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Bhattacharya D, Stephens TG, Chille EE, Benites LF, Chan CX. Facultative lifestyle drives diversity of coral algal symbionts. Trends Ecol Evol 2024; 39:239-247. [PMID: 37953106 DOI: 10.1016/j.tree.2023.10.005] [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: 07/11/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 11/14/2023]
Abstract
The photosynthetic symbionts of corals sustain biodiverse reefs in nutrient-poor, tropical waters. Recent genomic data illuminate the evolution of coral symbionts under genome size constraints and suggest that retention of the facultative lifestyle, widespread among these algae, confers a selective advantage when compared with a strict symbiotic existence. We posit that the coral symbiosis is analogous to a 'bioreactor' that selects winner genotypes and allows them to rise to high numbers in a sheltered habitat prior to release by the coral host. Our observations lead to a novel hypothesis, the 'stepping-stone model', which predicts that local adaptation under both the symbiotic and free-living stages, in a stepwise fashion, accelerates coral alga diversity and the origin of endemic strains and species.
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Affiliation(s)
- Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA.
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Erin E Chille
- Ecology and Evolution Graduate Program, Rutgers University, New Brunswick, NJ 08901, USA
| | - L Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, QLD, Australia.
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2
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González-Pech RA, Li VY, Garcia V, Boville E, Mammone M, Kitano H, Ritchie KB, Medina M. The Evolution, Assembly, and Dynamics of Marine Holobionts. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:443-466. [PMID: 37552896 DOI: 10.1146/annurev-marine-022123-104345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
The holobiont concept (i.e., multiple living beings in close symbiosis with one another and functioning as a unit) is revolutionizing our understanding of biology, especially in marine systems. The earliest marine holobiont was likely a syntrophic partnership of at least two prokaryotic members. Since then, symbiosis has enabled marine organisms to conquer all ocean habitats through the formation of holobionts with a wide spectrum of complexities. However, most scientific inquiries have focused on isolated organisms and their adaptations to specific environments. In this review, we attempt to illustrate why a holobiont perspective-specifically, the study of how numerous organisms form a discrete ecological unit through symbiosis-will be a more impactful strategy to advance our understanding of the ecology and evolution of marine life. We argue that this approach is instrumental in addressing the threats to marine biodiversity posed by the current global environmental crisis.
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Affiliation(s)
- Raúl A González-Pech
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Vivian Y Li
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Vanessa Garcia
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Elizabeth Boville
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Marta Mammone
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | | | - Kim B Ritchie
- Department of Natural Sciences, University of South Carolina, Beaufort, South Carolina, USA;
| | - Mónica Medina
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
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3
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Shah S, Dougan KE, Chen Y, Lo R, Laird G, Fortuin MDA, Rai SK, Murigneux V, Bellantuono AJ, Rodriguez-Lanetty M, Bhattacharya D, Chan CX. Massive genome reduction predates the divergence of Symbiodiniaceae dinoflagellates. THE ISME JOURNAL 2024; 18:wrae059. [PMID: 38655774 PMCID: PMC11114475 DOI: 10.1093/ismejo/wrae059] [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: 09/26/2023] [Revised: 01/22/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
Abstract
Dinoflagellates in the family Symbiodiniaceae are taxonomically diverse, predominantly symbiotic lineages that are well-known for their association with corals. The ancestor of these taxa is believed to have been free-living. The establishment of symbiosis (i.e. symbiogenesis) is hypothesized to have occurred multiple times during Symbiodiniaceae evolution, but its impact on genome evolution of these taxa is largely unknown. Among Symbiodiniaceae, the genus Effrenium is a free-living lineage that is phylogenetically positioned between two robustly supported groups of genera within which symbiotic taxa have emerged. The apparent lack of symbiogenesis in Effrenium suggests that the ancestral features of Symbiodiniaceae may have been retained in this lineage. Here, we present de novo assembled genomes (1.2-1.9 Gbp in size) and transcriptome data from three isolates of Effrenium voratum and conduct a comparative analysis that includes 16 Symbiodiniaceae taxa and the other dinoflagellates. Surprisingly, we find that genome reduction, which is often associated with a symbiotic lifestyle, predates the origin of Symbiodiniaceae. The free-living lifestyle distinguishes Effrenium from symbiotic Symbiodiniaceae vis-à-vis their longer introns, more-extensive mRNA editing, fewer (~30%) lineage-specific gene sets, and lower (~10%) level of pseudogenization. These results demonstrate how genome reduction and the adaptation to distinct lifestyles intersect to drive diversification and genome evolution of Symbiodiniaceae.
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Affiliation(s)
- Sarah Shah
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Katherine E Dougan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Yibi Chen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rosalyn Lo
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Gemma Laird
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Michael D A Fortuin
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Subash K Rai
- Genome Innovation Hub, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Valentine Murigneux
- Genome Innovation Hub, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Anthony J Bellantuono
- Biomolecular Science Institute, Department of Biological Sciences, Florida International University, Miami, FL 33099, United States
| | - Mauricio Rodriguez-Lanetty
- Biomolecular Science Institute, Department of Biological Sciences, Florida International University, Miami, FL 33099, United States
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, United States
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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4
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Ishida H, John U, Murray SA, Bhattacharya D, Chan CX. Developing model systems for dinoflagellates in the post-genomic era. JOURNAL OF PHYCOLOGY 2023; 59:799-808. [PMID: 37657822 DOI: 10.1111/jpy.13386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 09/03/2023]
Abstract
Dinoflagellates are a diverse group of eukaryotic microbes that are ubiquitous in aquatic environments. Largely photosynthetic, they encompass symbiotic, parasitic, and free-living lineages with a broad spectrum of trophism. Many free-living taxa can produce bioactive secondary metabolites such as biotoxins, some of which cause harmful algal blooms. In contrast, most symbiotic species are crucial for sustaining coral reef health. The year 2023 marked a decade since the first genome data of dinoflagellates became available. The growing genome-scale resources for these taxa are highlighting their remarkable evolutionary and genomic complexities. Here, we discuss the prospect of developing dinoflagellate models using the criteria of accessibility, tractability, resources, research support, and promise. Moving forward in the post-genomic era, we argue for the development of fit-to-purpose models that tailor to specific biological contexts, and that a one-size-fits-all model is inadequate for encapsulating the complex biology, ecology, and evolutionary history of dinoflagellates.
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Affiliation(s)
- Hisatake Ishida
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia
| | - Uwe John
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Shauna A Murray
- School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Cheong Xin Chan
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia
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5
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Shah S, Dougan KE, Chen Y, Bhattacharya D, Chan CX. Gene duplication is the primary driver of intraspecific genomic divergence in coral algal symbionts. Open Biol 2023; 13:230182. [PMID: 37751888 PMCID: PMC10522408 DOI: 10.1098/rsob.230182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/21/2023] [Indexed: 09/28/2023] Open
Abstract
Dinoflagellates in the order Suessiales include the family Symbiodiniaceae, which have essential roles as photosymbionts in corals, and their cold-adapted sister group, Polarella glacialis. These diverse taxa exhibit extensive genomic divergence, although their genomes are relatively small (haploid size < 3 Gbp) when compared with most other free-living dinoflagellates. Different strains of Symbiodiniaceae form symbiosis with distinct hosts and exhibit different regimes of gene expression, but intraspecific whole-genome divergence is poorly understood. Focusing on three Symbiodiniaceae species (the free-living Effrenium voratum and the symbiotic Symbiodinium microadriaticum and Durusdinium trenchii) and the free-living outgroup P. glacialis, for which whole-genome data from multiple isolates are available, we assessed intraspecific genomic divergence with respect to sequence and structure. Our analysis, based on alignment and alignment-free methods, revealed a greater extent of intraspecific sequence divergence in Symbiodiniaceae than in P. glacialis. Our results underscore the role of gene duplication in generating functional innovation, with a greater prevalence of tandemly duplicated single-exon genes observed in the genomes of free-living species than in symbionts. These results demonstrate the remarkable intraspecific genomic divergence in dinoflagellates under the constraint of reduced genome sizes, shaped by genetic duplications and symbiogenesis events during the diversification of Symbiodiniaceae.
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Affiliation(s)
- Sarah Shah
- School of Chemistry and Molecular Biosciences, and Australian Centre for Ecogenomics, The University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Katherine E. Dougan
- School of Chemistry and Molecular Biosciences, and Australian Centre for Ecogenomics, The University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Yibi Chen
- School of Chemistry and Molecular Biosciences, and Australian Centre for Ecogenomics, The University of Queensland, Brisbane, 4072 Queensland, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Cheong Xin Chan
- School of Chemistry and Molecular Biosciences, and Australian Centre for Ecogenomics, The University of Queensland, Brisbane, 4072 Queensland, Australia
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6
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McCauley M, Goulet TL, Jackson CR, Loesgen S. Systematic review of cnidarian microbiomes reveals insights into the structure, specificity, and fidelity of marine associations. Nat Commun 2023; 14:4899. [PMID: 37580316 PMCID: PMC10425419 DOI: 10.1038/s41467-023-39876-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 06/30/2023] [Indexed: 08/16/2023] Open
Abstract
Microorganisms play essential roles in the health and resilience of cnidarians. Understanding the factors influencing cnidarian microbiomes requires cross study comparisons, yet the plethora of protocols used hampers dataset integration. We unify 16S rRNA gene sequences from cnidarian microbiome studies under a single analysis pipeline. We reprocess 12,010 cnidarian microbiome samples from 186 studies, alongside 3,388 poriferan, 370 seawater samples, and 245 cultured Symbiodiniaceae, unifying ~6.5 billion sequence reads. Samples are partitioned by hypervariable region and sequencing platform to reduce sequencing variability. This systematic review uncovers an incredible diversity of 86 archaeal and bacterial phyla associated with Cnidaria, and highlights key bacteria hosted across host sub-phylum, depth, and microhabitat. Shallow (< 30 m) water Alcyonacea and Actinaria are characterized by highly shared and relatively abundant microbial communities, unlike Scleractinia and most deeper cnidarians. Utilizing the V4 region, we find that cnidarian microbial composition, richness, diversity, and structure are primarily influenced by host phylogeny, sampling depth, and ocean body, followed by microhabitat and sampling date. We identify host and geographical generalist and specific Endozoicomonas clades within Cnidaria and Porifera. This systematic review forms a framework for understanding factors governing cnidarian microbiomes and creates a baseline for assessing stress associated dysbiosis.
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Affiliation(s)
- M McCauley
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA.
- Department of Biology, University of Mississippi, University, MS, USA.
- U.S. Geological Survey, Wetland and Aquatic Research Centre, Gainesville, FL, USA.
| | - T L Goulet
- Department of Biology, University of Mississippi, University, MS, USA
| | - C R Jackson
- Department of Biology, University of Mississippi, University, MS, USA
| | - S Loesgen
- Department of Chemistry, Whitney Laboratory for Marine Bioscience, University of Florida, St. Augustine, FL, USA
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7
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Hernández Elizárraga VH, Olguín-López N, Hernández-Matehuala R, Caballero-Pérez J, Ibarra-Alvarado C, Rojas-Molina A. Transcriptomic differences between bleached and unbleached hydrozoan Millepora complanata following the 2015-2016 ENSO in the Mexican Caribbean. PeerJ 2023; 11:e14626. [PMID: 36691486 PMCID: PMC9864129 DOI: 10.7717/peerj.14626] [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: 04/27/2022] [Accepted: 12/02/2022] [Indexed: 01/19/2023] Open
Abstract
The 2015-2016 El Niño-southern oscillation or "ENSO" caused many M. complanata colonies that live in the Mexican Caribbean to experience extensive bleaching. The purpose of this work was to analyze the effect of bleaching on the cellular response of M. complanata, employing a transcriptomic approach with RNA-seq. As expected, bleached specimens contained a significantly lower chlorophyll content than unbleached hydrocorals. The presence of algae of the genera Durusdinium and Cladocopium was only found in tissues of unbleached M. complanata, which could be associated to the greater resistance that these colonies exhibited during bleaching. We found that 299 genes were differentially expressed in M. complanata bleached colonies following the 2015-2016 ENSO in the Mexican Caribbean. The differential expression analysis of bleached M. complanata specimens evidenced enriched terms for functional categories, such as ribosome, RNA polymerase and basal transcription factors, chaperone, oxidoreductase, among others. Our results suggest that the heat-shock response mechanisms displayed by M. complanata include: an up-regulation of endogenous antioxidant defenses; a higher expression of heat stress response genes; up-regulation of transcription-related genes, higher expression of genes associated to transport processes, inter alia. This study constitutes the first differential gene expression analysis of the molecular response of a reef-forming hydrozoan during bleaching.
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Affiliation(s)
| | - Norma Olguín-López
- Posgrado en Ciencias Químico Biológicas, Facultad de Química, Universidad Autónoma de Querétaro, Querétaro, México
| | - Rosalina Hernández-Matehuala
- Posgrado en Ciencias Químico Biológicas, Facultad de Química, Universidad Autónoma de Querétaro, Querétaro, México
| | | | - César Ibarra-Alvarado
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Querétaro, México
| | - Alejandra Rojas-Molina
- Laboratorio de Investigación Química y Farmacológica de Productos Naturales, Facultad de Química, Universidad Autónoma de Querétaro, Querétaro, México
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8
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Davies SW, Gamache MH, Howe-Kerr LI, Kriefall NG, Baker AC, Banaszak AT, Bay LK, Bellantuono AJ, Bhattacharya D, Chan CX, Claar DC, Coffroth MA, Cunning R, Davy SK, del Campo J, Díaz-Almeyda EM, Frommlet JC, Fuess LE, González-Pech RA, Goulet TL, Hoadley KD, Howells EJ, Hume BCC, Kemp DW, Kenkel CD, Kitchen SA, LaJeunesse TC, Lin S, McIlroy SE, McMinds R, Nitschke MR, Oakley CA, Peixoto RS, Prada C, Putnam HM, Quigley K, Reich HG, Reimer JD, Rodriguez-Lanetty M, Rosales SM, Saad OS, Sampayo EM, Santos SR, Shoguchi E, Smith EG, Stat M, Stephens TG, Strader ME, Suggett DJ, Swain TD, Tran C, Traylor-Knowles N, Voolstra CR, Warner ME, Weis VM, Wright RM, Xiang T, Yamashita H, Ziegler M, Correa AMS, Parkinson JE. Building consensus around the assessment and interpretation of Symbiodiniaceae diversity. PeerJ 2023; 11:e15023. [PMID: 37151292 PMCID: PMC10162043 DOI: 10.7717/peerj.15023] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 02/17/2023] [Indexed: 05/09/2023] Open
Abstract
Within microeukaryotes, genetic variation and functional variation sometimes accumulate more quickly than morphological differences. To understand the evolutionary history and ecology of such lineages, it is key to examine diversity at multiple levels of organization. In the dinoflagellate family Symbiodiniaceae, which can form endosymbioses with cnidarians (e.g., corals, octocorals, sea anemones, jellyfish), other marine invertebrates (e.g., sponges, molluscs, flatworms), and protists (e.g., foraminifera), molecular data have been used extensively over the past three decades to describe phenotypes and to make evolutionary and ecological inferences. Despite advances in Symbiodiniaceae genomics, a lack of consensus among researchers with respect to interpreting genetic data has slowed progress in the field and acted as a barrier to reconciling observations. Here, we identify key challenges regarding the assessment and interpretation of Symbiodiniaceae genetic diversity across three levels: species, populations, and communities. We summarize areas of agreement and highlight techniques and approaches that are broadly accepted. In areas where debate remains, we identify unresolved issues and discuss technologies and approaches that can help to fill knowledge gaps related to genetic and phenotypic diversity. We also discuss ways to stimulate progress, in particular by fostering a more inclusive and collaborative research community. We hope that this perspective will inspire and accelerate coral reef science by serving as a resource to those designing experiments, publishing research, and applying for funding related to Symbiodiniaceae and their symbiotic partnerships.
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Affiliation(s)
- Sarah W. Davies
- Department of Biology, Boston University, Boston, MA, United States
| | - Matthew H. Gamache
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
| | | | | | - Andrew C. Baker
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | - Anastazia T. Banaszak
- Unidad Académica de Sistemas Arrecifales, Universidad Nacional Autónoma de México, Puerto Morelos, Mexico
| | - Line Kolind Bay
- Australian Institute of Marine Science, Townsville, Australia
| | - Anthony J. Bellantuono
- Department of Biological Sciences, Florida International University, Miami, FL, United States
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Danielle C. Claar
- Nearshore Habitat Program, Washington State Department of Natural Resources, Olympia, WA, USA
| | | | - Ross Cunning
- Daniel P. Haerther Center for Conservation and Research, John G. Shedd Aquarium, Chicago, IL, United States
| | - Simon K. Davy
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Javier del Campo
- Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | | | - Jörg C. Frommlet
- Centre for Environmental and Marine Studies, Department of Biology, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Lauren E. Fuess
- Department of Biology, Texas State University, San Marcos, TX, United States
| | - Raúl A. González-Pech
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
- Department of Biology, Pennsylvania State University, State College, PA, United States
| | - Tamar L. Goulet
- Department of Biology, University of Mississippi, University, MS, United States
| | - Kenneth D. Hoadley
- Department of Biological Sciences, University of Alabama—Tuscaloosa, Tuscaloosa, AL, United States
| | - Emily J. Howells
- National Marine Science Centre, Faculty of Science and Engineering, Southern Cross University, Coffs Harbour, NSW, Australia
| | | | - Dustin W. Kemp
- Department of Biology, University of Alabama—Birmingham, Birmingham, Al, United States
| | - Carly D. Kenkel
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
| | - Sheila A. Kitchen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Todd C. LaJeunesse
- Department of Biology, Pennsylvania State University, University Park, PA, United States
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Mansfield, CT, United States
| | - Shelby E. McIlroy
- Swire Institute of Marine Science, School of Biological Sciences, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Ryan McMinds
- Center for Global Health and Infectious Disease Research, University of South Florida, Tampa, FL, United States
| | | | - Clinton A. Oakley
- School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Raquel S. Peixoto
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Carlos Prada
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | | | - Hannah G. Reich
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, United States
| | - James Davis Reimer
- Department of Biology, Chemistry and Marine Sciences, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | | | - Stephanie M. Rosales
- The Cooperative Institute For Marine and Atmospheric Studies, Miami, FL, United States
| | - Osama S. Saad
- Department of Biological Oceanography, Red Sea University, Port-Sudan, Sudan
| | - Eugenia M. Sampayo
- School of Biological Sciences, The University of Queensland, St. Lucia, QLD, Australia
| | - Scott R. Santos
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, United States
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Edward G. Smith
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Michael Stat
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW, Australia
| | - Timothy G. Stephens
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Marie E. Strader
- Department of Biology, Texas A&M University, College Station, TX, United States
| | - David J. Suggett
- Red Sea Research Center (RSRC), Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, Australia
| | - Timothy D. Swain
- Department of Marine and Environmental Science, Nova Southeastern University, Dania Beach, FL, United States
| | - Cawa Tran
- Department of Biology, University of San Diego, San Diego, CA, United States
| | - Nikki Traylor-Knowles
- Rosenstiel School of Marine, Atmospheric, and Earth Science, University of Miami, Miami, FL, United States
| | | | - Mark E. Warner
- School of Marine Science and Policy, University of Delaware, Lewes, DE, United States
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Rachel M. Wright
- Department of Biological Sciences, Southern Methodist University, Dallas, TX, United States
| | - Tingting Xiang
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Hiroshi Yamashita
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Ishigaki, Okinawa, Japan
| | - Maren Ziegler
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen (Germany), Giessen, Germany
| | | | - John Everett Parkinson
- Department of Integrative Biology, University of South Florida, Tampa, FL, United States
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9
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Chen Y, Shah S, Dougan KE, van Oppen MJH, Bhattacharya D, Chan CX. Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes. Microorganisms 2022; 10:microorganisms10081662. [PMID: 36014080 PMCID: PMC9412976 DOI: 10.3390/microorganisms10081662] [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: 07/01/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Dinoflagellates of the family Symbiodiniaceae are crucial photosymbionts in corals and other marine organisms. Of these, Cladocopium goreaui is one of the most dominant symbiont species in the Indo-Pacific. Here, we present an improved genome assembly of C. goreaui combining new long-read sequence data with previously generated short-read data. Incorporating new full-length transcripts to guide gene prediction, the C. goreaui genome (1.2 Gb) exhibits a high extent of completeness (82.4% based on BUSCO protein recovery) and better resolution of repetitive sequence regions; 45,322 gene models were predicted, and 327 putative, topologically associated domains of the chromosomes were identified. Comparison with other Symbiodiniaceae genomes revealed a prevalence of repeats and duplicated genes in C. goreaui, and lineage-specific genes indicating functional innovation. Incorporating 2,841,408 protein sequences from 96 taxonomically diverse eukaryotes and representative prokaryotes in a phylogenomic approach, we assessed the evolutionary history of C. goreaui genes. Of the 5246 phylogenetic trees inferred from homologous protein sets containing two or more phyla, 35–36% have putatively originated via horizontal gene transfer (HGT), predominantly (19–23%) via an ancestral Archaeplastida lineage implicated in the endosymbiotic origin of plastids: 10–11% are of green algal origin, including genes encoding photosynthetic functions. Our results demonstrate the utility of long-read sequence data in resolving structural features of a dinoflagellate genome, and highlight how genetic transfer has shaped genome evolution of a facultative symbiont, and more broadly of dinoflagellates.
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Affiliation(s)
- Yibi Chen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sarah Shah
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Katherine E. Dougan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Madeleine J. H. van Oppen
- School of Bioscience, The University of Melbourne, Parkville, VIC 3010, Australia
- Australian Institute of Marine Science, Townsville, QLD 4810, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
- Correspondence:
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10
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Lo R, Dougan KE, Chen Y, Shah S, Bhattacharya D, Chan CX. Alignment-Free Analysis of Whole-Genome Sequences From Symbiodiniaceae Reveals Different Phylogenetic Signals in Distinct Regions. FRONTIERS IN PLANT SCIENCE 2022; 13:815714. [PMID: 35557718 PMCID: PMC9087856 DOI: 10.3389/fpls.2022.815714] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/04/2022] [Indexed: 05/24/2023]
Abstract
Dinoflagellates of the family Symbiodiniaceae are predominantly essential symbionts of corals and other marine organisms. Recent research reveals extensive genome sequence divergence among Symbiodiniaceae taxa and high phylogenetic diversity hidden behind subtly different cell morphologies. Using an alignment-free phylogenetic approach based on sub-sequences of fixed length k (i.e. k-mers), we assessed the phylogenetic signal among whole-genome sequences from 16 Symbiodiniaceae taxa (including the genera of Symbiodinium, Breviolum, Cladocopium, Durusdinium and Fugacium) and two strains of Polarella glacialis as outgroup. Based on phylogenetic trees inferred from k-mers in distinct genomic regions (i.e. repeat-masked genome sequences, protein-coding sequences, introns and repeats) and in protein sequences, the phylogenetic signal associated with protein-coding DNA and the encoded amino acids is largely consistent with the Symbiodiniaceae phylogeny based on established markers, such as large subunit rRNA. The other genome sequences (introns and repeats) exhibit distinct phylogenetic signals, supporting the expected differential evolutionary pressure acting on these regions. Our analysis of conserved core k-mers revealed the prevalence of conserved k-mers (>95% core 23-mers among all 18 genomes) in annotated repeats and non-genic regions of the genomes. We observed 180 distinct repeat types that are significantly enriched in genomes of the symbiotic versus free-living Symbiodinium taxa, suggesting an enhanced activity of transposable elements linked to the symbiotic lifestyle. We provide evidence that representation of alignment-free phylogenies as dynamic networks enhances the ability to generate new hypotheses about genome evolution in Symbiodiniaceae. These results demonstrate the potential of alignment-free phylogenetic methods as a scalable approach for inferring comprehensive, unbiased whole-genome phylogenies of dinoflagellates and more broadly of microbial eukaryotes.
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Affiliation(s)
- Rosalyn Lo
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Katherine E. Dougan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Yibi Chen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Sarah Shah
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, United States
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD, Australia
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11
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Zaheri B, Veilleux-Trinh C, Morse D. A DINOFLAGELLATE TBP-LIKE FACTOR ACTIVATES TRANSCRIPTION FROM A TTTT-BOX IN YEAST. JOURNAL OF PHYCOLOGY 2022; 58:343-346. [PMID: 35146760 DOI: 10.1111/jpy.13243] [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: 11/16/2021] [Revised: 01/13/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Dinoflagellates do not have a typical TATA-binding protein (TBP), a subunit of the general transcription factor TFIID complex. Instead, they have a TBP-like factor (TLF) that has been shown to bind TTTT instead of TATA in vitro. The ability of TLF to act as a functional replacement of TBP in vivo has never been assessed, however. Here, we show that a dinoflagellate TLF can drive expression of a reporter gene controlled by a budding yeast promoter whose TATA box was mutated to TTTT. TLF is thus able to bind and activate the yeast RNA polymerase and appear to function normally in the TFIID complex.
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Affiliation(s)
- Bahareh Zaheri
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke est, Montréal, H1X 2B2, Canada
| | - Charlotte Veilleux-Trinh
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke est, Montréal, H1X 2B2, Canada
| | - David Morse
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, 4101 Sherbrooke est, Montréal, H1X 2B2, Canada
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12
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Dougan KE, González-Pech RA, Stephens TG, Shah S, Chen Y, Ragan MA, Bhattacharya D, Chan CX. Genome-powered classification of microbial eukaryotes: focus on coral algal symbionts. Trends Microbiol 2022; 30:831-840. [DOI: 10.1016/j.tim.2022.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/20/2022] [Accepted: 02/01/2022] [Indexed: 12/20/2022]
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13
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Shoguchi E. Gene clusters for biosynthesis of mycosporine-like amino acids in dinoflagellate nuclear genomes: Possible recent horizontal gene transfer between species of Symbiodiniaceae (Dinophyceae). JOURNAL OF PHYCOLOGY 2022; 58:1-11. [PMID: 34699617 PMCID: PMC9298759 DOI: 10.1111/jpy.13219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 10/01/2021] [Accepted: 10/12/2021] [Indexed: 05/12/2023]
Abstract
Global warming increases the temperature of the ocean surface, which can disrupt dinoflagellate-coral symbioses and result in coral bleaching. Photosynthetic dinoflagellates of the family Symbiodiniaceae include bleaching-tolerant and bleaching-sensitive coral symbionts. Therefore, understanding the molecular mechanisms for changing symbiont diversity is potentially useful to assist recovery of coral holobionts (corals and their associated microbes, including multiple species of Symbiodiniaceae), although sexual reproduction has not been observed in the Symbiodiniaceae. Recent molecular phylogenetic analyses estimate that the Symbiodiniaceae appeared 160 million years ago and diversified into 15 groups, five genera of which now have available draft genomes (i.e., Symbiodinium, Durusdinium, Breviolum, Fugacium, and Cladocopium). Comparative genomic analyses have suggested that crown groups have fewer gene families than early-diverging groups, although many genes that were probably acquired via gene duplications and horizontal gene transfers (HGTs) have been found in each decoded genome. Because UV stress is likely a contributor to coral bleaching, and because the highly conserved gene cluster for mycosporine-like amino acid (MAA) biosynthesis has been found in thermal-tolerant symbiont genomes, I reviewed genomic features of the Symbiodiniaceae, focusing on possible acquisition of a biosynthetic gene cluster for MAAs, which absorb UV radiation. On the basis of highly conserved noncoding sequences, I hypothesized that HGTs have occurred among members of the Symbiodiniaceae and have contributed to the diversification of Symbiodiniaceae-host relationships. Finally, I proposed that bleaching tolerance may be strengthened by multiple MAAs from both symbiotic dinoflagellates and corals.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaOkinawa904‐0495Japan
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14
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Zhang K, Shen Z, Yang W, Guo J, Yan Z, Li J, Lin J, Cao X, Tang J, Liu Z, Zhou Z, Lin S. Unraveling the metabolic effects of benzophenone-3 on the endosymbiotic dinoflagellate Cladocopium goreaui. Front Microbiol 2022; 13:1116975. [PMID: 36938131 PMCID: PMC10016356 DOI: 10.3389/fmicb.2022.1116975] [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: 12/06/2022] [Accepted: 12/28/2022] [Indexed: 03/05/2023] Open
Abstract
As a well-known pseudo-persistent environmental pollutant, oxybenzone (BP-3) and its related organic ultraviolet (UV) filters have been verified to directly contribute to the increasing mortality rate of coral reefs. Previous studies have revealed the potential role of symbiotic Symbiodiniaceae in protecting corals from the toxic effects of UV filters. However, the detailed protection mechanism(s) have not been explained. Here, the impacts of BP-3 on the symbiotic Symbiodiniaceae Cladocopium goreaui were explored. C. goreaui cells exhibited distinct cell growth at different BP-3 doses, with increasing growth at the lower concentration (2 mg L-1) and rapid death at a higher concentration (20 mg L-1). Furthermore, C. goreaui cells showed a significant BP-3 uptake at the lower BP-3 concentration. BP-3 absorbing cells exhibited elevated photosynthetic efficiency, and decreased cellular carbon and nitrogen contents. Besides, the derivatives of BP-3 and aromatic amino acid metabolism highly responded to BP-3 absorption and biodegradation. Our physiological and metabolic results reveal that the symbiotic Symbiodiniaceae could resist the toxicity of a range of BP-3 through promoting cell division, photosynthesis, and reprogramming amino acid metabolism. This study provides novel insights into the influences of organic UV filters to coral reef ecosystems, which urgently needs increasing attention and management.
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Affiliation(s)
- Kaidian Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan, Hainan University, Haikou, China
| | - Zhen Shen
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan, Hainan University, Haikou, China
| | - Weilu Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan, Hainan University, Haikou, China
| | - Jianing Guo
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan, Hainan University, Haikou, China
| | - Zhicong Yan
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan, Hainan University, Haikou, China
| | - Jiashun Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jiamin Lin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan, Hainan University, Haikou, China
| | - Xiaocong Cao
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan, Hainan University, Haikou, China
| | - Jia Tang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan, Hainan University, Haikou, China
| | - Zhaoqun Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan, Hainan University, Haikou, China
| | - Zhi Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan, Hainan University, Haikou, China
- *Correspondence: Zhi Zhou,
| | - Senjie Lin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
- Key Laboratory of Tropical Hydrobiology and Biotechnology of Hainan, Hainan University, Haikou, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, China
- Department of Marine Sciences, University of Connecticut, Groton, CT, United States
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15
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Scucchia F, Malik A, Putnam HM, Mass T. Genetic and physiological traits conferring tolerance to ocean acidification in mesophotic corals. GLOBAL CHANGE BIOLOGY 2021; 27:5276-5294. [PMID: 34310005 DOI: 10.1111/gcb.15812] [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: 05/08/2021] [Revised: 07/15/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
The integrity of coral reefs worldwide is jeopardized by ocean acidification (OA). Most studies conducted so far have focused on the vulnerability to OA of corals inhabiting shallow reefs while nothing is currently known about the response of mesophotic scleractinian corals. In this study, we assessed the susceptibility to OA of corals, together with their algal partners, inhabiting a wide depth range. We exposed fragments of the depth generalist coral Stylophora pistillata collected from either 5 or 45 m to simulated future OA conditions, and assessed key molecular, physiological and photosynthetic processes influenced by the lowered pH. Our comparative analysis reveals that mesophotic and shallow S. pistillata corals are genetically distinct and possess different symbiont types. Under the exposure to acidification conditions, we observed a 50% drop of metabolic rate in shallow corals, whereas mesophotic corals were able to maintain unaltered metabolic rates. Overall, our gene expression and physiological analyses show that mesophotic corals possess a greater capacity to cope with the effects of OA compared to their shallow counterparts. Such capability stems from physiological characteristics (i.e., biomass and lipids energetics), a greater capacity to regulate cellular acid-base parameters, and a higher baseline expression of cell adhesion and extracellular matrix genes. Moreover, our gene expression analysis suggests that the enhanced symbiont photochemical efficiency under high pCO2 levels could prevent acidosis of the host cells and it could support a greater translocation of photosynthates, increasing the energy pool available to the host. With this work, we provide new insights on the response to OA of corals living at mesophotic depths. Our investigation discloses key genetic and physiological traits underlying the potential for corals to cope with future OA conditions.
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Affiliation(s)
- Federica Scucchia
- Department of Marine Biology, Leon H. Charney school of Marine Sciences, University of Haifa, Haifa, Israel
- The Interuniversity Institute of Marine Sciences, Eilat, Israel
| | - Assaf Malik
- Department of Marine Biology, Leon H. Charney school of Marine Sciences, University of Haifa, Haifa, Israel
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - 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
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16
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Zhou Z, Zhang K, Wang L, Su Y, Wang J, Song T, Yang X, Tang J, Lin S. Nitrogen availability improves the physiological resilience of coral endosymbiont Cladocopium goreaui to high temperature. JOURNAL OF PHYCOLOGY 2021; 57:1187-1198. [PMID: 33650119 DOI: 10.1111/jpy.13156] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/15/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
The physiological response of symbiotic Symbiodiniaceae to high temperature is believed to result in coral bleaching. However, the potential effect of nitrogen availability on heat acclimatization of symbiotic Symbiodiniaceae is still unclear. In this study, physiological responses of Symbiodiniaceae Cladocopium goreaui to temperature and nitrogen nutrient stress conditions were investigated. Nitrogen deficiency caused significant declines in cell concentration and chlorophyll content per cell, but significant increases in nitric oxide synthase activity, caspase3 activation level, and cellular carbon content of C. goreaui at normal temperature. Algal cells under high temperature and nitrogen deficiency showed significant rises in Fv/Fm, catalase activity, and caspase3 activation level, but no significant changes in cell yield, cell size, chlorophyll content, superoxide dismutase, nitric oxide synthase activity, and cellular contents of nitrogen and carbon, in comparison with those under normal temperature and nitrogen deficiency. Growth, chlorophyll, and nitrogen contents of algal cells under the high temperature and nitrogen-replete conditions were significantly higher than those under high temperature or nitrogen deficiency alone, whereas nitric oxide synthase activity, superoxide dismutase activity, catalase activity, carbon content, and caspase3 activation level exhibited opposite trends of variation. Transcriptomic and network analyses revealed ion transport and metabolic processes mainly involved in regulating these physiological activities under different temperature and nitrogen nutrient. The totality of results shows that high temperature activates stress responses, induces antioxidant capacity of apoptosis, and limits the growth rate of C. goreaui. Adequate nitrogen nutrient can improve the resilience of this Symbiodiniaceae against heat stress through repressed apoptosis, promoted ion transport, and optimized metabolism.
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Affiliation(s)
- Zhi Zhou
- Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan, 570228, China
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
| | - Kaidian Zhang
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, 361102, China
| | - Lingui Wang
- Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan, 570228, China
| | - Yilu Su
- Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan, 570228, China
| | - Jierui Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, 361102, China
| | - Tingting Song
- Hainan Aquaculture Breeding Engineering Research Center, College of Marine Sciences, Hainan University, Haikou, Hainan, 570228, China
| | - Xiaohong Yang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, 361102, China
| | - Jia Tang
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, 264003, China
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, 361102, China
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17
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Reich HG, Kitchen SA, Stankiewicz KH, Devlin-Durante M, Fogarty ND, Baums IB. Genomic variation of an endosymbiotic dinoflagellate (Symbiodinium 'fitti') among closely related coral hosts. Mol Ecol 2021; 30:3500-3514. [PMID: 33964051 DOI: 10.1111/mec.15952] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 12/20/2022]
Abstract
Mutualisms where hosts are coupled metabolically to their symbionts often exhibit high partner fidelity. Most reef-building coral species form obligate symbioses with a specific species of photosymbionts, dinoflagellates in the family Symbiodiniaceae, despite needing to acquire symbionts early in their development from environmental sources. Three Caribbean acroporids (Acropora palmata, A. cervicornis and their F1 hybrid) are sympatric across much of their range, but often occupy different depth and light habitats. Throughout this range, both species and their hybrid associate with the endosymbiotic dinoflagellate Symbiodinium 'fitti'. Because light (and therefore depth) influences the physiology of dinoflagellates, we investigated whether S. 'fitti' populations from each host taxon were differentiated genetically. Single nucleotide polymorphisms (SNPs) among S. 'fitti' strains were identified by aligning shallow metagenomic sequences of acroporid colonies sampled from across the Caribbean to a ~600-Mb draft assembly of the S. 'fitti' genome (from the CFL14120 A. cervicornis metagenome). Phylogenomic and multivariate analyses revealed that genomic variation among S. 'fitti' strains partitioned to each host taxon rather than by biogeographical origin. This is particularly noteworthy because the hybrid has a sparse fossil record and may be of relatively recent origin. A subset (37.6%) of the SNPs putatively under selection were nonsynonymous mutations predicted to alter protein efficiency. Differences in genomic variation of S. 'fitti' strains from each host taxon may reflect the unique selection pressures created by the microenvironments associated with each host. The nonrandom sorting among S. 'fitti' strains to different hosts could be the basis for lineage diversification via disruptive selection, leading to ecological specialization and ultimately speciation.
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Affiliation(s)
- Hannah G Reich
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sheila A Kitchen
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | | | | | - Nicole D Fogarty
- Department of Biology and Marine Biology, Center for Marine Science, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Iliana B Baums
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
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18
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González-Pech RA, Stephens TG, Chen Y, Mohamed AR, Cheng Y, Shah S, Dougan KE, Fortuin MDA, Lagorce R, Burt DW, Bhattacharya D, Ragan MA, Chan CX. Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium. BMC Biol 2021; 19:73. [PMID: 33849527 PMCID: PMC8045281 DOI: 10.1186/s12915-021-00994-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/25/2021] [Indexed: 02/07/2023] Open
Abstract
Background Dinoflagellates in the family Symbiodiniaceae are important photosynthetic symbionts in cnidarians (such as corals) and other coral reef organisms. Breakdown of the coral-dinoflagellate symbiosis due to environmental stress (i.e. coral bleaching) can lead to coral death and the potential collapse of reef ecosystems. However, evolution of Symbiodiniaceae genomes, and its implications for the coral, is little understood. Genome sequences of Symbiodiniaceae remain scarce due in part to their large genome sizes (1–5 Gbp) and idiosyncratic genome features. Results Here, we present de novo genome assemblies of seven members of the genus Symbiodinium, of which two are free-living, one is an opportunistic symbiont, and the remainder are mutualistic symbionts. Integrating other available data, we compare 15 dinoflagellate genomes revealing high sequence and structural divergence. Divergence among some Symbiodinium isolates is comparable to that among distinct genera of Symbiodiniaceae. We also recovered hundreds of gene families specific to each lineage, many of which encode unknown functions. An in-depth comparison between the genomes of the symbiotic Symbiodinium tridacnidorum (isolated from a coral) and the free-living Symbiodinium natans reveals a greater prevalence of transposable elements, genetic duplication, structural rearrangements, and pseudogenisation in the symbiotic species. Conclusions Our results underscore the potential impact of lifestyle on lineage-specific gene-function innovation, genome divergence, and the diversification of Symbiodinium and Symbiodiniaceae. The divergent features we report, and their putative causes, may also apply to other microbial eukaryotes that have undergone symbiotic phases in their evolutionary history. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-00994-6.
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Affiliation(s)
- Raúl A González-Pech
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia. .,Present address: Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA.
| | - Timothy G Stephens
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,Present address: Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Yibi Chen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, 4072, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Amin R Mohamed
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD, 4072, Australia.,Present address: Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Yuanyuan Cheng
- UQ Genomics Initiative, The University of Queensland, Brisbane, QLD, 4072, Australia.,Present address: School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Sarah Shah
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, 4072, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Katherine E Dougan
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, 4072, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Michael D A Fortuin
- Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, 4072, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Rémi Lagorce
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,École Polytechnique Universitaire de l'Université de Nice, Université Nice-Sophia-Antipolis, 06410, Nice, Provence-Alpes-Côte d'Azur, France
| | - David W Burt
- UQ Genomics Initiative, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, 4072, Australia. .,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
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19
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Shoguchi E, Yoshioka Y, Shinzato C, Arimoto A, Bhattacharya D, Satoh N. Correlation between Organelle Genetic Variation and RNA Editing in Dinoflagellates Associated with the Coral Acropora digitifera. Genome Biol Evol 2021; 12:203-209. [PMID: 32108224 PMCID: PMC7144361 DOI: 10.1093/gbe/evaa042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2020] [Indexed: 12/11/2022] Open
Abstract
In order to develop successful strategies for coral reef preservation, it is critical that the biology of both host corals and symbiotic algae are investigated. In the Ryukyu Archipelago, which encompasses many islands spread over ∼500 km of the Pacific Ocean, four major populations of the coral Acropora digitifera have been studied using whole-genome shotgun (WGS) sequence analysis (Shinzato C, Mungpakdee S, Arakaki N, Satoh N. 2015. Genome-wide single-nucleotide polymorphism (SNP) analysis explains coral diversity and recovery in the Ryukyu Archipelago. Sci Rep. 5:18211.). In contrast, the diversity of the symbiotic dinoflagellates associated with these A. digitifera populations is unknown. It is therefore unclear if these two core components of the coral holobiont share a common evolutionary history. This issue can be addressed for the symbiotic algal populations by studying the organelle genomes of their mitochondria and plastids. Here, we analyzed WGS data from ∼150 adult A. digitifera, and by mapping reads to the available reference genome sequences, we extracted 2,250 sequences representing 15 organelle genes of Symbiodiniaceae. Molecular phylogenetic analyses of these mitochondrial and plastid gene sets revealed that A. digitifera from the southern Yaeyama islands harbor a different Symbiodiniaceae population than the islands of Okinawa and Kerama in the north, indicating that the distribution of symbiont populations partially matches that of the four host populations. Interestingly, we found that numerous SNPs correspond to known RNA-edited sites in 14 of the Symbiodiniaceae organelle genes, with mitochondrial genes showing a stronger correspondence than plastid genes. These results suggest a possible correlation between RNA editing and SNPs in the two organelle genomes of symbiotic dinoflagellates.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Yuki Yoshioka
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha, Kashiwa, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwanoha, Kashiwa, Japan
| | - Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
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20
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Shoguchi E, Beedessee G, Hisata K, Tada I, Narisoko H, Satoh N, Kawachi M, Shinzato C. A New Dinoflagellate Genome Illuminates a Conserved Gene Cluster Involved in Sunscreen Biosynthesis. Genome Biol Evol 2020; 13:5955767. [PMID: 33146374 PMCID: PMC7875005 DOI: 10.1093/gbe/evaa235] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2020] [Indexed: 12/18/2022] Open
Abstract
Photosynthetic dinoflagellates of the Family Symbiodiniaceae live symbiotically with many organisms that inhabit coral reefs and are currently classified into fifteen groups, including seven genera. Draft genomes from four genera, Symbiodinium, Breviolum, Fugacium, and Cladocopium, which have been isolated from corals, have been reported. However, no genome is available from the genus Durusdinium, which occupies an intermediate phylogenetic position in the Family Symbiodiniaceae and is well known for thermal tolerance (resistance to bleaching). We sequenced, assembled, and annotated the genome of Durusdinium trenchii, isolated from the coral, Favia speciosa, in Okinawa, Japan. Assembled short reads amounted to 670 Mb with ∼47% GC content. This GC content was intermediate among taxa belonging to the Symbiodiniaceae. Approximately 30,000 protein-coding genes were predicted in the D. trenchii genome, fewer than in other genomes from the Symbiodiniaceae. However, annotations revealed that the D. trenchii genome encodes a cluster of genes for synthesis of mycosporine-like amino acids, which absorb UV radiation. Interestingly, a neighboring gene in the cluster encodes a glucose-methanol-choline oxidoreductase with a flavin adenine dinucleotide domain that is also found in Symbiodinium tridacnidorum. This conservation seems to partially clarify an ancestral genomic structure in the Symbiodiniaceae and its loss in late-branching lineages, including Breviolum and Cladocopium, after splitting from the Durusdinium lineage. Our analysis suggests that approximately half of the taxa in the Symbiodiniaceae may maintain the ability to synthesize mycosporine-like amino acids. Thus, this work provides a significant genomic resource for understanding the genomic diversity of Symbiodiniaceae in corals.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Ipputa Tada
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.,Department of Genetics, The Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka, Japan
| | - Haruhi Narisoko
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
| | - Chuya Shinzato
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan.,Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan
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21
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Pierangelini M, Thiry M, Cardol P. Different levels of energetic coupling between photosynthesis and respiration do not determine the occurrence of adaptive responses of Symbiodiniaceae to global warming. THE NEW PHYTOLOGIST 2020; 228:855-868. [PMID: 32535971 PMCID: PMC7590187 DOI: 10.1111/nph.16738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 05/30/2020] [Indexed: 05/06/2023]
Abstract
Disentangling the metabolic functioning of corals' endosymbionts (Symbiodiniaceae) is relevant to understanding the response of coral reefs to warming oceans. In this work, we first question whether there is an energetic coupling between photosynthesis and respiration in Symbiodiniaceae (Symbiodinium, Durusdinium and Effrenium), and second, how different levels of energetic coupling will affect their adaptive responses to global warming. Coupling between photosynthesis and respiration was established by determining the variation of metabolic rates during thermal response curves, and how inhibition of respiration affects photosynthesis. Adaptive (irreversible) responses were studied by exposing two Symbiodinium species with different levels of photosynthesis-respiration interaction to high temperature conditions (32°C) for 1 yr. We found that some Symbiodiniaceae have a high level of energetic coupling; that is, photosynthesis and respiration have the same temperature dependency, and photosynthesis is negatively affected when respiration is inhibited. Conversely, photosynthesis and respiration are not coupled in other species. In any case, prolonged exposure to high temperature caused adjustments in both photosynthesis and respiration, but these changes were fully reversible. We conclude that energetic coupling between photosynthesis and respiration exhibits wide variation amongst Symbiodiniaceae and does not determine the occurrence of adaptive responses in Symbiodiniaceae to temperature increase.
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Affiliation(s)
- Mattia Pierangelini
- Génétique et Physiologie des MicroalguesInBioS/PhytosystemsInstitut de BotaniqueUniversité de LiègeB22Liège4000Belgium
| | - Marc Thiry
- Unit of Cell BiologyGIGA‐NeurosciencesCHU Sart‐TilmanUniversity of LiègeLiègeB36, 4000Belgium
| | - Pierre Cardol
- Génétique et Physiologie des MicroalguesInBioS/PhytosystemsInstitut de BotaniqueUniversité de LiègeB22Liège4000Belgium
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22
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Mohamed AR, Andrade N, Moya A, Chan CX, Negri AP, Bourne DG, Ying H, Ball EE, Miller DJ. Dual RNA-sequencing analyses of a coral and its native symbiont during the establishment of symbiosis. Mol Ecol 2020; 29:3921-3937. [PMID: 32853430 DOI: 10.1111/mec.15612] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 08/16/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022]
Abstract
Despite the ecological significance of the mutualistic relationship between Symbiodiniaceae and reef-building corals, the molecular interactions during establishment of this relationship are not well understood. This is particularly true of the transcriptional changes that occur in the symbiont. In the current study, a dual RNA-sequencing approach was used to better understand transcriptional changes on both sides of the coral-symbiont interaction during the colonization of Acropora tenuis by a compatible Symbiodiniaceae strain (Cladocopium goreaui; ITS2 type C1). Comparison of transcript levels of the in hospite symbiont 3, 12, 48 and 72 hr after exposure to those of the same strain in culture revealed that extensive and generalized down-regulation of symbiont gene expression occurred during the infection process. Included in this "symbiosis-derived transcriptional repression" were a range of stress response and immune-related genes. In contrast, a suite of symbiont genes implicated in metabolism was upregulated in the symbiotic state. The coral data support the hypothesis that immune-suppression and arrest of phagosome maturation play important roles during the establishment of compatible symbioses, and additionally imply the involvement of some SCRiP family members in the colonization process. Consistent with previous ecological studies, the transcriptomic data suggest that active translocation of metabolites to the host may begin early in the colonization process, and thus that the mutualistic relationship can be established at the larval stage. This dual RNA-sequencing study provides insights into the transcriptomic remodelling that occurs in C. goreaui during transition to a symbiotic lifestyle and the novel coral genes implicated in symbiosis.
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Affiliation(s)
- Amin R Mohamed
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Qld, Australia.,Zoology Department, Faculty of Science, Benha University, Benha, Egypt.,ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, AIMS@JCU, Australian Institute of Marine Science, James Cook University, Townsville, Qld, Australia
| | - Natalia Andrade
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, Australia
| | - Aurelie Moya
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, Australia
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, Australia
| | - Andrew P Negri
- Australian Institute of Marine Science, Townsville, Qld, Australia
| | - David G Bourne
- Australian Institute of Marine Science, Townsville, Qld, Australia.,Department of Marine Ecosystems and Impacts, James Cook University, Townsville, Qld, Australia
| | - Hua Ying
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, Australia
| | - Eldon E Ball
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia.,Department of Molecular and Cell Biology, James Cook University, Townsville, Qld, Australia
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23
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Mohamed AR, Chan CX, Ragan MA, Zhang J, Cooke I, Ball EE, Miller DJ. Comparative transcriptomic analyses of Chromera and Symbiodiniaceae. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:435-443. [PMID: 32452166 DOI: 10.1111/1758-2229.12859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 05/12/2020] [Accepted: 05/21/2020] [Indexed: 06/11/2023]
Abstract
Reef-building corals live in a mutualistic relationship with photosynthetic algae (family Symbiodiniaceae) that usually provide most of the energy required by the coral host. This relationship is sensitive to temperature stress; as little as a 1°C increase often leads to the collapse of the association. This sensitivity has led to an interest in the potential of more stress-tolerant algae to supplement or substitute for the normal Symbiodiniaceae mutualists. In this respect, the apicomplexan-like microalga Chromera is of particular interest due to its greater temperature tolerance. We generated a de novo transcriptome for a Chromera strain isolated from a GBR coral ('GBR Chromera') and compared with those of the reference strain of Chromera ('Sydney Chromera'), and to those of Symbiodiniaceae (Fugacium kawagutii, Cladocopium goreaui and Breviolum minutum), as well as the apicomplexan parasite, Plasmodium falciparum. In contrast to the high sequence divergence amongst representatives of different genera within the family Symbiodiniaceae, the two Chromera strains featured low sequence divergence at orthologous genes, implying that they are likely to be conspecifics. Although KEGG categories provide few criteria by which true coral mutualists might be identified, they do supply a molecular rationalization that explains the ecological dominance of Cladocopium spp. amongst Indo-Pacific reef corals. The presence of HSP20 genes may contribute to the high thermal tolerance of Chromera.
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Affiliation(s)
- Amin R Mohamed
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St Lucia, Brisbane, Qld, 4067, Australia
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia
- Molecular and Cell Biology, James Cook University, Townsville, Qld, 4811, Australia
- Department of Molecular and Cell Biology, AIMS@JCU, Australian Institute of Marine Science, James Cook University, Townsville, Qld, 4811, Australia
- Zoology Department, Faculty of Science, Benha University, Benha, 13518, Egypt
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Jia Zhang
- Molecular and Cell Biology, James Cook University, Townsville, Qld, 4811, Australia
| | - Ira Cooke
- Molecular and Cell Biology, James Cook University, Townsville, Qld, 4811, Australia
| | - Eldon E Ball
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia
- Division of Ecology and Evolution, Research School of Biology, Australian National University, Acton ACT, 2601, Australia
| | - David J Miller
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, 4811, Australia
- Molecular and Cell Biology, James Cook University, Townsville, Qld, 4811, Australia
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24
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Su Y, Zhang K, Zhou Z, Wang J, Yang X, Tang J, Li H, Lin S. Microplastic exposure represses the growth of endosymbiotic dinoflagellate Cladocopium goreaui in culture through affecting its apoptosis and metabolism. CHEMOSPHERE 2020; 244:125485. [PMID: 31809929 DOI: 10.1016/j.chemosphere.2019.125485] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/29/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
Microplastics are widespread emerging marine pollutants that have been found in the coral reef ecosystem. In the present study, using Cladocopium goreaui as a symbiont representative, we investigated cytological, physiological, and molecular responses of a Symbiodiniaceae species to weeklong microplastic exposure (Polystyrene, diameter 1.0 μm, 9.0 × 109 particles L-1). The density and size of algal cells decreased significantly at 7 d and 6-7 d of microplastic exposure, respectively. Chlorophyll a content increased significantly at 7 d of exposure, whereas Fv/Fm did not change significantly during the entire exposure period. We observed significant increases in superoxide dismutase activity and caspase3 activation level, significant decrease in glutathione S-transferase activity, but no change in catalase activity during the whole exposure period. Transcriptomic analysis revealed 191 significantly upregulated and 71 significantly downregulated genes at 7 d after microplastic exposure. Fifteen GO terms were overrepresented for these significantly upregulated genes, which were grouped into four categories including transmembrane ion transport, substrate-specific transmembrane transporter activity, calcium ion binding, and calcium-dependent cysteine-type endopeptidase activity. Thirteen of the significantly upregulated genes encode metal ion transporter and ammonium transporter, and five light-harvesting protein genes were among the significantly downregulated genes. These results demonstrate that microplastics can act as an exogenous stressor, suppress detoxification activity, nutrient uptake, and photosynthesis, elevate oxidative stress, and raise the apoptosis level through upregulating ion transport and apoptotic enzymes to repress the growth of C. goreaui. These effects have implications in negative impacts of microplastics on coral-Symbiodiniaceae symbiosis that involves C. goreaui.
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Affiliation(s)
- Yilu Su
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
| | - Kaidian Zhang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China; Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Zhi Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China; Department of Marine Sciences, University of Connecticut, Groton, CT, USA.
| | - Jierui Wang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Xiaohong Yang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Jia Tang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, Hainan, China
| | - Hongfei Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, Fujian, China
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA.
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25
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Matthews JL, Raina J, Kahlke T, Seymour JR, Oppen MJH, Suggett DJ. Symbiodiniaceae‐bacteria interactions: rethinking metabolite exchange in reef‐building corals as multi‐partner metabolic networks. Environ Microbiol 2020; 22:1675-1687. [DOI: 10.1111/1462-2920.14918] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 11/29/2022]
Affiliation(s)
- Jennifer L. Matthews
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
| | - Jean‐Baptiste Raina
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
| | - Tim Kahlke
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
| | - Justin R. Seymour
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
| | - Madeleine J. H. Oppen
- The University of Melbourne Parkville 3010 Victoria Australia
- Australian Institute of Marine Science PMB No 3 Townsville MC 4810 QLD Australia
| | - David J. Suggett
- Climate Change Cluster University of Technology Sydney 2007 New South Wales Australia
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