1
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Williams A. Multiomics data integration, limitations, and prospects to reveal the metabolic activity of the coral holobiont. FEMS Microbiol Ecol 2024; 100:fiae058. [PMID: 38653719 PMCID: PMC11067971 DOI: 10.1093/femsec/fiae058] [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: 09/26/2023] [Revised: 03/25/2024] [Accepted: 04/22/2024] [Indexed: 04/25/2024] Open
Abstract
Since their radiation in the Middle Triassic period ∼240 million years ago, stony corals have survived past climate fluctuations and five mass extinctions. Their long-term survival underscores the inherent resilience of corals, particularly when considering the nutrient-poor marine environments in which they have thrived. However, coral bleaching has emerged as a global threat to coral survival, requiring rapid advancements in coral research to understand holobiont stress responses and allow for interventions before extensive bleaching occurs. This review encompasses the potential, as well as the limits, of multiomics data applications when applied to the coral holobiont. Synopses for how different omics tools have been applied to date and their current restrictions are discussed, in addition to ways these restrictions may be overcome, such as recruiting new technology to studies, utilizing novel bioinformatics approaches, and generally integrating omics data. Lastly, this review presents considerations for the design of holobiont multiomics studies to support lab-to-field advancements of coral stress marker monitoring systems. Although much of the bleaching mechanism has eluded investigation to date, multiomic studies have already produced key findings regarding the holobiont's stress response, and have the potential to advance the field further.
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Affiliation(s)
- Amanda Williams
- Microbial Biology Graduate Program, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, United States
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2
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Han T, Liao X, Guo Z, Chen JY, He C, Lu Z. Comparative transcriptome analysis reveals deep molecular landscapes in stony coral Montipora clade. Front Genet 2023; 14:1297483. [PMID: 38028626 PMCID: PMC10662330 DOI: 10.3389/fgene.2023.1297483] [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: 09/20/2023] [Accepted: 10/25/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Coral reefs, among the most invaluable ecosystems in the world, face escalating threats from climate change and anthropogenic activities. To decipher the genetic underpinnings of coral adaptation and resilience, we undertook comprehensive transcriptome profiling of two emblematic coral species, Montipora foliosa and Montipora capricornis, leveraging PacBio Iso-Seq technology. These species were strategically selected for their ecological significance and their taxonomic proximity within the Anthozoa class. Methods: Our study encompassed the generation of pristine transcriptomes, followed by thorough functional annotation via diverse databases. Subsequently, we quantified transcript abundance and scrutinized gene expression patterns, revealing notable distinctions between the two species. Results: Intriguingly, shared orthologous genes were identified across a spectrum of coral species, highlighting a substantial genetic conservation within scleractinian corals. Importantly, a subset of genes, integral to biomineralization processes, emerged as exclusive to scleractinian corals, shedding light on their intricate evolutionary history. Furthermore, we discerned pronounced upregulation of genes linked to immunity, stress response, and oxidative-reduction processes in M. foliosa relative to M. capricornis. These findings hint at the presence of more robust mechanisms in M. foliosa for maintaining internal equilibrium and effectively navigating external challenges, underpinning its potential ecological advantage. Beyond elucidating genetic adaptation in corals, our research underscores the urgency of preserving genetic diversity within coral populations. Discussion: These insights hold promise for informed conservation strategies aimed at safeguarding these imperiled ecosystems, bearing ecological and economic significance. In synthesis, our study seamlessly integrates genomic inquiry with ecological relevance, bridging the gap between molecular insights and the imperative to conserve coral reefs in the face of mounting threats.
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Affiliation(s)
- Tingyu Han
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xin Liao
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Beihai, China
| | - Zhuojun Guo
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - J.-Y. Chen
- Nanjing Institute of Geology and Paleontology, Nanjing, China
| | - Chunpeng He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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3
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Ricci F, Leggat W, Page CE, Ainsworth TD. Coral growth anomalies, neoplasms, and tumors in the Anthropocene. Trends Microbiol 2022; 30:1160-1173. [PMID: 35718641 DOI: 10.1016/j.tim.2022.05.013] [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: 02/18/2022] [Revised: 05/19/2022] [Accepted: 05/23/2022] [Indexed: 01/13/2023]
Abstract
One of the most widespread coral diseases linked to anthropogenic activities and recorded on reefs worldwide is characterized by anomalous growth formations in stony corals, referred to as coral growth anomalies (GAs). The biological functions of GA tissue include limited reproduction, reduced access to resources, and weakened ability to defend against predators. Transcriptomic analyses have revealed that, in some cases, disease progression can involve host genes related to oncogenesis, suggesting that the GA tissues may be malignant neoplasms such as those developed by vertebrates. The number of studies reporting the presence of GAs in common reef-forming species highlights the urgency of a thorough understanding of the pathology and causative factors of this disease and its parallels to higher organism malignant tissue growth. Here, we review the current state of knowledge on the etiology and holobiont features of GAs in reef-building corals.
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Affiliation(s)
- Francesco Ricci
- University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington 2033, NSW, Australia.
| | - William Leggat
- University of Newcastle, School of Environmental and Life Sciences, Callaghan 2309, NSW, Australia
| | - Charlotte E Page
- University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington 2033, NSW, Australia
| | - Tracy D Ainsworth
- University of New South Wales, School of Biological, Earth and Environmental Sciences, Kensington 2033, NSW, Australia
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4
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Wong YH, Zhang Y, Lun JCY, Qiu JW. A proteomic analysis of skeletal tissue anomaly in the brain coral Platygyra carnosa. MARINE POLLUTION BULLETIN 2021; 164:111982. [PMID: 33517085 DOI: 10.1016/j.marpolbul.2021.111982] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 12/19/2020] [Accepted: 12/20/2020] [Indexed: 06/12/2023]
Abstract
Coral skeletal growth anomaly (GA) is a common coral disease. It has been considered as a pathological condition comparable to abnormal tissue growth in mammals, but little is known about the molecular changes underlying coral GA. To investigate the molecular pathology of GA, we compared the proteome between normal and GA-affected tissues of the brain coral Platygyra carnosa using iTRAQ-labeling and LC-MS/MS, which quantified 818 proteins and identified 117 differentially expressed proteins (DEPs). GO analyses revealed DEPs that might be related to GA included "translational elongation", "proteasome core complex", "amine metabolic processes" and "lysosome". Several proteins implicated in calcification and fluorescence were differentially expressed at both protein and mRNA level. Protein-protein interaction network suggested possible involvement of TNF receptor signaling in GA. Overall, our results provided novel insights into the molecular pathology of coral GA, which will pave the way for determination of the causative agent(s) of this coral disease.
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Affiliation(s)
- Yue-Him Wong
- Institute for Advance Study, Shenzhen University, Shenzhen, China
| | - Yu Zhang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-environmental Science, Guangdong Engineering Research Center for Marine Algal Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China.
| | - Janice C Y Lun
- Agriculture, Fishery and Conservation Department, The Government of the Hong Kong Special Administrative Region, China
| | - Jian-Wen Qiu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China; Department of Biology, Hong Kong Baptist University, Hong Kong, China; HKBU Institute of Research and Continuing Education, Shenzhen, China.
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5
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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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6
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Young BD, Serrano XM, Rosales SM, Miller MW, Williams D, Traylor-Knowles N. Innate immune gene expression in Acropora palmata is consistent despite variance in yearly disease events. PLoS One 2020; 15:e0228514. [PMID: 33091033 PMCID: PMC7580945 DOI: 10.1371/journal.pone.0228514] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022] Open
Abstract
Coral disease outbreaks are expected to increase in prevalence, frequency and severity due to climate change and other anthropogenic stressors. This is especially worrying for the Caribbean branching coral Acropora palmata which has already seen an 80% decrease in cover primarily due to disease. Despite the importance of this keystone species, there has yet to be a characterization of its transcriptomic response to disease exposure. In this study we provide the first transcriptomic analysis of 12 A. palmata genotypes and their symbiont Symbiodiniaceae exposed to disease in 2016 and 2017. Year was the primary driver of gene expression variance for A. palmata and the Symbiodiniaceae. We hypothesize that lower expression of ribosomal genes in the coral, and higher expression of transmembrane ion transport genes in the Symbiodiniaceae indicate that a compensation or dysbiosis may be occurring between host and symbiont. Disease response was the second driver of gene expression variance for A. palmata and included a core set of 422 genes that were significantly differentially expressed. Of these, 2 genes (a predicted cyclin-dependent kinase 11b and aspartate 1-decarboxylase) showed negative Log2 fold changes in corals showing transmission of disease, and positive Log2 fold changes in corals showing no transmission of disease, indicating that these may be important in disease resistance. Co-expression analysis identified two modules positively correlated to disease exposure, one enriched for lipid biosynthesis genes, and the other enriched in innate immune genes. The hub gene in the immune module was identified as D-amino acid oxidase, a gene implicated in phagocytosis and microbiome homeostasis. The role of D-amino acid oxidase in coral immunity has not been characterized but could be an important enzyme for responding to disease. Our results indicate that A. palmata mounts a core immune response to disease exposure despite differences in the disease type and virulence between 2016 and 2017. These identified genes may be important for future biomarker development in this Caribbean keystone species.
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Affiliation(s)
- Benjamin D. Young
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
| | - Xaymara M. Serrano
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanographic and Atmospheric Administration, Miami, Florida, United States of America
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, Florida, United States of America
| | - Stephanie M. Rosales
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, Florida, United States of America
| | - Margaret W. Miller
- Southeast Fisheries Science Center, NOAA-National Marine Fisheries Service, Miami, FL, United States of America
- SECORE International, Miami, FL, United States of America
| | - Dana Williams
- Cooperative Institute for Marine and Atmospheric Studies, University of Miami, Miami, Florida, United States of America
- Southeast Fisheries Science Center, NOAA-National Marine Fisheries Service, Miami, FL, United States of America
| | - Nikki Traylor-Knowles
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
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7
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Li J, Long L, Zou Y, Zhang S. Microbial community and transcriptional responses to increased temperatures in coral Pocillopora damicornis holobiont. Environ Microbiol 2020; 23:826-843. [PMID: 32686311 PMCID: PMC7984454 DOI: 10.1111/1462-2920.15168] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 05/31/2020] [Accepted: 07/14/2020] [Indexed: 12/14/2022]
Abstract
A few studies have holistically examined successive changes in coral holobionts in response to increased temperatures. Here, responses of the coral host Pocillopora damicornis, its Symbiodiniaceae symbionts, and associated bacteria to increased water temperatures were investigated. High temperatures induced bleaching, but no coral mortality was observed. Transcriptome analyses showed that P. damicornis responded more quickly to elevated temperatures than its algal symbionts. Numerous genes putatively associated with apoptosis, exocytosis, and autophagy were upregulated in P. damicornis, suggesting that Symbiodiniaceae can be eliminated or expelled through these mechanisms when P. damicornis experiences heat stress. Furthermore, apoptosis in P. damicornis is presumably induced through tumour necrosis factor and p53 signalling and caspase pathways. The relative abundances of several coral disease-associated bacteria increased at 32°C, which may affect immune responses in heat-stressed corals and potentially accelerates the loss of algal symbionts. Additionally, consistency of Symbiodiniaceae community structures under heat stress suggests non-selective loss of Symbiodiniaceae. We propose that heat stress elicits interrelated response mechanisms in all parts of the coral holobiont.
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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.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Lijuan Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, Guangdong, China.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, Guangdong, 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
| | - 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.,Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, Guangdong, China
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8
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Morphological, elemental, and boron isotopic insights into pathophysiology of diseased coral growth anomalies. Sci Rep 2020; 10:8252. [PMID: 32427852 PMCID: PMC7237652 DOI: 10.1038/s41598-020-65118-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 04/15/2020] [Indexed: 11/08/2022] Open
Abstract
Coral growth anomalies (GAs) are tumor-like lesions that are detrimental to colony fitness and are commonly associated with high human population density, yet little is known about the disease pathology or calcification behavior. SEM imagery, skeletal trace elements and boron isotopes (δ11B) have been combined as a novel approach to study coral disease. Low Mg/Ca, and high U/Ca, Mo/Ca, and V/Ca potentially suggest a decreased abundance of "centers of calcification" and nitrogen-fixation in GAs. Estimates of carbonate system parameters from δ11B and B/Ca measurements indicate reduced pH (-0.05 units) and [CO32-] within GA calcifying fluid. We theorize GAs re-allocate resources away from internal pH upregulation to sustain elevated tissue growth, resulting in a porous and fragile skeleton. Our findings show that dystrophic calcification processes could explain structural differences seen in GA skeletons and highlight the use of skeletal geochemistry to shed light on disease pathophysiology in corals.
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9
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Xie JY, Yeung YH, Kwok CK, Kei K, Ang P, Chan LL, Cheang CC, Chow WK, Qiu JW. Localized bleaching and quick recovery in Hong Kong's coral communities. MARINE POLLUTION BULLETIN 2020; 153:110950. [PMID: 32056854 DOI: 10.1016/j.marpolbul.2020.110950] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 06/10/2023]
Abstract
During the summer of 2017 we visited 33 sites with substantial coral cover across Hong Kong waters. At six sites where coral bleaching was observed, video-transect surveys were conducted, which revealed 18.7% to 56.1% bleached colonies and 5.9% to 57.6% bleached coral covered area per site. Mainly affected were three plate-like and three massive coral species. Water quality parameters were analyzed, which indicated that hyposalinity might have triggered the bleaching event. Tagging and follow-up field observation revealed a pattern of recovery depending on coral growth form, with high recovery rates (>93%) at five sites dominated by massive and submassive corals, but moderate (70%) at a site dominated by plate-like corals. Our study shows that the corals of Hong Kong exhibit differential susceptibility to bleaching and ability to recover, therefore it is imperative to establish a long-term monitoring programme to detect the changes in community structure over time.
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Affiliation(s)
- James Y Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yip Hung Yeung
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Chun Kit Kwok
- Agriculture, Fisheries and Conservation Department, Hong Kong, China
| | - Keith Kei
- College of International Education, Hong Kong Baptist University, Hong Kong, China
| | - Put Ang
- Institute of Space and Earth Information Science, The Chinese University of Hong Kong, Hong Kong, China
| | - Leo Lai Chan
- State Key Laboratory of Marine Pollution and Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Chi Chiu Cheang
- Department of Science and Environmental Studies, The Education University of Hong Kong, Hong Kong, China
| | - Wing-Kuen Chow
- Agriculture, Fisheries and Conservation Department, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China.
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10
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Zhang Y, Chen Q, Xie JY, Yeung YH, Xiao B, Liao B, Xu J, Qiu JW. Development of a transcriptomic database for 14 species of scleractinian corals. BMC Genomics 2019; 20:387. [PMID: 31101011 PMCID: PMC6525400 DOI: 10.1186/s12864-019-5744-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 04/29/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Scleractinian corals are important reef builders, but around the world they are under the threat of global climate change as well as local stressors. Molecular resources are critical for understanding a species' stress responses and resilience to the changing environment, but such resources are unavailable for most scleractinian corals, especially those distributed in the South China Sea. We therefore aimed to provide transcriptome resources for 14 common species, including a few structure forming species, in the South China Sea. DESCRIPTION We sequenced the transcriptome of 14 species of scleractinian corals using high-throughput RNA-seq and conducted de novo assembly. For each species, we produced 7.4 to 12.0 gigabases of reads, and assembled them into 271 to 762 thousand contigs with a N50 value of 629 to 1427 bp. These contigs included 66 to 114 thousand unigenes with a predicted open reading frame, and 74.3 to 80.5% of the unigenes were functionally annotated. In the azooxanthelate species Tubastraea coccinea, 41.5% of the unigenes had at least a best-hit sequence from corals. In the other thirteen species, 20.2 to 48.9% of the annotated unigenes had best-hit sequences from corals, and 28.3 to 51.6% from symbiotic algae belonging to the family Symbiodinaceae. With these resources, we developed a transcriptome database (CoralTBase) which features online BLAST and keyword search for unigenes/functional terms through a user friendly Internet interface. SHORT CONCLUSION We developed comprehensive transcriptome resources for 14 species of scleractinian corals and constructed a publicly accessible database ( www.comp.hkbu.edu.hk/~db/CoralTBase ). CoralTBase will facilitate not only functional studies using these corals to understand the molecular basis of stress responses and adaptation, but also comparative transcriptomic studies with other species of corals and more distantly related cnidarians.
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Affiliation(s)
- Yanjie Zhang
- HKBU Institute of Research and Continuing Education, Virtual University Park, Gaoxin South 4th Road, Shenzhen, 518057, China.,Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Qian Chen
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China.,Present address: Google China, Beijing, China
| | - James Y Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yip Hung Yeung
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Baohua Xiao
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, China
| | - Baoling Liao
- Shenzhen Institute of Guangdong Ocean University, Shenzhen, China
| | - Jianliang Xu
- Department of Computer Science, Hong Kong Baptist University, Hong Kong, China.
| | - Jian-Wen Qiu
- HKBU Institute of Research and Continuing Education, Virtual University Park, Gaoxin South 4th Road, Shenzhen, 518057, China. .,Department of Biology, Hong Kong Baptist University, Hong Kong, China.
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11
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Yuan X, Huang H, Zhou W, Guo Y, Yuan T, Liu S. Gene Expression Profiles of Two Coral Species with Varied Resistance to Ocean Acidification. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:151-160. [PMID: 30612219 DOI: 10.1007/s10126-018-9864-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/15/2018] [Indexed: 06/09/2023]
Abstract
Recent studies have indicated that various corals might have different degrees of resistance to elevated CO2 levels. However, the underlying molecular mechanism accounting for these differences is still poorly understood. In this study, RNA-seq data were analyzed to identify differentially expressed genes in two coral species (Acropora austera and Acropora cerealis) in response to high CO2 levels. The calcification rates were higher in high CO2 treatment than the control in A. austera, but was not significantly different in A. cerealis. A KEGG database search revealed that in both coral species, most Ca2+ transporters were present in the calcium signaling pathway, which could be important in the CO2 regulation of coral calcification. The gene expression levels of many CO2 and HCO3- transporters were not affected by elevated CO2. Nevertheless, high CO2 levels did have an effect on the expression of certain Ca2+ transporters. The upregulation of Ca2+ transporters likely explained the higher resistance of A. austera to high CO2 than A. cerealis.
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Affiliation(s)
- Xiangcheng Yuan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China.
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China.
| | - Hui Huang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China.
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China.
- Tropical Marine Biological Research Station in Hainan, Chinese Academy of Sciences, Sanya, 572000, China.
| | - Weihua Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
| | - Yajuan Guo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
- Equipment Public Service Center, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Tao Yuan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
| | - Sheng Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
- Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510000, China
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12
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Xie JY, Lau DCC, Kei K, Yu VPF, Chow WK, Qiu JW. The 2014 summer coral bleaching event in subtropical Hong Kong. MARINE POLLUTION BULLETIN 2017; 124:653-659. [PMID: 28392092 DOI: 10.1016/j.marpolbul.2017.03.061] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 03/27/2017] [Accepted: 03/29/2017] [Indexed: 06/07/2023]
Abstract
We reported a coral bleaching event that occurred in August-September 2014 in Hong Kong waters based on video transect surveys conducted at eight sites. The bleaching affected eight species of corals with different growth forms. Bleaching at seven of the eight study sites was minor, affecting only 0.4-5.2% colonies and 0.8-10.0% coral-covered area. Sharp Island East, however, suffered from a moderate level of bleaching, with 13.1% colonies and 30.1% coral-covered area affected. Examination of the government's environmental monitoring data indicated abnormal water quality conditions preceding and during the bleaching event. Follow-up field surveys of tagged colonies showed that 76% of them had fully recovered, 12% partially recovered, and 12% suffered from mortality. These results indicate that the subtropical corals of Hong Kong are not immune to bleaching, and there is a need to study their responses under climate change scenarios.
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Affiliation(s)
- James Y Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, P.R. China
| | - Dickey C C Lau
- Agriculture, Fisheries and Conservation Department, Hong Kong SAR Government, P.R. China
| | - Keith Kei
- College of International Education, Hong Kong Baptist University, Hong Kong, P.R. China
| | - Vriko P F Yu
- College of International Education, Hong Kong Baptist University, Hong Kong, P.R. China
| | - Wing-Kuen Chow
- Agriculture, Fisheries and Conservation Department, Hong Kong SAR Government, P.R. China.
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, P.R. China.
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Frazier M, Helmkampf M, Bellinger MR, Geib SM, Takabayashi M. De novo metatranscriptome assembly and coral gene expression profile of Montipora capitata with growth anomaly. BMC Genomics 2017; 18:710. [PMID: 28893194 PMCID: PMC5594617 DOI: 10.1186/s12864-017-4090-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/25/2017] [Indexed: 11/10/2022] Open
Abstract
Background Scleractinian corals are a vital component of coral reef ecosystems, and of significant cultural and economic value worldwide. As anthropogenic and natural stressors are contributing to a global decline of coral reefs, understanding coral health is critical to help preserve these ecosystems. Growth anomaly (GA) is a coral disease that has significant negative impacts on coral biology, yet our understanding of its etiology and pathology is lacking. In this study we used RNA-seq along with de novo metatranscriptome assembly and homology assignment to identify coral genes that are expressed in three distinct coral tissue types: tissue from healthy corals (“healthy”), GA lesion tissue from diseased corals (“GA-affected”) and apparently healthy tissue from diseased corals (“GA-unaffected”). We conducted pairwise comparisons of gene expression among these three tissue types to identify genes and pathways that help us to unravel the molecular pathology of this coral disease. Results The quality-filtered de novo-assembled metatranscriptome contained 76,063 genes, of which 13,643 were identified as putative coral genes. Overall gene expression profiles of coral genes revealed high similarity between healthy tissue samples, in contrast to high variance among diseased samples. This indicates GA has a variety of genetic effects at the colony level, including on seemingly healthy (GA-unaffected) tissue. A total of 105 unique coral genes were found differentially expressed among tissue types. Pairwise comparisons revealed the greatest number of differentially expressed genes between healthy and GA-affected tissue (93 genes), followed by healthy and GA-unaffected tissue (33 genes), and GA-affected and -unaffected tissue (7 genes). The putative function of these genes suggests GA is associated with changes in the activity of genes involved in developmental processes and activation of the immune system. Conclusion This is one of the first transcriptome-level studies to investigate coral GA, and the first metatranscriptome assembly for the M. capitata holobiont. The gene expression data, metatranscriptome assembly and methodology developed through this study represent a significant addition to the molecular information available to further our understanding of this coral disease. Electronic supplementary material The online version of this article (10.1186/s12864-017-4090-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Monika Frazier
- Tropical Conservation Biology and Environmental Science, University of Hawai'i at Hilo, 200 West Kāwili Street, Hilo, HI, 96720, USA
| | - Martin Helmkampf
- Tropical Conservation Biology and Environmental Science, University of Hawai'i at Hilo, 200 West Kāwili Street, Hilo, HI, 96720, USA
| | - M Renee Bellinger
- Tropical Conservation Biology and Environmental Science, University of Hawai'i at Hilo, 200 West Kāwili Street, Hilo, HI, 96720, USA
| | - Scott M Geib
- United States Department of Agriculture, Agriculture Research Service, Daniel K Inouye U.S. Pacific Basin Agricultural Research Center, 64 Nowelo St, Hilo, HI, 96720, USA
| | - Misaki Takabayashi
- Tropical Conservation Biology and Environmental Science, University of Hawai'i at Hilo, 200 West Kāwili Street, Hilo, HI, 96720, USA. .,Marine Science Department, University of Hawai'i at Hilo, 200 West Kāwili Street, Hilo, HI, 96720, USA.
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