating indicates that the Acropora ancestor survived warm periods without sea ice from the mid or late Cretaceous to the Early Eocene and that diversification of Acropora may have been enhanced by subsequent cooling periods. In general, the scleractinian gene repertoire is highly conserved; however, coral- or cnidarian-specific possible stress response genes are tandemly duplicated in Acropora. Enzymes that cleave dimethlysulfonioproprionate into dimethyl sulfide, which promotes cloud formation and combats greenhouse gasses, are the most duplicated genes in the Acropora ancestor. These may have been acquired by horizontal gene transfer from algal symbionts belonging to the family Symbiodiniaceae, or from coccolithophores, suggesting that although functions of this enzyme in Acropora are unclear, Acropora may have survived warmer marine environments in the past by enhancing cloud formation. In addition, possible antimicrobial peptides and symbiosis-related genes are under positive selection in Acropora, perhaps enabling adaptation to diverse environments. Our results suggest unique Acropora adaptations to ancient, warm marine environments and provide insights into its capacity to adjust to rising seawater temperatures.
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Affiliation(s)
- Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan
| | - Konstantin Khalturin
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Jun Inoue
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan.,Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Yuna Zayasu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Miyuki Kanda
- DNA Sequence Section (SQC), Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Mayumi Kawamitsu
- DNA Sequence Section (SQC), Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, Japan.,Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Hiroshi Yamashita
- Research Center for Subtropical Fisheries, Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Okinawa, Japan
| | - Go Suzuki
- Research Center for Subtropical Fisheries, Seikai National Fisheries Research Institute, Japan Fisheries Research and Education Agency, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
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43
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Roger LM, Reich HG, Lawrence E, Li S, Vizgaudis W, Brenner N, Kumar L, Klein-Seetharaman J, Yang J, Putnam HM, Lewinski NA. Applying model approaches in non-model systems: A review and case study on coral cell culture. PLoS One 2021; 16:e0248953. [PMID: 33831033 PMCID: PMC8031391 DOI: 10.1371/journal.pone.0248953] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/09/2021] [Indexed: 12/19/2022] Open
Abstract
Model systems approaches search for commonality in patterns underlying biological diversity and complexity led by common evolutionary paths. The success of the approach does not rest on the species chosen but on the scalability of the model and methods used to develop the model and engage research. Fine-tuning approaches to improve coral cell cultures will provide a robust platform for studying symbiosis breakdown, the calcification mechanism and its disruption, protein interactions, micronutrient transport/exchange, and the toxicity of nanoparticles, among other key biological aspects, with the added advantage of minimizing the ethical conundrum of repeated testing on ecologically threatened organisms. The work presented here aimed to lay the foundation towards development of effective methods to sort and culture reef-building coral cells with the ultimate goal of obtaining immortal cell lines for the study of bleaching, disease and toxicity at the cellular and polyp levels. To achieve this objective, the team conducted a thorough review and tested the available methods (i.e. cell dissociation, isolation, sorting, attachment and proliferation). The most effective and reproducible techniques were combined to consolidate culture methods and generate uncontaminated coral cell cultures for ~7 days (10 days maximum). The tests were conducted on scleractinian corals Pocillopora acuta of the same genotype to harmonize results and reduce variation linked to genetic diversity. The development of cell separation and identification methods in conjunction with further investigations into coral cell-type specific metabolic requirements will allow us to tailor growth media for optimized monocultures as a tool for studying essential reef-building coral traits such as symbiosis, wound healing and calcification at multiple scales.
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Affiliation(s)
- Liza M. Roger
- Life Science and Engineering, Virginia Commonwealth University, Richmond, Virginia, United States of America
- * E-mail: ,
| | - Hannah G. Reich
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States of America
| | - Evan Lawrence
- Life Science and Engineering, Virginia Commonwealth University, Richmond, Virginia, United States of America
| | - Shuaifeng Li
- Aeronautics and Astronautics, University of Washington, Seattle, Washington, United States of America
| | - Whitney Vizgaudis
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, United States of America
| | - Nathan Brenner
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, United States of America
| | - Lokender Kumar
- Department of Chemistry, Colorado School of Mines, Golden, Colorado, United States of America
| | | | - Jinkyu Yang
- Aeronautics and Astronautics, University of Washington, Seattle, Washington, United States of America
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States of America
| | - Nastassja A. Lewinski
- Life Science and Engineering, Virginia Commonwealth University, Richmond, Virginia, United States of America
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44
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Silva-Lima AW, Froes AM, Garcia GD, Tonon LAC, Swings J, Cosenza CAN, Medina M, Penn K, Thompson JR, Thompson CC, Thompson FL. Mussismilia braziliensis White Plague Disease Is Characterized by an Affected Coral Immune System and Dysbiosis. MICROBIAL ECOLOGY 2021; 81:795-806. [PMID: 33000311 DOI: 10.1007/s00248-020-01588-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/14/2020] [Indexed: 06/11/2023]
Abstract
Infectious diseases are one of the major drivers of coral reef decline worldwide. White plague-like disease (WPL) is a widespread disease with a complex etiology that infects several coral species, including the Brazilian endemic species Mussismilia braziliensis. Gene expression profiles of healthy and WPL-affected M. braziliensis were analyzed in winter and summer seasons. The de novo assembly of the M. braziliensis transcriptome from healthy and white plague samples produced a reference transcriptome containing 119,088 transcripts. WPL-diseased samples were characterized by repression of immune system and cellular defense processes. Autophagy and cellular adhesion transcripts were also repressed in WPL samples, suggesting exhaustion of the coral host defenses. Seasonal variation leads to plasticity in transcription with upregulation of intracellular signal transduction, apoptosis regulation, and oocyte development in the summer. Analysis of the active bacterial rRNA indicated that Pantoea bacteria were more abundant in WPL corals, while Tistlia, Fulvivirga, and Gammaproteobacteria Ga0077536 were more abundant in healthy samples. Cyanobacteria proliferation was also observed in WPL, mostly in the winter. These results indicate a scenario of dysbiosis in WPL-affected M. braziliensis, with the loss of potentially symbiotic bacteria and proliferation of opportunistic microbes after the start of the infection process.
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Affiliation(s)
- A W Silva-Lima
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Fo. S/N-CCS-IB-Lab de Microbiologia-BLOCO A (Anexo) A3-sl 102, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil
| | - A M Froes
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Fo. S/N-CCS-IB-Lab de Microbiologia-BLOCO A (Anexo) A3-sl 102, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil
| | - G D Garcia
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Fo. S/N-CCS-IB-Lab de Microbiologia-BLOCO A (Anexo) A3-sl 102, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil
- Sage/Coppe, Centro de Gestão Tecnológica-CT2, Rua Moniz de Aragão, no. 360-Bloco 2, Ilha do Fundão-Cidade Universitária, Rio de Janeiro, 21941-972, Brazil
| | - L A C Tonon
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Fo. S/N-CCS-IB-Lab de Microbiologia-BLOCO A (Anexo) A3-sl 102, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil
- Sage/Coppe, Centro de Gestão Tecnológica-CT2, Rua Moniz de Aragão, no. 360-Bloco 2, Ilha do Fundão-Cidade Universitária, Rio de Janeiro, 21941-972, Brazil
| | - J Swings
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Fo. S/N-CCS-IB-Lab de Microbiologia-BLOCO A (Anexo) A3-sl 102, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil
- Sage/Coppe, Centro de Gestão Tecnológica-CT2, Rua Moniz de Aragão, no. 360-Bloco 2, Ilha do Fundão-Cidade Universitária, Rio de Janeiro, 21941-972, Brazil
| | - C A N Cosenza
- Sage/Coppe, Centro de Gestão Tecnológica-CT2, Rua Moniz de Aragão, no. 360-Bloco 2, Ilha do Fundão-Cidade Universitária, Rio de Janeiro, 21941-972, Brazil
| | - M Medina
- Pennsylvania State University, 324 Mueller Lab, University Park, PA, 16802, USA
| | - K Penn
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - J R Thompson
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - C C Thompson
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Fo. S/N-CCS-IB-Lab de Microbiologia-BLOCO A (Anexo) A3-sl 102, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil
- Sage/Coppe, Centro de Gestão Tecnológica-CT2, Rua Moniz de Aragão, no. 360-Bloco 2, Ilha do Fundão-Cidade Universitária, Rio de Janeiro, 21941-972, Brazil
| | - F L Thompson
- Laboratório de Microbiologia, Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Av. Carlos Chagas Fo. S/N-CCS-IB-Lab de Microbiologia-BLOCO A (Anexo) A3-sl 102, Cidade Universitária, Rio de Janeiro, RJ, 21941-599, Brazil.
- Sage/Coppe, Centro de Gestão Tecnológica-CT2, Rua Moniz de Aragão, no. 360-Bloco 2, Ilha do Fundão-Cidade Universitária, Rio de Janeiro, 21941-972, Brazil.
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Yu X, Yu K, Chen B, Liao Z, Qin Z, Yao Q, Huang Y, Liang J, Huang W. Nanopore long-read RNAseq reveals regulatory mechanisms of thermally variable reef environments promoting heat tolerance of scleractinian coral Pocillopora damicornis. ENVIRONMENTAL RESEARCH 2021; 195:110782. [PMID: 33503412 DOI: 10.1016/j.envres.2021.110782] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Some scleractinian corals exhibit high thermal adaptability to climate changes, although the mechanism of their adaptation is unclear. This study investigated the adaptability of scleractinian coral Pocillopora damicornis to thermally variable reef environments by applying a nanopore-based RNA sequencing method to characterize different transcription responses that promote heat tolerance of P. damicornis. We identified 1414 novel genes and optimized 6256 mis-annotated loci. Based on full-length transcriptome data, we identified complex alternative polyadenylation and alternative splicing events, which can improve our understanding of the genome annotation and gene structures of P. damicornis. Furthermore, we constructed differentially expressed lncRNA-mRNA co-expression networks, which may play a crucial role in the P. damicornis thermal adaptive response. KEGG function enrichment analysis revealed that P. damicornis from the high-temperature pool had a lower metabolic rate than that from the low-temperature pool. We hypothesize that metabolic readjustment, in the form of a lower metabolic rate, positively correlated with increased heat tolerance in P. damicornis in thermally variable reef environments. Our study provides novel insights into lncRNAs that promote thermally tolerance of scleractinian corals in the thermally variable reef environment, suggesting potential mechanisms for their adaptation to global warming in the future.
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Affiliation(s)
- Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China.
| | - Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Qiucui Yao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Yanhua Huang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Wen Huang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
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46
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Selmoni O, Lecellier G, Magalon H, Vigliola L, Oury N, Benzoni F, Peignon C, Joost S, Berteaux-Lecellier V. Seascape genomics reveals candidate molecular targets of heat stress adaptation in three coral species. Mol Ecol 2021; 30:1892-1906. [PMID: 33619812 PMCID: PMC8252710 DOI: 10.1111/mec.15857] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 02/02/2021] [Accepted: 02/16/2021] [Indexed: 12/14/2022]
Abstract
Anomalous heat waves are causing a major decline of hard corals around the world and threatening the persistence of coral reefs. There are, however, reefs that have been exposed to recurrent thermal stress over the years and whose corals appear to have been tolerant against heat. One of the mechanisms that could explain this phenomenon is local adaptation, but the underlying molecular mechanisms are poorly known. In this work, we applied a seascape genomics approach to study heat stress adaptation in three coral species of New Caledonia (southwestern Pacific) and to uncover the molecular actors potentially involved. We used remote sensing data to characterize the environmental trends across the reef system, and sampled corals living at the most contrasted sites. These samples underwent next generation sequencing to reveal single nucleotide polymorphisms (SNPs), frequencies of which were associated with heat stress gradients. As these SNPs might underpin an adaptive role, we characterized the functional roles of the genes located in their genomic region. In each of the studied species, we found heat stress-associated SNPs located in proximity of genes involved in pathways well known to contribute to the cellular responses against heat, such as protein folding, oxidative stress homeostasis, inflammatory and apoptotic pathways, and DNA damage-repair. In some cases, the same candidate molecular targets of heat stress adaptation recurred among species. Together, these results underline the relevance and the power of the seascape genomics approach for the discovery of adaptive traits that could allow corals to persist across wider thermal ranges.
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Affiliation(s)
- Oliver Selmoni
- Laboratory of Geographic Information Systems (LASIG, School of Architecture, Civil and Environmental Engineering (ENAC, Ecole Polytechnique Fédérale de Lausanne (EPFL, Lausanne, Switzerland.,UMR250/9220, ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, Nouméa, France
| | - Gaël Lecellier
- UMR250/9220, ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, Nouméa, France.,Université Paris-Saclay, UVSQ, Versailles, France
| | - Hélène Magalon
- UMR250/9220, ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, St Denis de la Réunion, France
| | - Laurent Vigliola
- UMR250/9220, ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, Nouméa, France
| | - Nicolas Oury
- UMR250/9220, ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, St Denis de la Réunion, France
| | - Francesca Benzoni
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Christophe Peignon
- UMR250/9220, ENTROPIE IRD-CNRS-Ifremer-UNC-UR, Labex CORAIL, Nouméa, France
| | - Stéphane Joost
- Laboratory of Geographic Information Systems (LASIG, School of Architecture, Civil and Environmental Engineering (ENAC, Ecole Polytechnique Fédérale de Lausanne (EPFL, Lausanne, Switzerland
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47
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Ma H, Liao H, Dellisanti W, Sun Y, Chan LL, Zhang L. Characterizing the Host Coral Proteome of Platygyra carnosa Using Suspension Trapping (S-Trap). J Proteome Res 2021; 20:1783-1791. [PMID: 33630606 DOI: 10.1021/acs.jproteome.0c00812] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Stony corals form the foundation of coral reefs, which are of prominent ecological and economic significance. A robust workflow for investigating the coral proteome is essential in understanding coral biology. Here we investigated different preparative workflows and characterized the proteome of Platygyra carnosa, a common stony coral of the South China Sea. We found that a combination of bead homogenization with suspension trapping (S-Trap) preparation could yield more than 2700 proteins from coral samples. Annotation using a P. carnosa transcriptome database revealed that the majority of proteins were from the coral host cells (2140, 212, and 427 proteins from host coral, dinoflagellate, and other compartments, respectively). Label-free quantification and functional annotations indicated that a high proportion were involved in protein and redox homeostasis. Furthermore, the S-Trap method achieved good reproducibility in quantitative analysis. Although yielding a low symbiont:host ratio, the method is efficient in characterizing the coral host proteomic landscape, which provides a foundation to explore the molecular basis of the responses of coral host tissues to environmental stressors.
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Affiliation(s)
- Haiying Ma
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China.,State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China.,Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Herui Liao
- Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Walter Dellisanti
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China.,State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China.,Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
| | - Yanni Sun
- Department of Electronic Engineering, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Leo Lai Chan
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China.,State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong, China.,Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China.,Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Hong Kong, China
| | - Liang Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, City University of Hong Kong Shenzhen Research Institute, Shenzhen 518057, China
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48
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Novel methods to establish whole-body primary cell cultures for the cnidarians Nematostella vectensis and Pocillopora damicornis. Sci Rep 2021; 11:4086. [PMID: 33603013 PMCID: PMC7893170 DOI: 10.1038/s41598-021-83549-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 01/06/2021] [Indexed: 11/15/2022] Open
Abstract
Cnidarians are emerging model organisms for cell and molecular biology research. However, successful cell culture development has been challenging due to incomplete tissue dissociation and contamination. In this report, we developed and tested several different methodologies to culture primary cells from all tissues of two species of Cnidaria: Nematostella vectensis and Pocillopora damicornis. In over 170 replicated cell cultures, we demonstrate that physical dissociation was the most successful method for viable and diverse N. vectensis cells while antibiotic-assisted dissociation was most successful for viable and diverse P. damicornis cells. We also demonstrate that a rigorous antibiotic pretreatment results in less initial contamination in cell cultures. Primary cultures of both species averaged 12–13 days of viability, showed proliferation, and maintained high cell diversity including cnidocytes, nematosomes, putative gastrodermal, and epidermal cells. Overall, this work will contribute a needed tool for furthering functional cell biology experiments in Cnidaria.
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Satoh N, Kinjo K, Shintaku K, Kezuka D, Ishimori H, Yokokura A, Hagiwara K, Hisata K, Kawamitsu M, Koizumi K, Shinzato C, Zayasu Y. Color morphs of the coral, Acropora tenuis, show different responses to environmental stress and different expression profiles of fluorescent-protein genes. G3 (BETHESDA, MD.) 2021; 11:jkab018. [PMID: 33621334 PMCID: PMC8022974 DOI: 10.1093/g3journal/jkab018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/06/2021] [Indexed: 11/21/2022]
Abstract
Corals of the family Acroporidae are key structural components of reefs that support the most diverse marine ecosystems. Due to increasing anthropogenic stresses, coral reefs are in decline. Along the coast of Okinawa, Japan, three different color morphs of Acropora tenuis have been recognized for decades. These include brown (N morph), yellow green (G), and purple (P) forms. The tips of axial polyps of each morph exhibit specific fluorescence spectra. This attribute is inherited asexually, and color morphs do not change seasonally. In Okinawa Prefecture, during the summer of 2017, N and P morphs experienced bleaching, in which many N morphs died. Dinoflagellates (Symbiodiniaceae) are essential partners of scleractinian corals, and photosynthetic activity of symbionts was reduced in N and P morphs. In contrast, G morphs successfully withstood the stress. Examination of the clade and type of Symbiodiniaceae indicated that the three color-morphs host similar sets of Clade-C symbionts, suggesting that beaching of N and P morphs is unlikely attributable to differences in the clade of Symbiodiniaceae the color morphs hosted. Fluorescent proteins play pivotal roles in physiological regulation of corals. Since the A. tenuis genome has been decoded, we identified five genes for green fluorescent proteins (GFPs), two for cyan fluorescent proteins (CFPs), three for red fluorescent proteins (RFPs), and seven genes for chromoprotein (ChrP). A summer survey of gene expression profiles under outdoor aquarium conditions demonstrated that (a) expression of CFP and REP was quite low during the summer in all three morphs, (b) P morphs expressed higher levels of ChrP than N and G morphs, (c) both N and G morphs expressed GFP more highly than P morphs, and (d) GFP expression in N morphs was reduced during summer whereas G morphs maintained high levels of GFP expression throughout the summer. Although further studies are required to understand the biological significance of these color morphs of A. tenuis, our results suggest that thermal stress resistance is modified by genetic mechanisms that coincidentally lead to diversification of color morphs of this coral.
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Affiliation(s)
- Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Koji Kinjo
- Umino-Tane Co. Ltd, Okinawa 905-0888, Japan
| | - Kohei Shintaku
- IDEA Consultants, Inc., Okinawa Branch Office, Okinawa 900-0003, Japan
| | - Daisuke Kezuka
- IDEA Consultants, Inc., Okinawa Branch Office, Okinawa 900-0003, Japan
| | - Hiroo Ishimori
- IDEA Consultants, Inc., Okinawa Branch Office, Okinawa 900-0003, Japan
| | - Atsushi Yokokura
- IDEA Consultants, Inc., Institute of Environmental Informatics, Kanagawa 224-0025, Japan
| | | | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Mayumi Kawamitsu
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Koji Koizumi
- Imaging Section, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba 277-8564, Japan
| | - Yuna Zayasu
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan
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50
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Chiu YL, Shikina S, Yoshioka Y, Shinzato C, Chang CF. De novo transcriptome assembly from the gonads of a scleractinian coral, Euphyllia ancora: molecular mechanisms underlying scleractinian gametogenesis. BMC Genomics 2020; 21:732. [PMID: 33087060 PMCID: PMC7579821 DOI: 10.1186/s12864-020-07113-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 09/29/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Sexual reproduction of scleractinians has captured the attention of researchers and the general public for decades. Although extensive ecological data has been acquired, underlying molecular and cellular mechanisms remain largely unknown. In this study, to better understand mechanisms underlying gametogenesis, we isolated ovaries and testes at different developmental phases from a gonochoric coral, Euphyllia ancora, and adopted a transcriptomic approach to reveal sex- and phase-specific gene expression profiles. In particular, we explored genes associated with oocyte development and maturation, spermiogenesis, sperm motility / capacitation, and fertilization. RESULTS 1.6 billion raw reads were obtained from 24 gonadal samples. De novo assembly of trimmed reads, and elimination of contigs derived from symbiotic dinoflagellates (Symbiodiniaceae) and other organisms yielded a reference E. ancora gonadal transcriptome of 35,802 contigs. Analysis of 4 developmental phases identified 2023 genes that were differentially expressed during oogenesis and 678 during spermatogenesis. In premature/mature ovaries, 631 genes were specifically upregulated, with 538 in mature testes. Upregulated genes included those involved in gametogenesis, gamete maturation, sperm motility / capacitation, and fertilization in other metazoans, including humans. Meanwhile, a large number of genes without homology to sequences in the SWISS-PROT database were also observed among upregulated genes in premature / mature ovaries and mature testes. CONCLUSIONS Our findings show that scleractinian gametogenesis shares many molecular characteristics with that of other metazoans, but it also possesses unique characteristics developed during cnidarian and/or scleractinian evolution. To the best of our knowledge, this study is the first to create a gonadal transcriptome assembly from any scleractinian. This study and associated datasets provide a foundation for future studies regarding gametogenesis and differences between male and female colonies from molecular and cellular perspectives. Furthermore, our transcriptome assembly will be a useful reference for future development of sex-specific and/or stage-specific germ cell markers that can be used in coral aquaculture and ecological studies.
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Affiliation(s)
- Yi-Ling Chiu
- Doctoral Program in Marine Biotechnology, National Taiwan Ocean University, Keelung, 20224, Taiwan.,Doctoral Program in Marine Biotechnology, Academia Sinica, Taipei, 11529, Taiwan
| | - Shinya Shikina
- Institute of Marine Environment and Ecology, National Taiwan Ocean University, Keelung, Taiwan. .,Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Rd, Keelung, 20224, Taiwan.
| | - Yuki Yoshioka
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan
| | - Chuya Shinzato
- Atmosphere and Ocean Research Institute, The University of Tokyo, Chiba, 277-8564, Japan.
| | - Ching-Fong Chang
- Center of Excellence for the Oceans, National Taiwan Ocean University, 2 Pei-Ning Rd, Keelung, 20224, Taiwan. .,Department of Aquaculture, National Taiwan Ocean University, Keelung, Taiwan.
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