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Lin S. A decade of dinoflagellate genomics illuminating an enigmatic eukaryote cell. BMC Genomics 2024; 25:932. [PMID: 39367346 PMCID: PMC11453091 DOI: 10.1186/s12864-024-10847-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2024] [Accepted: 09/27/2024] [Indexed: 10/06/2024] Open
Abstract
Dinoflagellates are a remarkable group of protists, not only for their association with harmful algal blooms and coral reefs but also for their numerous characteristics deviating from the rules of eukaryotic biology. Genome research on dinoflagellates has lagged due to their immense genome sizes in most species (~ 1-250 Gbp). Nevertheless, the last decade marked a fruitful era of dinoflagellate genomics, with 27 genomes sequenced and many insights attained. This review aims to synthesize information from these genomes, along with other omic data, to reflect on where we are now in understanding dinoflagellates and where we are heading in the future. The most notable insights from the decade-long genomics work include: (1) dinoflagellate genomes have been expanded in multiple times independently, probably by a combination of rampant retroposition, accumulation of repetitive DNA, and genome duplication; (2) Symbiodiniacean genomes are highly divergent, but share about 3,445 core unigenes concentrated in 219 KEGG pathways; (3) Most dinoflagellate genes are encoded unidirectionally and are not intron-poor; (4) The dinoflagellate nucleus has undergone extreme evolutionary changes, including complete or nearly complete loss of nucleosome and histone H1, and acquisition of dinoflagellate viral nuclear protein (DVNP); (5) Major basic nuclear protein (MBNP), histone-like protein (HLP), and bacterial HU-like protein (HCc) belong to the same protein family, and MBNP can be the unifying name; (6) Dinoflagellate gene expression is regulated by poorly understood mechanisms, but microRNA and other epigenetic mechanisms are likely important; (7) Over 50% of dinoflagellate genes are "dark" and their functions remain to be deciphered using functional genetics; (8) Initial insights into the genomic basis of parasitism and mutualism have emerged. The review then highlights functionally unique and interesting genes. Future research needs to obtain a finished genome, tackle large genomes, characterize the unknown genes, and develop a quantitative molecular ecological model for addressing ecological questions.
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Affiliation(s)
- Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT, 06340, USA.
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González-Pech RA, Shepherd J, Fuller ZL, LaJeunesse TC, Parkinson JE. The genome of a giant clam zooxanthella (Cladocopium infistulum) offers few clues to adaptation as an extracellular symbiont with high thermotolerance. BMC Genomics 2024; 25:914. [PMID: 39354409 PMCID: PMC11443893 DOI: 10.1186/s12864-024-10822-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 09/20/2024] [Indexed: 10/03/2024] Open
Abstract
BACKGROUND Cladocopium infistulum (Symbiodiniaceae) is a dinoflagellate specialized to live in symbiosis with western Pacific giant clams (Tridacnidae). Unlike coral-associated symbionts, which reside within the host cells, C. infistulum inhabits the extracellular spaces of the clam's digestive diverticula. It is phylogenetically basal to a large species complex of stress-tolerant Cladocopium, many of which are associated with important reef-building corals in the genus Porites. This close phylogenetic relationship may explain why C. infistulum exhibits high thermotolerance relative to other tridacnid symbionts. Moreover, past analyses of microsatellite loci indicated that Cladocopium underwent whole-genome duplication prior to the adaptive radiations that led to its present diversity. RESULTS A draft genome assembly of C. infistulum was produced using long- and short-read sequences to explore the genomic basis for adaptations underlying thermotolerance and extracellular symbiosis among dinoflagellates and to look for evidence of genome duplication. Comparison to three other Cladocopium genomes revealed no obvious over-representation of gene groups or families whose functions would be important for maintaining C. infistulum's unique physiological and ecological properties. Preliminary analyses support the existence of partial or whole-genome duplication among Cladocopium, but additional high-quality genomes are required to substantiate these findings. CONCLUSION Although this investigation of Cladocopium infistulum revealed no patterns diagnostic of heat tolerance or extracellular symbiosis in terms of overrepresentation of gene functions or genes under selection, it provided a valuable genomic resource for comparative analyses. It also indicates that ecological divergence among Cladocopium species, and potentially among other dinoflagellates, is partially governed by mechanisms other than gene content. Thus, additional high-quality, multiomic data are needed to explore the molecular basis of key phenotypes among symbiotic microalgae.
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Affiliation(s)
- Raúl A González-Pech
- Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA.
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Jihanne Shepherd
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
- Miller School of Medicine, University of Miami, Miami, FL, 33136, USA
| | - Zachary L Fuller
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Todd C LaJeunesse
- Department of Biology, Pennsylvania State University, University Park, PA, 16802, USA
- Institute of Energy and the Environment, The Pennsylvania State University, University Park, PA, 16802, USA
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Frail S, Steele-Ogus M, Doenier J, Moulin SLY, Braukmann T, Xu S, Yeh E. Genomes of nitrogen-fixing eukaryotes reveal a non-canonical model of organellogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.27.609708. [PMID: 39253440 PMCID: PMC11383321 DOI: 10.1101/2024.08.27.609708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Endosymbiont gene transfer and import of host-encoded proteins are considered hallmarks of organelles necessary for stable integration of two cells. However, newer endosymbiotic models have challenged the origin and timing of such genetic integration during organellogenesis. Epithemia diatoms contain diazoplasts, closely related to recently-described nitrogen-fixing organelles, that are also stably integrated and co-speciating with their host algae. We report genomic analyses of two species, freshwater E.clementina and marine E.pelagica, which are highly divergent but share a common endosymbiotic origin. We found minimal evidence of genetic integration: nonfunctional diazoplast-to-nuclear DNA transfers in the E.clementina genome and 6 host-encoded proteins of unknown function in the E.clementina diazoplast proteome, far fewer than in other recently-acquired organelles. Epithemia diazoplasts are a valuable counterpoint to existing organellogenesis models, demonstrating that endosymbionts can be stably integrated and inherited absent significant genetic integration. The minimal genetic integration makes diazoplasts valuable blueprints for bioengineering endosymbiotic compartments de novo.
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Affiliation(s)
- Sarah Frail
- Department of Biochemistry, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Melissa Steele-Ogus
- Department of Pathology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Jon Doenier
- Department of Biochemistry, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Solène L Y Moulin
- Department of Pathology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Tom Braukmann
- Department of Biochemistry, Stanford School of Medicine, Stanford, CA 94305, USA
- Department of Pathology, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Shouling Xu
- Department of Plant Biology, Carnegie Institution, Stanford, CA 94305, USA
| | - Ellen Yeh
- Department of Pathology, Stanford School of Medicine, Stanford, CA 94305, USA
- Department of Microbiology & Immunology, Stanford School of Medicine, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub - San Francisco, San Francisco, California 94158, USA
- Lead contact
- Senior author
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van Oppen MJH. Shining light on the coral photosymbiont family Symbiodiniaceae. Nat Microbiol 2024:10.1038/s41564-024-01745-3. [PMID: 39095497 DOI: 10.1038/s41564-024-01745-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Affiliation(s)
- Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville, Queensland, Australia.
- School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia.
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Kalvelage J, Rabus R. Multifaceted Dinoflagellates and the Marine Model Prorocentrum cordatum. Microb Physiol 2024; 34:197-242. [PMID: 39047710 DOI: 10.1159/000540520] [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: 06/01/2024] [Accepted: 07/20/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Dinoflagellates are a monophyletic group within the taxon Alveolata, which comprises unicellular eukaryotes. Dinoflagellates have long been studied for their organismic and morphologic diversity as well as striking cellular features. They have a main size range of 10-100 µm, a complex "cell covering", exceptionally large genomes (∼1-250 Gbp with a mean of 50,000 protein-encoding genes) spread over a variable number of highly condensed chromosomes, and perform a closed mitosis with extranuclear spindles (dinomitosis). Photosynthetic, marine, and free-living Prorocentrum cordatum is a ubiquitously occurring, bloom-forming dinoflagellate, and an emerging model system, particularly with respect to systems biology. SUMMARY Focused ion beam/scanning electron microscopy (FIB/SEM) analysis of P. cordatum recently revealed (i) a flattened nucleus with unusual structural features and a total of 62 tightly packed chromosomes, (ii) a single, barrel-shaped chloroplast devoid of grana and harboring multiple starch granules, (iii) a single, highly reticular mitochondrion, and (iv) multiple phosphate and lipid storage bodies. Comprehensive proteomics of subcellular fractions suggested (i) major basic nuclear proteins to participate in chromosome condensation, (ii) composition of nuclear pores to differ from standard knowledge, (iii) photosystems I and II, chloroplast complex I, and chlorophyll a-b binding light-harvesting complex to form a large megacomplex (>1.5 MDa), and (iv) an extraordinary richness in pigment-binding proteins. Systems biology-level investigation of heat stress response demonstrated a concerted down-regulation of CO2-concentrating mechanisms, CO2-fixation, central metabolism, and monomer biosynthesis, which agrees with reduced growth yields. KEY MESSAGES FIB/SEM analysis revealed new insights into the remarkable subcellular architecture of P. cordatum, complemented by proteogenomic unraveling of novel nuclear structures and a photosynthetic megacomplex. These recent findings are put in the wider context of current understanding of dinoflagellates.
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Affiliation(s)
- Jana Kalvelage
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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Dougan KE, Bellantuono AJ, Kahlke T, Abbriano RM, Chen Y, Shah S, Granados-Cifuentes C, van Oppen MJH, Bhattacharya D, Suggett DJ, Rodriguez-Lanetty M, Chan CX. Whole-genome duplication in an algal symbiont bolsters coral heat tolerance. SCIENCE ADVANCES 2024; 10:eadn2218. [PMID: 39028812 PMCID: PMC11259175 DOI: 10.1126/sciadv.adn2218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 06/14/2024] [Indexed: 07/21/2024]
Abstract
The algal endosymbiont Durusdinium trenchii enhances the resilience of coral reefs under thermal stress. D. trenchii can live freely or in endosymbiosis, and the analysis of genetic markers suggests that this species has undergone whole-genome duplication (WGD). However, the evolutionary mechanisms that underpin the thermotolerance of this species are largely unknown. Here, we present genome assemblies for two D. trenchii isolates, confirm WGD in these taxa, and examine how selection has shaped the duplicated genome regions using gene expression data. We assess how the free-living versus endosymbiotic lifestyles have contributed to the retention and divergence of duplicated genes, and how these processes have enhanced the thermotolerance of D. trenchii. Our combined results suggest that lifestyle is the driver of post-WGD evolution in D. trenchii, with the free-living phase being the most important, followed by endosymbiosis. Adaptations to both lifestyles likely enabled D. trenchii to provide enhanced thermal stress protection to the host coral.
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Affiliation(s)
- Katherine E. Dougan
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
- Department of Biological Sciences, Biomolecular Science Institute, Florida International University, Miami, FL 33099, USA
| | - Anthony J. Bellantuono
- Department of Biological Sciences, Biomolecular Science Institute, Florida International University, Miami, FL 33099, USA
| | - Tim Kahlke
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Raffaela M. Abbriano
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Yibi Chen
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sarah Shah
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Camila Granados-Cifuentes
- Department of Biological Sciences, Biomolecular Science Institute, Florida International University, Miami, FL 33099, USA
| | - Madeleine J. H. van Oppen
- School of Biosciences, 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
| | - David J. Suggett
- Climate Change Cluster, University of Technology Sydney, Sydney, NSW 2007, Australia
- KAUST Reefscape Restoration Initiative (KRRI) and Red Sea Research Center (RSRC), King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | - Mauricio Rodriguez-Lanetty
- Department of Biological Sciences, Biomolecular Science Institute, Florida International University, Miami, FL 33099, USA
| | - Cheong Xin Chan
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD 4072, Australia
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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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Wang H, Wu P, Xiong L, Kim HS, Kim JH, Ki JS. Nuclear genome of dinoflagellates: Size variation and insights into evolutionary mechanisms. Eur J Protistol 2024; 93:126061. [PMID: 38394997 DOI: 10.1016/j.ejop.2024.126061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024]
Abstract
Recent progress in high-throughput sequencing technologies has dramatically increased availability of genome data for prokaryotes and eukaryotes. Dinoflagellates have distinct chromosomes and a huge genome size, which make their genomic analysis complicated. Here, we reviewed the nuclear genomes of core dinoflagellates, focusing on the genome and cell size. Till now, the genome sizes of several dinoflagellates (more than 25) have been measured by certain methods (e.g., flow cytometry), showing a range of 3-250 pg of genomic DNA per cell. In contrast to their relatively small cell size, their genomes are huge (about 1-80 times the human haploid genome). In the present study, we collected the genome and cell size data of dinoflagellates and compared their relationships. We found that dinoflagellate genome size exhibits a positive correlation with cell size. On the other hand, we recognized that the genome size is not correlated with phylogenetic relatedness. These may be caused by genome duplication, increased gene copy number, repetitive non-coding DNA, transposon expansion, horizontal gene transfer, organelle-to-nucleus gene transfer, and/or mRNA reintegration into the genome. Ultimate verification of these factors as potential causative mechanisms would require sequencing of more dinoflagellate genomes in the future.
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Affiliation(s)
- Hui Wang
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China; Department of Life Science, Sangmyung University, Seoul 03016, Republic of Korea
| | - Peiling Wu
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Lu Xiong
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Han-Sol Kim
- Department of Life Science, Sangmyung University, Seoul 03016, Republic of Korea
| | - Jin Ho Kim
- Department of Earth and Marine Science, College of Ocean Sciences, Jeju National University, Jeju 63243, Republic of Korea
| | - Jang-Seu Ki
- Department of Life Science, Sangmyung University, Seoul 03016, Republic of Korea; Department of Biotechnology, Sangmyung University, Seoul 03016, Republic of Korea.
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Burgunter-Delamare B, Shetty P, Vuong T, Mittag M. Exchange or Eliminate: The Secrets of Algal-Bacterial Relationships. PLANTS (BASEL, SWITZERLAND) 2024; 13:829. [PMID: 38592793 PMCID: PMC10974524 DOI: 10.3390/plants13060829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024]
Abstract
Algae and bacteria have co-occurred and coevolved in common habitats for hundreds of millions of years, fostering specific associations and interactions such as mutualism or antagonism. These interactions are shaped through exchanges of primary and secondary metabolites provided by one of the partners. Metabolites, such as N-sources or vitamins, can be beneficial to the partner and they may be assimilated through chemotaxis towards the partner producing these metabolites. Other metabolites, especially many natural products synthesized by bacteria, can act as toxins and damage or kill the partner. For instance, the green microalga Chlamydomonas reinhardtii establishes a mutualistic partnership with a Methylobacterium, in stark contrast to its antagonistic relationship with the toxin producing Pseudomonas protegens. In other cases, as with a coccolithophore haptophyte alga and a Phaeobacter bacterium, the same alga and bacterium can even be subject to both processes, depending on the secreted bacterial and algal metabolites. Some bacteria also influence algal morphology by producing specific metabolites and micronutrients, as is observed in some macroalgae. This review focuses on algal-bacterial interactions with micro- and macroalgal models from marine, freshwater, and terrestrial environments and summarizes the advances in the field. It also highlights the effects of temperature on these interactions as it is presently known.
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Affiliation(s)
- Bertille Burgunter-Delamare
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (P.S.); (T.V.)
| | - Prateek Shetty
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (P.S.); (T.V.)
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Trang Vuong
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (P.S.); (T.V.)
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (P.S.); (T.V.)
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, 07743 Jena, Germany
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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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Valadez-Ingersoll M, Aguirre Carrión PJ, Bodnar CA, Desai NA, Gilmore TD, Davies SW. Starvation differentially affects gene expression, immunity and pathogen susceptibility across symbiotic states in a model cnidarian. Proc Biol Sci 2024; 291:20231685. [PMID: 38412969 PMCID: PMC10898965 DOI: 10.1098/rspb.2023.1685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 01/29/2024] [Indexed: 02/29/2024] Open
Abstract
Mutualistic symbioses between cnidarians and photosynthetic algae are modulated by complex interactions between host immunity and environmental conditions. Here, we investigate how symbiosis interacts with food limitation to influence gene expression and stress response programming in the sea anemone Exaiptasia pallida (Aiptasia). Transcriptomic responses to starvation were similar between symbiotic and aposymbiotic Aiptasia; however, aposymbiotic anemone responses were stronger. Starved Aiptasia of both symbiotic states exhibited increased protein levels of immune-related transcription factor NF-κB, its associated gene pathways, and putative target genes. However, this starvation-induced increase in NF-κB correlated with increased immunity only in symbiotic anemones. Furthermore, starvation had opposite effects on Aiptasia susceptibility to pathogen and oxidative stress challenges, suggesting distinct energetic priorities under food scarce conditions. Finally, when we compared starvation responses in Aiptasia to those of a facultative coral and non-symbiotic anemone, 'defence' responses were similarly regulated in Aiptasia and the facultative coral, but not in the non-symbiotic anemone. This pattern suggests that capacity for symbiosis influences immune responses in cnidarians. In summary, expression of certain immune pathways-including NF-κB-does not necessarily predict susceptibility to pathogens, highlighting the complexities of cnidarian immunity and the influence of symbiosis under varying energetic demands.
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Affiliation(s)
| | | | - Caoimhe A. Bodnar
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
| | - Niharika A. Desai
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
| | - Thomas D. Gilmore
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
| | - Sarah W. Davies
- Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA
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Hoepner CM, Stewart ZK, Qiao R, Fobert EK, Prentis PJ, Colella A, Chataway T, Burke da Silva K, Abbott CA. Proteotransciptomics of the Most Popular Host Sea Anemone Entacmaea quadricolor Reveals Not All Toxin Genes Expressed by Tentacles Are Recruited into Its Venom Arsenal. Toxins (Basel) 2024; 16:85. [PMID: 38393163 PMCID: PMC10893224 DOI: 10.3390/toxins16020085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
While the unique symbiotic relationship between anemonefishes and sea anemones is iconic, it is still not fully understood how anemonefishes can withstand and thrive within the venomous environment of their host sea anemone. In this study, we used a proteotranscriptomics approach to elucidate the proteinaceous toxin repertoire from the most common host sea anemone, Entacmaea quadricolor. Although 1251 different toxin or toxin-like RNA transcripts were expressed in E. quadricolor tentacles (0.05% of gene clusters, 1.8% of expression) and 5375 proteins were detected in milked venom, only 4% of proteins detected in venom were putative toxins (230), and they only represent on average 14% of the normalised protein expression in the milked venom samples. Thus, most proteins in milked venom do not appear to have a toxin function. This work raises the perils of defining a dominant venom phenotype based on transcriptomics data alone in sea anemones, as we found that the dominant venom phenotype differs between the transcriptome and proteome abundance data. E. quadricolor venom contains a mixture of toxin-like proteins of unknown and known function. A newly identified toxin protein family, Z3, rich in conserved cysteines of unknown function, was the most abundant at the RNA transcript and protein levels. The venom was also rich in toxins from the Protease S1, Kunitz-type and PLA2 toxin protein families and contains toxins from eight venom categories. Exploring the intricate venom toxin components in other host sea anemones will be crucial for improving our understanding of how anemonefish adapt to the venomous environment.
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Affiliation(s)
- Cassie M. Hoepner
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Zachary K. Stewart
- Centre for Agriculture and Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Robert Qiao
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Emily K. Fobert
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Peter J. Prentis
- Centre for Agriculture and Bioeconomy, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Alex Colella
- Flinders Proteomics Facility, College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Tim Chataway
- Flinders Proteomics Facility, College of Medicine and Public Health, Flinders University, Bedford Park, SA 5042, Australia
| | - Karen Burke da Silva
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
| | - Catherine A. Abbott
- College of Science and Engineering, Flinders University, Bedford Park, SA 5042, Australia
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13
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Matthews JL, Ueland M, Bartels N, Lawson CA, Lockwood TE, Wu Y, Camp EF. Multi-Chemical Omics Analysis of the Symbiodiniaceae Durusdinium trenchii under Heat Stress. Microorganisms 2024; 12:317. [PMID: 38399721 PMCID: PMC10893086 DOI: 10.3390/microorganisms12020317] [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: 12/31/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The urgency of responding to climate change for corals necessitates the exploration of innovative methods to swiftly enhance our understanding of crucial processes. In this study, we employ an integrated chemical omics approach, combining elementomics, metabolomics, and volatilomics methodologies to unravel the biochemical pathways associated with the thermal response of the coral symbiont, Symbiodiniaceae Durusdinium trenchii. We outline the complimentary sampling approaches and discuss the standardised data corrections used to allow data integration and comparability. Our findings highlight the efficacy of individual methods in discerning differences in the biochemical response of D. trenchii under both control and stress-inducing temperatures. However, a deeper insight emerges when these methods are integrated, offering a more comprehensive understanding, particularly regarding oxidative stress pathways. Employing correlation network analysis enhanced the interpretation of volatile data, shedding light on the potential metabolic origins of volatiles with undescribed functions and presenting promising candidates for further exploration. Elementomics proves to be less straightforward to integrate, likely due to no net change in elements but rather elements being repurposed across compounds. The independent and integrated data from this study informs future omic profiling studies and recommends candidates for targeted research beyond Symbiodiniaceae biology. This study highlights the pivotal role of omic integration in advancing our knowledge, addressing critical gaps, and guiding future research directions in the context of climate change and coral reef preservation.
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Affiliation(s)
- Jennifer L. Matthews
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Maiken Ueland
- Centre for Forensic Sciences, School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
- Hyphenated Mass Spectrometry Laboratory, School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Natasha Bartels
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Caitlin A. Lawson
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
- School of Environmental and Life Sciences, University of Newcastle, Ourimbah, NSW 2258, Australia
| | - Thomas E. Lockwood
- Hyphenated Mass Spectrometry Laboratory, School of Mathematical and Physical Sciences, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Yida Wu
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
| | - Emma F. Camp
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
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14
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Gong S, Liang J, Li G, Xu L, Tan Y, Zheng X, Jin X, Yu K, Xia X. Linking coral fluorescence phenotypes to thermal bleaching in the reef-building Galaxea fascicularis from the northern South China Sea. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:155-167. [PMID: 38433965 PMCID: PMC10902222 DOI: 10.1007/s42995-023-00190-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 07/31/2023] [Indexed: 03/05/2024]
Abstract
Coral fluorescence phenotypes have been suggested as an adaptation to a broad range of environmental conditions, yet the mechanisms linking thermal bleaching tolerance in reef-building coral populations, associated with fluorescence phenotypes due to GFP-like proteins, remains unclear. In this study, the relationship between the thermal sensitivity and phenotypic plasticity of corals was investigated using two phenotypes of Galaxea fascicularis, green and brown. The results reveal that brown G. fascicularis was more susceptible to bleaching than green G. fascicularis when exposed to a higher growth temperature of 32 °C. Both phenotypes of G. fascicularis were associated with the thermotolerant Symbiodiniaceae symbiont, Durusdinium trenchii. However, the brown G. fascicularis showed a significant decrease in Symbiodiniaceae cell density and a significant increase in pathogenic bacteria abundance when the growth temperature was raised from 29 to 32 °C. The physiological traits and transcriptomic profiles of Symbiodiniaceae were not notably affected, but there were differences in the transcriptional levels of certain genes between the two phenotype hosts of G. fascicularis. Under heat stress of 32 °C, the gene encoding green fluorescent protein (GFP)-like and chromosome-associated proteins, as well as genes related to oxidative phosphorylation, cell growth and death showed lower transcriptional levels in the brown G. fascicularis compared to the green G. fascicularis. Overall, the results demonstrate that the green form of G. fascicularis is better able to tolerate ocean warming and defend against pathogenic bacteria, likely due to higher gene transcription levels and defense ability. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00190-1.
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Affiliation(s)
- Sanqiang Gong
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301 China
| | - Jiayuan Liang
- Coral Reef Research Center of China, Guangxi University, Nanning, 53004 China
| | - Gang Li
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301 China
| | - Lijia Xu
- South China Institute of Environmental Sciences, The Ministry of Ecology and Environment of PRC, Guangzhou, 510530 China
| | - Yehui Tan
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301 China
| | - Xinqing Zheng
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
| | - Xuejie Jin
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
| | - Kefu Yu
- Coral Reef Research Center of China, Guangxi University, Nanning, 53004 China
| | - Xiaomin Xia
- Key Laboratory of Tropical Marine Bio-Resources and Ecology & Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 510301 China
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15
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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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16
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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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17
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Cuadrado Á, Montiel EE, Mora P, Figueroa RI, Lorite P, de Bustos A. Contribution of the satellitome to the exceptionally large genome of dinoflagellates: The case of the harmful alga Alexandrium minutum. HARMFUL ALGAE 2023; 130:102543. [PMID: 38061820 DOI: 10.1016/j.hal.2023.102543] [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: 06/28/2023] [Revised: 10/30/2023] [Accepted: 11/11/2023] [Indexed: 12/18/2023]
Abstract
Dinoflagellates are known to possess an exceptionally large genome organized in permanently condensed chromosomes. Focusing on the contribution of satellite DNA (satDNA) to the whole DNA content of genomes and its potential role in the architecture of the chromosomes, we present the characterization of the satellitome of Alexandriun minutum strain VGO577. To achieve this, we analyzed Illumina reads using graph-based clustering and performed complementary bioinformatic analyses. In this way, we discovered 180 satDNAs occupying 17.38 % of the genome. The 12 most abundant satDNAs represent the half of the satellitome but no satDNA is overrepresented, with the most abundant contributing ∼1.56 % of the genome. The largest repeat unit is 517 bp long but more than the half of the satDNAs (101) have repeat units shorter than 20 bp. We used FISH to map a selected set of 26 satDNAs. Although some satDNAs generate discrete hybridization signals at specific chromosomal locations (hybridization sites, HS), our cytological analysis showed that most satDNAs are dispersed throughout the genome, probably forming short arrays. Two satDNAs co-localize with the 45S rDNA. With the exception of telomeric DNA, no other satDNA yields HS on all chromosomes. In addition, we analyzed nine satDNAs yielding HS in VGO577 in four other A. minutum strains. Polymorphism at the intraspecific level was found for the presence/absence and/or abundance of some satDNAs, suggesting the amplification/deletion of these satDNAs following geographic separation or during culture maintenance of the strains. We also discuss how these results contribute to the understanding of chromosome architecture and evolution of dinoflagellate genomes.
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Affiliation(s)
- Ángeles Cuadrado
- Department of Biomedicine and Biotecnology, Universidad de Alcalá (UAH), Alcalá de Henares, Madrid 28805, Spain.
| | - Eugenia E Montiel
- Department of Experimental Biology (Genetics Area), Human and Animal Molecular Genetic Group (RNM-924), Universidad de Jaén, Jaén 23071, Spain; Departamento de Biología (Genética), Universidad Autonoma de Madrid, Madrid 28049, Spain
| | - Pablo Mora
- Department of Experimental Biology (Genetics Area), Human and Animal Molecular Genetic Group (RNM-924), Universidad de Jaén, Jaén 23071, Spain
| | - Rosa I Figueroa
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía (IEO-CSIC), Subida a Radio Faro 50, Vigo 36390, Spain
| | - Pedro Lorite
- Department of Experimental Biology (Genetics Area), Human and Animal Molecular Genetic Group (RNM-924), Universidad de Jaén, Jaén 23071, Spain
| | - Alfredo de Bustos
- Department of Biomedicine and Biotecnology, Universidad de Alcalá (UAH), Alcalá de Henares, Madrid 28805, Spain
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18
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Dougan KE, Deng ZL, Wöhlbrand L, Reuse C, Bunk B, Chen Y, Hartlich J, Hiller K, John U, Kalvelage J, Mansky J, Neumann-Schaal M, Overmann J, Petersen J, Sanchez-Garcia S, Schmidt-Hohagen K, Shah S, Spröer C, Sztajer H, Wang H, Bhattacharya D, Rabus R, Jahn D, Chan CX, Wagner-Döbler I. Multi-omics analysis reveals the molecular response to heat stress in a "red tide" dinoflagellate. Genome Biol 2023; 24:265. [PMID: 37996937 PMCID: PMC10666404 DOI: 10.1186/s13059-023-03107-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 11/10/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND "Red tides" are harmful algal blooms caused by dinoflagellate microalgae that accumulate toxins lethal to other organisms, including humans via consumption of contaminated seafood. These algal blooms are driven by a combination of environmental factors including nutrient enrichment, particularly in warm waters, and are increasingly frequent. The molecular, regulatory, and evolutionary mechanisms that underlie the heat stress response in these harmful bloom-forming algal species remain little understood, due in part to the limited genomic resources from dinoflagellates, complicated by the large sizes of genomes, exhibiting features atypical of eukaryotes. RESULTS We present the de novo assembled genome (~ 4.75 Gbp with 85,849 protein-coding genes), transcriptome, proteome, and metabolome from Prorocentrum cordatum, a globally abundant, bloom-forming dinoflagellate. Using axenic algal cultures, we study the molecular mechanisms that underpin the algal response to heat stress, which is relevant to current ocean warming trends. We present the first evidence of a complementary interplay between RNA editing and exon usage that regulates the expression and functional diversity of biomolecules, reflected by reduction in photosynthesis, central metabolism, and protein synthesis. These results reveal genomic signatures and post-transcriptional regulation for the first time in a pelagic dinoflagellate. CONCLUSIONS Our multi-omics analyses uncover the molecular response to heat stress in an important bloom-forming algal species, which is driven by complex gene structures in a large, high-G+C genome, combined with multi-level transcriptional regulation. The dynamics and interplay of molecular regulatory mechanisms may explain in part how dinoflagellates diversified to become some of the most ecologically successful organisms on Earth.
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Affiliation(s)
- Katherine E Dougan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Zhi-Luo Deng
- Helmholtz-Center for Infection Research (HZI), Inhoffenstraße 7, Braunschweig, 38124, Germany
| | - Lars Wöhlbrand
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, 26129, Oldenburg, Germany
| | - Carsten Reuse
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Boyke Bunk
- German Culture Collection for Microorganisms and Cell Cultures (DSMZ), Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Yibi Chen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Juliane Hartlich
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Karsten Hiller
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Uwe John
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstraße 231, 26129, Oldenburg, Germany
| | - Jana Kalvelage
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, 26129, Oldenburg, Germany
| | - Johannes Mansky
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Meina Neumann-Schaal
- German Culture Collection for Microorganisms and Cell Cultures (DSMZ), Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Jörg Overmann
- German Culture Collection for Microorganisms and Cell Cultures (DSMZ), Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Jörn Petersen
- German Culture Collection for Microorganisms and Cell Cultures (DSMZ), Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Selene Sanchez-Garcia
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Kerstin Schmidt-Hohagen
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Sarah Shah
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Cathrin Spröer
- German Culture Collection for Microorganisms and Cell Cultures (DSMZ), Inhoffenstraße 7B, 38124, Braunschweig, Germany
| | - Helena Sztajer
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Hui Wang
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, 26129, Oldenburg, Germany
| | - Dieter Jahn
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Irene Wagner-Döbler
- Braunschweig Center for Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, 38106, Brunswick, Germany.
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19
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Van Etten J, Stephens TG, Bhattacharya D. A k-mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data. Syst Biol 2023; 72:1101-1118. [PMID: 37314057 DOI: 10.1093/sysbio/syad037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/20/2023] [Accepted: 06/12/2023] [Indexed: 06/15/2023] Open
Abstract
In the age of genome sequencing, whole-genome data is readily and frequently generated, leading to a wealth of new information that can be used to advance various fields of research. New approaches, such as alignment-free phylogenetic methods that utilize k-mer-based distance scoring, are becoming increasingly popular given their ability to rapidly generate phylogenetic information from whole-genome data. However, these methods have not yet been tested using environmental data, which often tends to be highly fragmented and incomplete. Here, we compare the results of one alignment-free approach (which utilizes the D2 statistic) to traditional multi-gene maximum likelihood trees in 3 algal groups that have high-quality genome data available. In addition, we simulate lower-quality, fragmented genome data using these algae to test method robustness to genome quality and completeness. Finally, we apply the alignment-free approach to environmental metagenome assembled genome data of unclassified Saccharibacteria and Trebouxiophyte algae, and single-cell amplified data from uncultured marine stramenopiles to demonstrate its utility with real datasets. We find that in all instances, the alignment-free method produces phylogenies that are comparable, and often more informative, than those created using the traditional multi-gene approach. The k-mer-based method performs well even when there are significant missing data that include marker genes traditionally used for tree reconstruction. Our results demonstrate the value of alignment-free approaches for classifying novel, often cryptic or rare, species, that may not be culturable or are difficult to access using single-cell methods, but fill important gaps in the tree of life.
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Affiliation(s)
- Julia Van Etten
- Graduate Program in Ecology and Evolution, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ 08901, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ 08901, USA
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20
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Castillo-Medina RE, Islas-Flores T, Morales-Ruiz E, Villanueva MA. Biochemical and molecular characterization of the SBiP1 chaperone from Symbiodinium microadriaticum CassKB8 and light parameters that modulate its phosphorylation. PLoS One 2023; 18:e0293299. [PMID: 37862348 PMCID: PMC10588850 DOI: 10.1371/journal.pone.0293299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 10/10/2023] [Indexed: 10/22/2023] Open
Abstract
The coding and promoter region sequences from the BiP-like protein SBiP1 from Symbiodinium microadriaticum CassKB8 were obtained by PCR, sequenced and compared with annotated sequences. The nucleotides corresponding to the full sequence were correctly annotated and the main SBiP1 features determined at the nucleotide and amino acid level. The translated protein was organized into the typical domains of the BiP/HSP70 family including a signal peptide, a substrate- and a nucleotide-binding domain, and an ER localization sequence. Conserved motifs included a highly conserved Thr513 phosphorylation site and two ADP-ribosylation sites from eukaryotic BiP's. Molecular modeling showed the corresponding domain regions and main exposed post-translational target sites in its three-dimensional structure, which also closely matched Homo sapiens BiP further indicating that it indeed corresponds to a BiP/HSP70 family protein. The gene promoter region showed at least eight light regulation-related sequences consistent with the molecule being highly phosphorylated in Thr under dark conditions and dephosphorylated upon light stimuli. We tested light parameter variations that could modulate the light mediated phosphorylation effect and found that SBiP1 Thr dephosphorylation was only significantly detected after 15-30 min light stimulation. Such light-induced dephosphorylation was observed even when dichlorophenyl dimethyl urea, a photosynthesis inhibitor, was also present in the cells during the light stimulation. Dephosphorylation occurred indistinctly under red, yellow, blue or the full visible light spectra. In additon, it was observed at a light intensity of as low as 1 μmole photon m-2 s-1. Our results indicate that: a) SBiP1 is a chaperone belonging to the BiP/HSP70 family proteins; b) its light-modulated phosphorylation/dephosphorylation most likely functions as an activity switch for the chaperone; c) this light-induced modulation occurs relatively slow but is highly sensitive to the full spectrum of visible light; and d) the light induced Thr dephosphorylation is independent of photosynthetic activity in these cells.
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Affiliation(s)
- Raúl Eduardo Castillo-Medina
- Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México-UNAM, Puerto Morelos, Quintana Roo, México
| | - Tania Islas-Flores
- Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México-UNAM, Puerto Morelos, Quintana Roo, México
| | - Estefanía Morales-Ruiz
- Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México-UNAM, Puerto Morelos, Quintana Roo, México
| | - Marco A. Villanueva
- Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México-UNAM, Puerto Morelos, Quintana Roo, México
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21
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Fourreau CJL, Kise H, Santander MD, Pirro S, Maronna MM, Poliseno A, Santos ME, Reimer JD. Genome sizes and repeatome evolution in zoantharians (Cnidaria: Hexacorallia: Zoantharia). PeerJ 2023; 11:e16188. [PMID: 37868064 PMCID: PMC10586311 DOI: 10.7717/peerj.16188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/06/2023] [Indexed: 10/24/2023] Open
Abstract
Across eukaryotes, large variations of genome sizes have been observed even between closely related species. Transposable elements as part of the repeated DNA have been proposed and confirmed as one of the most important contributors to genome size variation. However, the evolutionary implications of genome size variation and transposable element dynamics are not well understood. Together with phenotypic traits, they are commonly referred to as the "C-value enigma". The order Zoantharia are benthic cnidarians found from intertidal zones to the deep sea, and some species are particularly abundant in coral reefs. Despite their high ecological relevance, zoantharians have yet to be largely studied from the genomic point of view. This study aims at investigating the role of the repeatome (total content of repeated elements) in genome size variations across the order Zoantharia. To this end, whole-genomes of 32 zoantharian species representing five families were sequenced. Genome sizes were estimated and the abundances of different repeat classes were assessed. In addition, the repeat overlap between species was assessed by a sequence clustering method. The genome sizes in the dataset varied up to 2.4 fold magnitude. Significant correlations between genome size, repeated DNA content and transposable elements, respectively (Pearson's correlation test R2 = 0.47, p = 0.0016; R2 = 0.22, p = 0.05) were found, suggesting their involvement in the dynamics of genome expansion and reduction. In all species, long interspersed nuclear elements and DNA transposons were the most abundant identified elements. These transposable elements also appeared to have had a recent expansion event. This was in contrast to the comparative clustering analysis which revealed species-specific patterns of satellite elements' amplification. In summary, the genome sizes of zoantharians likely result from the complex dynamics of repeated elements. Finally, the majority of repeated elements (up to 70%) could not be annotated to a known repeat class, highlighting the need to further investigate non-model cnidarian genomes. More research is needed to understand how repeated DNA dynamics relate to zoantharian evolution and their biology.
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Affiliation(s)
- Chloé Julie Loïs Fourreau
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Hiroki Kise
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- AIST Tsukuba Central, Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, Japan
| | - Mylena Daiana Santander
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Stacy Pirro
- Iridian Genomes, Bethesda, United States of America
| | - Maximiliano M. Maronna
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Faculdade de Ciências, Universidade Estadual Paulista (UNESP), Bauru, Brazil
| | - Angelo Poliseno
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Maria E.A. Santos
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Okinawa Institute of Science and Technology, Onna, Okinawa, Japan
| | - James Davis Reimer
- Molecular Invertebrate Systematics and Ecology (MISE) Lab, Graduate School of Engineering and Science, University of the Ryukyus, Nishihara, Okinawa, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, United States of America
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22
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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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23
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Vollmer SV, Selwyn JD, Despard BA, Roesel CL. Genomic signatures of disease resistance in endangered staghorn corals. Science 2023; 381:1451-1454. [PMID: 37769073 DOI: 10.1126/science.adi3601] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/09/2023] [Indexed: 09/30/2023]
Abstract
White band disease (WBD) has caused unprecedented declines in the Caribbean Acropora corals, which are now listed as critically endangered species. Highly disease-resistant Acropora cervicornis genotypes exist, but the genetic underpinnings of disease resistance are not understood. Using transmission experiments, a newly assembled genome, and whole-genome resequencing of 76 A. cervicornis genotypes from Florida and Panama, we identified 10 genomic regions and 73 single-nucleotide polymorphisms that are associated with disease resistance and that include functional protein-coding changes in four genes involved in coral immunity and pathogen detection. Polygenic scores calculated from 10 genomic loci indicate that genetic screens can detect disease resistance in wild and nursery stocks of A. cervicornis across the Caribbean.
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Affiliation(s)
- Steven V Vollmer
- Department of Marine and Environmental Sciences, Northeastern University, 430 Nahant Road, Nahant, MA 01908, USA
| | - Jason D Selwyn
- Department of Marine and Environmental Sciences, Northeastern University, 430 Nahant Road, Nahant, MA 01908, USA
| | - Brecia A Despard
- Department of Marine and Environmental Sciences, Northeastern University, 430 Nahant Road, Nahant, MA 01908, USA
| | - Charles L Roesel
- Department of Marine and Environmental Sciences, Northeastern University, 430 Nahant Road, Nahant, MA 01908, USA
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24
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Milner DS, Galindo LJ, Irwin NAT, Richards TA. Transporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes. Annu Rev Microbiol 2023; 77:45-66. [PMID: 36944262 DOI: 10.1146/annurev-micro-032421-115538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Here we review two connected themes in evolutionary microbiology: (a) the nature of gene repertoire variation within species groups (pangenomes) and (b) the concept of metabolite transporters as accessory proteins capable of providing niche-defining "bolt-on" phenotypes. We discuss the need for improved sampling and understanding of pangenome variation in eukaryotic microbes. We then review the factors that shape the repertoire of accessory genes within pangenomes. As part of this discussion, we outline how gene duplication is a key factor in both eukaryotic pangenome variation and transporter gene family evolution. We go on to outline how, through functional characterization of transporter-encoding genes, in combination with analyses of how transporter genes are gained and lost from accessory genomes, we can reveal much about the niche range, the ecology, and the evolution of virulence of microbes. We advocate for the coordinated systematic study of eukaryotic pangenomes through genome sequencing and the functional analysis of genes found within the accessory gene repertoire.
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Affiliation(s)
- David S Milner
- Department of Biology, University of Oxford, Oxford, United Kingdom;
| | | | - Nicholas A T Irwin
- Department of Biology, University of Oxford, Oxford, United Kingdom;
- Merton College, University of Oxford, Oxford, United Kingdom
| | - Thomas A Richards
- Department of Biology, University of Oxford, Oxford, United Kingdom;
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25
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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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26
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Saldivia P, Hernández M, Isla A, Fritz R, Varela D, González-Jartín JM, Figueroa J, Botana LM, Vargas C, Yañez AJ. Proteomic and toxicological analysis of the response of dinoflagellate Alexandrium catenella to changes in NaNO 3 concentration. HARMFUL ALGAE 2023; 125:102428. [PMID: 37220981 DOI: 10.1016/j.hal.2023.102428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 03/05/2023] [Accepted: 03/18/2023] [Indexed: 05/25/2023]
Abstract
Dinoflagellates of the genus Alexandrium cause Harmful Algal Blooms (HABs) in coastal waters worldwide, damaging marine environments, aquaculture, and human health. They synthesize potent neurotoxic alkaloids known as PSTs (i.e., Paralytic Shellfish Toxins), the etiological agents of PSP (i.e., Paralytic Shellfish Poisoning). In recent decades, the eutrophication of coastal waters with inorganic nitrogen (e.g., nitrate, nitrite, and ammonia) has increased the frequency and scale of HABs. PSTs concentrations within Alexandrium cells can increase by up to 76% after a nitrogen enrichment event; however, the mechanisms that underlie their biosynthesis in dinoflagellates remains unclear. This study combines mass spectrometry, bioinformatics, and toxicology and investigates the expression profiles of PSTs in Alexandrium catenella grown in 0.4, 0.9 and 1.3 mM NaNO3. Pathway analysis of protein expression revealed that tRNA amino acylation, glycolysis, TCA cycle and pigment biosynthesis were upregulated in 0.4 mM and downregulated in 1.3 mM NaNO3 compared to those grown in 0.9 mM NaNO3. Conversely, ATP synthesis, photosynthesis and arginine biosynthesis were downregulated in 0.4 mM and upregulated in 1.3 mM NaNO3. Additionally, the expression of proteins involved in PST biosynthesis (sxtA, sxtG, sxtV, sxtW and sxtZ) and overall PST production like STX, NEO, C1, C2, GTX1-6 and dcGTX2 was higher at lower nitrate concentrations. Therefore, increased nitrogen concentrations increase protein synthesis, photosynthesis, and energy metabolism and decrease enzyme expression in PST biosynthesis and production. This research provides new clues about how the changes in the nitrate concentration can modulate different metabolic pathways and the expression of PST biosynthesis in toxigenic dinoflagellates.
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Affiliation(s)
- Pablo Saldivia
- Division of Biotechnology, MELISA Institute, Concepción, Chile; Programa de Doctorado en Biotecnología Molecular, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | | | - Adolfo Isla
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Valdivia, Chile; Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile; Laboratorio de Diagnóstico y Terapia, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Rocío Fritz
- Vicerrectoría de Investigación y Postgrado, Universidad Católica de la Santísima Concepción, Concepción, Chile
| | - Daniel Varela
- Centro i∼mar, Universidad de Los Lagos, Puerto Montt, Chile
| | - Jesús M González-Jartín
- Departamento de Farmacología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
| | - Jaime Figueroa
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile; Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Luis M Botana
- Departamento de Farmacología, Facultad de Veterinaria, Universidad de Santiago de Compostela, Lugo, Spain
| | - Cristian Vargas
- Division of Biotechnology, MELISA Institute, Concepción, Chile
| | - Alejandro J Yañez
- Interdisciplinary Center for Aquaculture Research (INCAR), Concepción, Chile; Laboratorio de Diagnóstico y Terapia, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile.
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27
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Veglia AJ, Bistolas KSI, Voolstra CR, Hume BCC, Ruscheweyh HJ, Planes S, Allemand D, Boissin E, Wincker P, Poulain J, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Zoccola D, Correa AMS, Vega Thurber RL. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes. Commun Biol 2023; 6:566. [PMID: 37264063 DOI: 10.1038/s42003-023-04917-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.
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Affiliation(s)
- Alex J Veglia
- BioSciences Department, Rice University, Houston, TX, USA
| | | | | | | | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, F-06230, Villefranche-sur-Mer, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road H91 TK33, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
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28
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Mohamed AR, Ochsenkühn MA, Kazlak AM, Moustafa A, Amin SA. The coral microbiome: towards an understanding of the molecular mechanisms of coral-microbiota interactions. FEMS Microbiol Rev 2023; 47:fuad005. [PMID: 36882224 PMCID: PMC10045912 DOI: 10.1093/femsre/fuad005] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 03/09/2023] Open
Abstract
Corals live in a complex, multipartite symbiosis with diverse microbes across kingdoms, some of which are implicated in vital functions, such as those related to resilience against climate change. However, knowledge gaps and technical challenges limit our understanding of the nature and functional significance of complex symbiotic relationships within corals. Here, we provide an overview of the complexity of the coral microbiome focusing on taxonomic diversity and functions of well-studied and cryptic microbes. Mining the coral literature indicate that while corals collectively harbour a third of all marine bacterial phyla, known bacterial symbionts and antagonists of corals represent a minute fraction of this diversity and that these taxa cluster into select genera, suggesting selective evolutionary mechanisms enabled these bacteria to gain a niche within the holobiont. Recent advances in coral microbiome research aimed at leveraging microbiome manipulation to increase coral's fitness to help mitigate heat stress-related mortality are discussed. Then, insights into the potential mechanisms through which microbiota can communicate with and modify host responses are examined by describing known recognition patterns, potential microbially derived coral epigenome effector proteins and coral gene regulation. Finally, the power of omics tools used to study corals are highlighted with emphasis on an integrated host-microbiota multiomics framework to understand the underlying mechanisms during symbiosis and climate change-driven dysbiosis.
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Affiliation(s)
- Amin R Mohamed
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Michael A Ochsenkühn
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
| | - Ahmed M Kazlak
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Ahmed Moustafa
- Systems Genomics Laboratory, American University in Cairo, New Cairo 11835, Egypt
- Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
- Department of Biology, American University in Cairo, New Cairo 11835, Egypt
| | - Shady A Amin
- Biology Program, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
- Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates
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29
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de la Fuente R, Díaz-Villanueva W, Arnau V, Moya A. Genomic Signature in Evolutionary Biology: A Review. BIOLOGY 2023; 12:biology12020322. [PMID: 36829597 PMCID: PMC9953303 DOI: 10.3390/biology12020322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023]
Abstract
Organisms are unique physical entities in which information is stored and continuously processed. The digital nature of DNA sequences enables the construction of a dynamic information reservoir. However, the distinction between the hardware and software components in the information flow is crucial to identify the mechanisms generating specific genomic signatures. In this work, we perform a bibliometric analysis to identify the different purposes of looking for particular patterns in DNA sequences associated with a given phenotype. This study has enabled us to make a conceptual breakdown of the genomic signature and differentiate the leading applications. On the one hand, it refers to gene expression profiling associated with a biological function, which may be shared across taxa. This signature is the focus of study in precision medicine. On the other hand, it also refers to characteristic patterns in species-specific DNA sequences. This interpretation plays a key role in comparative genomics, identifying evolutionary relationships. Looking at the relevant studies in our bibliographic database, we highlight the main factors causing heterogeneities in genome composition and how they can be quantified. All these findings lead us to reformulate some questions relevant to evolutionary biology.
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Affiliation(s)
- Rebeca de la Fuente
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
- Correspondence:
| | - Wladimiro Díaz-Villanueva
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
| | - Vicente Arnau
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
| | - Andrés Moya
- Institute of Integrative Systems Biology (I2Sysbio), University of Valencia and Spanish Research Council (CSIC), 46980 Valencia, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of the Valencian Community (FISABIO), 46020 Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBEResp), 28029 Madrid, Spain
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30
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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: 18] [Impact Index Per Article: 18.0] [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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31
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Puntin G, Sweet M, Fraune S, Medina M, Sharp K, Weis VM, Ziegler M. Harnessing the Power of Model Organisms To Unravel Microbial Functions in the Coral Holobiont. Microbiol Mol Biol Rev 2022; 86:e0005322. [PMID: 36287022 PMCID: PMC9769930 DOI: 10.1128/mmbr.00053-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Stony corals build the framework of coral reefs, ecosystems of immense ecological and economic importance. The existence of these ecosystems is threatened by climate change and other anthropogenic stressors that manifest in microbial dysbiosis such as coral bleaching and disease, often leading to coral mortality. Despite a significant amount of research, the mechanisms ultimately underlying these destructive phenomena, and what could prevent or mitigate them, remain to be resolved. This is mostly due to practical challenges in experimentation on corals and the highly complex nature of the coral holobiont that also includes bacteria, archaea, protists, and viruses. While the overall importance of these partners is well recognized, their specific contributions to holobiont functioning and their interspecific dynamics remain largely unexplored. Here, we review the potential of adopting model organisms as more tractable systems to address these knowledge gaps. We draw on parallels from the broader biological and biomedical fields to guide the establishment, implementation, and integration of new and emerging model organisms with the aim of addressing the specific needs of coral research. We evaluate the cnidarian models Hydra, Aiptasia, Cassiopea, and Astrangia poculata; review the fast-evolving field of coral tissue and cell cultures; and propose a framework for the establishment of "true" tropical reef-building coral models. Based on this assessment, we also suggest future research to address key aspects limiting our ability to understand and hence improve the response of reef-building corals to future ocean conditions.
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Affiliation(s)
- Giulia Puntin
- Department of Animal Ecology and Systematics, Marine Holobiomics Lab, Justus Liebig University Giessen, Giessen, Germany
| | - Michael Sweet
- Aquatic Research Facility, Environmental Sustainability Research Centre, University of Derby, Derby, United Kingdom
| | - Sebastian Fraune
- Institute for Zoology and Organismic Interactions, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Mónica Medina
- Department of Biology, Pennsylvania State University, State College, Pennsylvania, USA
| | - Koty Sharp
- Department of Biology, Marine Biology, and Environmental Science, Roger Williams University, Bristol, Rhode Island, USA
| | - Virginia M. Weis
- Department of Integrative Biology, Oregon State University, Corvallis, Oregon, USA
| | - Maren Ziegler
- Department of Animal Ecology and Systematics, Marine Holobiomics Lab, Justus Liebig University Giessen, Giessen, Germany
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32
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Stephens TG, Lee J, Jeong Y, Yoon HS, Putnam HM, Majerová E, Bhattacharya D. High-quality genome assembles from key Hawaiian coral species. Gigascience 2022; 11:6815755. [PMID: 36352542 PMCID: PMC9646523 DOI: 10.1093/gigascience/giac098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/11/2022] [Accepted: 09/22/2022] [Indexed: 11/11/2022] Open
Abstract
Background Coral reefs house about 25% of marine biodiversity and are critical for the livelihood of many communities by providing food, tourism revenue, and protection from wave surge. These magnificent ecosystems are under existential threat from anthropogenic climate change. Whereas extensive ecological and physiological studies have addressed coral response to environmental stress, high-quality reference genome data are lacking for many of these species. The latter issue hinders efforts to understand the genetic basis of stress resistance and to design informed coral conservation strategies. Results We report genome assemblies from 4 key Hawaiian coral species, Montipora capitata, Pocillopora acuta, Pocillopora meandrina, and Porites compressa. These species, or members of these genera, are distributed worldwide and therefore of broad scientific and ecological importance. For M. capitata, an initial assembly was generated from short-read Illumina and long-read PacBio data, which was then scaffolded into 14 putative chromosomes using Omni-C sequencing. For P. acuta, P. meandrina, and P. compressa, high-quality assemblies were generated using short-read Illumina and long-read PacBio data. The P. acuta assembly is from a triploid individual, making it the first reference genome of a nondiploid coral animal. Conclusions These assemblies are significant improvements over available data and provide invaluable resources for supporting multiomics studies into coral biology, not just in Hawaiʻi but also in other regions, where related species exist. The P. acuta assembly provides a platform for studying polyploidy in corals and its role in genome evolution and stress adaptation in these organisms.
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Affiliation(s)
- Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, NJ 08901, USA
| | - JunMo Lee
- Department of Oceanography, Kyungpook National University , Daegu, Buk-gu 41566, Korea
| | - YuJin Jeong
- Department of Oceanography, Kyungpook National University , Daegu, Buk-gu 41566, Korea
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University , Suwon 16419, Korea
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island , Kingston, RI 02881, USA
| | - Eva Majerová
- Hawaiʻi Institute of Marine Biology , Kāneʻohe, HI 96744, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University , New Brunswick, NJ 08901, USA
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33
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Benites LF, Stephens TG, Bhattacharya D. Multiple waves of viral invasions in Symbiodiniaceae algal genomes. Virus Evol 2022; 8:veac101. [PMID: 36381231 PMCID: PMC9651163 DOI: 10.1093/ve/veac101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/29/2022] [Accepted: 10/25/2022] [Indexed: 08/13/2023] Open
Abstract
Dinoflagellates from the family Symbiodiniaceae are phototrophic marine protists that engage in symbiosis with diverse hosts. Their large and distinct genomes are characterized by pervasive gene duplication and large-scale retroposition events. However, little is known about the role and scale of horizontal gene transfer (HGT) in the evolution of this algal family. In other dinoflagellates, high levels of HGTs have been observed, linked to major genomic transitions, such as the appearance of a viral-acquired nucleoprotein that originated via HGT from a large DNA algal virus. Previous work showed that Symbiodiniaceae from different hosts are actively infected by viral groups, such as giant DNA viruses and ssRNA viruses, that may play an important role in coral health. Latent viral infections may also occur, whereby viruses could persist in the cytoplasm or integrate into the host genome as a provirus. This hypothesis received experimental support; however, the cellular localization of putative latent viruses and their taxonomic affiliation are still unknown. In addition, despite the finding of viral sequences in some genomes of Symbiodiniaceae, viral origin, taxonomic breadth, and metabolic potential have not been explored. To address these questions, we searched for putative viral-derived proteins in thirteen Symbiodiniaceae genomes. We found fifty-nine candidate viral-derived HGTs that gave rise to twelve phylogenies across ten genomes. We also describe the taxonomic affiliation of these virus-related sequences, their structure, and their genomic context. These results lead us to propose a model to explain the origin and fate of Symbiodiniaceae viral acquisitions.
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Affiliation(s)
- L Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
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34
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Jadhav DB, Sriramkumar Y, Roy S. The enigmatic clock of dinoflagellates, is it unique? Front Microbiol 2022; 13:1004074. [PMID: 36338102 PMCID: PMC9627503 DOI: 10.3389/fmicb.2022.1004074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/29/2022] [Indexed: 12/01/2022] Open
Abstract
Dinoflagellate clocks are unique as they show no resemblance to any known model eukaryotic or prokaryotic clock architecture. Dinoflagellates are unicellular, photosynthetic, primarily marine eukaryotes are known for their unique biology and rhythmic physiology. Their physiological rhythms are driven by an internal oscillator whose molecular underpinnings are yet unknown. One of the primary reasons that slowed the progression of their molecular studies is their extremely large and repetitive genomes. Dinoflagellates are primary contributors to the global carbon cycle and oxygen levels, therefore, comprehending their internal clock architecture and its interaction with their physiology becomes a subject of utmost importance. The advent of high throughput Omics technology provided the momentum to understand the molecular architecture and functioning of the dinoflagellate clocks. We use these extensive databases to perform meta-analysis to reveal the status of clock components in dinoflagellates. In this article, we will delve deep into the various “Omics” studies that catered to various breakthroughs in the field of circadian biology in these organisms that were not possible earlier. The overall inference from these omics studies points toward an uncommon eukaryotic clock model, which can provide promising leads to understand the evolution of molecular clocks.
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35
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Full-Length Transcriptome Maps of Reef-Building Coral Illuminate the Molecular Basis of Calcification, Symbiosis, and Circa-Dian Genes. Int J Mol Sci 2022; 23:ijms231911135. [PMID: 36232445 PMCID: PMC9570262 DOI: 10.3390/ijms231911135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/08/2022] [Accepted: 09/19/2022] [Indexed: 11/17/2022] Open
Abstract
Coral transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Here, we sequence the full-length transcriptomes of four common and frequently dominant reef-building corals using the PacBio Sequel II platform. We obtain information on reported gene functions, structures, and expression profiles. Among them, a comparative analysis of biomineralization-related genes provides insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiont Symbiodiniaceae are also isolated and annotated from the holobiont sequence data. Finally, a phylogenetic analysis of key circadian clock genes among 40 evolutionarily representative species indicates that there are four key members in early metazoans, including cry genes; Clock or Npas2; cyc or Arntl; and tim, while per, as the fifth member, occurs in Bilateria. In summary, this work provides a foundation for further work on the manipulation of skeleton production or symbiosis to promote the survival of these important organisms.
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36
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Yang F, Wei Z, Long L. Response mechanisms to ocean warming exposure in Effrenium voratum (Symbiodiniaceae). MARINE POLLUTION BULLETIN 2022; 182:114032. [PMID: 35969902 DOI: 10.1016/j.marpolbul.2022.114032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 07/31/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Ocean warming is an extreme environment event that has profound and lasting impacts on Symbiodiniaceae. However, their response mechanisms to elevated temperature exposure are poorly understood. In this study, the physiological and transcriptional responses of Effrenium voratum (Symbiodiniaceae) to ocean warming were examined. After exposure to 30 °C, no significant variations in growth, chlorophyll a, or photosynthetic and respiration rates were observed, while a higher temperature (34 °C) significantly reduced these physiological measurements. Meanwhile, lipid content and fatty acid composition were altered at high temperature (i.e., elevated degree of fatty acid saturation). Such biochemical constituents likely contributed to the mitigation of the negative effects of elevated temperatures. Furthermore, higher expression levels of genes related to the synthesis and elongation of fatty acids were detected at high temperature. The adjustment of lipids and fatty acid composition may be a potential mechanism by which E. voratum may survive under future global warming. ONE SENTENCE SUMMARY: The adjustment of lipids and fatty acid composition may be a potential mechanism by which E. voratum acclimate to future global warming.
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Affiliation(s)
- Fangfang Yang
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China
| | - Zhangliang Wei
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Lijuan Long
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Southern Marine Science and Engineering Guangdong Laboratory, Guangzhou 511458, China.
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37
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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: 9] [Impact Index Per Article: 4.5] [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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38
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Wu X, Li L, Lin S. Energy metabolism and genetic information processing mark major transitions in the life history of Scrippsiella acuminata (Dinophyceae). HARMFUL ALGAE 2022; 116:102248. [PMID: 35710202 DOI: 10.1016/j.hal.2022.102248] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 05/01/2022] [Accepted: 05/05/2022] [Indexed: 06/15/2023]
Abstract
Many dinoflagellates perform sexual reproduction and form cysts as a life history strategy to survive adverse environmental conditions and seed annual harmful algal blooms (HABs). The molecular mechanisms underpinning the life stage transitions can provide clues about how key environmental factors induce encystment and initiation of a HAB but are still poorly understood. Here, we conducted an integrated physiological and transcriptomic study to unravel the mechanisms in Scrippsiella acuminata. We established a culture from a bloom, induced cyst formation, and divided the process into four life stages. Transcriptomic analysis of these stages revealed 19,900 differentially expressed genes (DEGs). The expression of genes related to photosynthesis was significantly up-regulated from vegetative stage to immature cyst stage, consistent with the marked increase in cell contents of energy-storing macromolecules (carbohydrates and lipids). When proceeding to resting cysts, most photosynthesis genes were down-regulated while "genetic information processing" related genes were up-regulated. Comparing germinating cysts with resting cysts revealed 100 DEGs involved in energy metabolism, indicating a high energy requirement of germination. In addition, the transition from germinating cysts to vegetative cells featured up-regulation of photosynthesis. Our results demonstrate that energy storage and consumption play a pivotal role in cyst formation and germination respectively and genetic information processing is crucial in cyst dormancy.
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Affiliation(s)
- Xiaomei Wu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
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39
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Shah S, Lonhienne T, Murray CE, Chen Y, Dougan KE, Low YS, Williams CM, Schenk G, Walter GH, Guddat LW, Chan CX. Genome-Guided Analysis of Seven Weed Species Reveals Conserved Sequence and Structural Features of Key Gene Targets for Herbicide Development. FRONTIERS IN PLANT SCIENCE 2022; 13:909073. [PMID: 35845697 PMCID: PMC9277346 DOI: 10.3389/fpls.2022.909073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Herbicides are commonly deployed as the front-line treatment to control infestations of weeds in native ecosystems and among crop plants in agriculture. However, the prevalence of herbicide resistance in many species is a major global challenge. The specificity and effectiveness of herbicides acting on diverse weed species are tightly linked to targeted proteins. The conservation and variance at these sites among different weed species remain largely unexplored. Using novel genome data in a genome-guided approach, 12 common herbicide-target genes and their coded proteins were identified from seven species of Weeds of National Significance in Australia: Alternanthera philoxeroides (alligator weed), Lycium ferocissimum (African boxthorn), Senecio madagascariensis (fireweed), Lantana camara (lantana), Parthenium hysterophorus (parthenium), Cryptostegia grandiflora (rubber vine), and Eichhornia crassipes (water hyacinth). Gene and protein sequences targeted by the acetolactate synthase (ALS) inhibitors and glyphosate were recovered. Compared to structurally resolved homologous proteins as reference, high sequence conservation was observed at the herbicide-target sites in the ALS (target for ALS inhibitors), and in 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase (target for glyphosate). Although the sequences are largely conserved in the seven phylogenetically diverse species, mutations observed in the ALS proteins of fireweed and parthenium suggest resistance of these weeds to ALS-inhibiting and other herbicides. These protein sites remain as attractive targets for the development of novel inhibitors and herbicides. This notion is reinforced by the results from the phylogenetic analysis of the 12 proteins, which reveal a largely consistent vertical inheritance in their evolutionary histories. These results demonstrate the utility of high-throughput genome sequencing to rapidly identify and characterize gene targets by computational methods, bypassing the experimental characterization of individual genes. Data generated from this study provide a useful reference for future investigations in herbicide discovery and development.
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Affiliation(s)
- Sarah Shah
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Thierry Lonhienne
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Cody-Ellen Murray
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yibi Chen
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Katherine E. Dougan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Yu Shang Low
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Gerhard Schenk
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- Sustainable Minerals Institute, The University of Queensland, Brisbane, QLD, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Gimme H. Walter
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Luke W. Guddat
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
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Cowen LJ, Putnam HM. Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience. Annu Rev Biomed Data Sci 2022; 5:205-231. [PMID: 35537462 DOI: 10.1146/annurev-biodatasci-122120-030732] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coral reefs are home to over two million species and provide habitat for roughly 25% of all marine animals, but they are being severely threatened by pollution and climate change. A large amount of genomic, transcriptomic, and other omics data is becoming increasingly available from different species of reef-building corals, the unicellular dinoflagellates, and the coral microbiome (bacteria, archaea, viruses, fungi, etc.). Such new data present an opportunity for bioinformatics researchers and computational biologists to contribute to a timely, compelling, and urgent investigation of critical factors that influence reef health and resilience. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 5 is August 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Lenore J Cowen
- Department of Computer Science, Tufts University, Medford, Massachusetts, USA;
| | - Hollie M Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, USA;
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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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Proteome metabolome and transcriptome data for three Symbiodiniaceae under ambient and heat stress conditions. Sci Data 2022; 9:153. [PMID: 35383179 PMCID: PMC8983644 DOI: 10.1038/s41597-022-01258-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 03/14/2022] [Indexed: 12/12/2022] Open
Abstract
The Symbiodiniaceae are a taxonomically and functionally diverse family of marine dinoflagellates. Their symbiotic relationship with invertebrates such as scleractinian corals has made them the focus of decades of research to resolve the underlying biology regulating their sensitivity to stressors, particularly thermal stress. Research to-date suggests that Symbiodiniaceae stress sensitivity is governed by a complex interplay between phylogenetic dependent and independent traits (diversity of characteristics of a species). Consequently, there is a need for datasets that simultaneously broadly resolve molecular and physiological processes under stressed and non-stressed conditions. Therefore, we provide a dataset simultaneously generating transcriptome, metabolome, and proteome data for three ecologically important Symbiodiniaceae isolates under nutrient replete growth conditions and two temperature treatments (ca. 26 °C and 32 °C). Elevated sea surface temperature is primarily responsible for coral bleaching events that occur when the coral-Symbiodiniaceae relationship has been disrupted. Symbiodiniaceae can strongly influence their host's response to thermal stress and consequently it is necessary to resolve drivers of Symbiodiniaceae heat stress tolerance. We anticipate these datasets to expand our understanding on the key genotypic and functional properties that influence the sensitivities of Symbiodiniaceae to thermal stress.
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Marangoni LFB, Beraud E, Ferrier-Pagès C. Polystyrene nanoplastics impair the photosynthetic capacities of Symbiodiniaceae and promote coral bleaching. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:152136. [PMID: 34921886 DOI: 10.1016/j.scitotenv.2021.152136] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 11/15/2021] [Accepted: 11/28/2021] [Indexed: 06/14/2023]
Abstract
Reef-building corals are increasingly threatened by global and regional stresses, which affect the stability of the coral-Symbiodiniaceae association. Among them, plastic pollution has been an ongoing and growing concern. Whereas several studies have highlighted the detrimental impact of microplastics (0.1 μm-5 mm) on corals and their symbiotic dinoflagellate algae, the physiological changes induced by nanoplastic (NP, <0.1 μm) pollution are still poorly known. Long-term experiments (4 weeks) were conducted to investigate the effects of ecologically relevant NP concentrations (0 to 0.5 mg/L of 20 nm polystyrene NPs) on two Symbiodiniaceae in culture [CCMP2467 or Clade A1 and pd44b or Clade F1]. The effects of 0.5 mg/L NPs were also evaluated on Clade A1 living in symbiosis with the coral Stylophora pistillata, to assess the in hospite effects of NPs on coral symbionts. The photosynthetic efficiency of photosystem II, the oxidative status of the Symbiodiniaceae and the coral host, as well as the host-symbiont stability were evaluated at the end of the experiment. Symbiodiniaceae in culture exhibited a significant decrease in the maximal electron transport rate (ETRmax) at NP concentrations as low as 0.005 mg/L, highlighting an impairment of the photosynthetic capacities of the dinoflagellates in presence of nanoplastics. Also, Clade A1 exhibited a significant decrease in its Total Antioxidant Capacity (TAC) and an increase in Lipid Peroxidation (LPO), which evidence oxidative stress and cellular damage. Interestingly, Clade A1 in hospite did not show any signs of oxidative stress, however, the coral host exhibited increased TAC and LPO. Additionally, exposure of S. pistillata to 0.5 mg/L NPs induced significant bleaching (loss of symbionts and photosynthetic pigments). Overall, NPs were detrimental for both the Symbiodiniaceae in culture and the host-symbiont association. In the future, the persistence of reef corals may be severely impacted by the cumulative effects of nanoplastic pollution along with global warming.
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Affiliation(s)
- Laura F B Marangoni
- Centre Scientifique de Monaco, Coral Ecophysiology Team, 8 Quai Antoine 1er, MC-98000, Monaco; Smithsonian Tropical Research Institute, Smithsonian Institution, Ciudad de Panamá, 0843-03092, Panama.
| | - Eric Beraud
- Centre Scientifique de Monaco, Coral Ecophysiology Team, 8 Quai Antoine 1er, MC-98000, Monaco
| | - Christine Ferrier-Pagès
- Centre Scientifique de Monaco, Coral Ecophysiology Team, 8 Quai Antoine 1er, MC-98000, Monaco
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Cuadrado Á, Figueroa RI, Sixto M, Bravo I, De Bustos A. First record of the spatial organization of the nucleosome-less chromatin of dinoflagellates: The nonrandom distribution of microsatellites and bipolar arrangement of telomeres in the nucleus of Gambierdiscus australes (Dinophyceae). JOURNAL OF PHYCOLOGY 2022; 58:297-307. [PMID: 35038777 DOI: 10.1111/jpy.13236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Dinoflagellates are a group of protists whose exceptionally large genome is organized in permanently condensed nucleosome-less chromosomes. In this study, we examined the potential role of repetitive DNAs in both the structure of dinoflagellate chromosomes and the architecture of the dinoflagellate nucleus. Non-denaturing fluorescent in situ hybridization (ND-FSH) was used to determine the abundance and physical distribution of telomeric DNA and 16 microsatellites (1- to 4-bp repeats) in the nucleus of Gambierdiscus australes. The results showed an increased relative abundance of the different microsatellite motifs with increasing GC content. Two ND-FISH probes, (A)20 and (AAT)5 , did not yield signals whereas the remainder revealed a dispersed but nonrandom distribution of the microsatellites, mostly in clusters. The bean-shaped interphase nucleus of G. australes contained a region with a high density of trinucleotides. This nuclear compartment was located between the nucleolar organizer region (NOR), located on the concave side of the nucleus, and the convex side. Telomeric DNA was grouped in multiple foci and distributed in two polarized compartments: one associated with the NOR and the other peripherally located along the convex side of the nucleus. Changes in the position of the telomeres during cell division evidenced their dynamic distribution and thus that of the chromosomes during dinomitosis. These insights into the spatial organization of microsatellites and telomeres and thus into the nuclear architecture of G. australes will open up new lines of research into the structure and function of the nucleosome-less chromatin of dinoflagellates.
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Affiliation(s)
- Ángeles Cuadrado
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá (UAH), Alcalá de Henares, Madrid, 28805, Spain
| | - Rosa I Figueroa
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía (IEO-CSIC), Subida a Radio Faro 50, Vigo, 36390, Spain
| | - Marta Sixto
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía (IEO-CSIC), Subida a Radio Faro 50, Vigo, 36390, Spain
- Campus do Mar, Facultad de Ciencias del Mar, Universidad de Vigo, Vigo, 36311, Spain
| | - Isabel Bravo
- Centro Oceanográfico de Vigo, Instituto Español de Oceanografía (IEO-CSIC), Subida a Radio Faro 50, Vigo, 36390, Spain
| | - Alfredo De Bustos
- Departamento de Biomedicina y Biotecnología, Universidad de Alcalá (UAH), Alcalá de Henares, Madrid, 28805, Spain
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45
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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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46
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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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47
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Coelho JC, Calhoun ED, Calhoun GN, Poole AZ. Patchy Distribution of GTPases of Immunity Associated Proteins (GIMAP) within Cnidarians and Dinoflagellates Suggests a Complex Evolutionary History. Genome Biol Evol 2022; 14:6500283. [PMID: 35015849 PMCID: PMC8857920 DOI: 10.1093/gbe/evac002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 11/24/2022] Open
Abstract
GTPases of Immunity-Associated Proteins (GIMAP) are a group of small GTP-binding proteins found in a variety of organisms, including vertebrates, invertebrates, and plants. These proteins are characterized by the highly conserved AIG1 domain, and in vertebrates, have been implicated in regulation of the immune system as well as apoptosis and autophagy, though their exact mechanism of action remains unclear. Recent work on cnidarian GIMAPs suggests a conserved role in immunity, apoptosis, and autophagy—three processes involved in coral bleaching, or the breakdown of cnidarian-dinoflagellate symbiosis. Therefore, to further understand the evolution of GIMAPs in this group of organisms, the purpose of this study was to characterize GIMAP or GIMAP-like sequences utilizing publicly available genomic and transcriptomic data in species across the cnidarian phylogeny. The results revealed a patchy distribution of GIMAPs in cnidarians, with three distinct types referred to as L-GIMAP, S-GIMAP, and GIMAP-like. Additionally, GIMAPs were present in most dinoflagellate species and formed seven well-supported clades. Overall, these results elucidate the distribution of GIMAPs within two distantly related eukaryotic groups and represent the first in-depth investigation on the evolution of these proteins within both protists and basal metazoans.
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Affiliation(s)
- Jenny C Coelho
- Department of Biology, Berry College, 2277 Martha Berry Highway NW, Mt. Berry GA, 30149, USA.,Department of Biology, University of North Carolina at Chapel Hill, 120 South Rd, Chapel Hill, NC 27599, USA
| | - Ethan D Calhoun
- Department of Biology, Berry College, 2277 Martha Berry Highway NW, Mt. Berry GA, 30149, USA
| | - Grant N Calhoun
- Department of Biology, Berry College, 2277 Martha Berry Highway NW, Mt. Berry GA, 30149, USA
| | - Angela Z Poole
- Department of Biology, Berry College, 2277 Martha Berry Highway NW, Mt. Berry GA, 30149, USA
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Erlendson AA, Freitag M. Not all Is SET for Methylation: Evolution of Eukaryotic Protein Methyltransferases. Methods Mol Biol 2022; 2529:3-40. [PMID: 35733008 DOI: 10.1007/978-1-0716-2481-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Dynamic posttranslational modifications to canonical histones that constitute the nucleosome (H2A, H2B, H3, and H4) control all aspects of enzymatic transactions with DNA. Histone methylation has been studied heavily for the past 20 years, and our mechanistic understanding of the control and function of individual methylation events on specific histone arginine and lysine residues has been greatly improved over the past decade, driven by excellent new tools and methods. Here, we will summarize what is known about the distribution and some of the functions of protein methyltransferases from all major eukaryotic supergroups. The main conclusion is that protein, and specifically histone, methylation is an ancient process. Many taxa in all supergroups have lost some subfamilies of both protein arginine methyltransferases (PRMT) and the heavily studied SET domain lysine methyltransferases (KMT). Over time, novel subfamilies, especially of SET domain proteins, arose. We use the interactions between H3K27 and H3K36 methylation as one example for the complex circuitry of histone modifications that make up the "histone code," and we discuss one recent example (Paramecium Ezl1) for how extant enzymes that may resemble more ancient SET domain KMTs are able to modify two lysine residues that have divergent functions in plants, fungi, and animals. Complexity of SET domain KMT function in the well-studied plant and animal lineages arose not only by gene duplication but also acquisition of novel DNA- and histone-binding domains in certain subfamilies.
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Affiliation(s)
- Allyson A Erlendson
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, USA.
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Liu Y, Liao X, Han T, Su A, Guo Z, Lu N, He C, Lu Z. Full-Length Transcriptome Sequencing of the Scleractinian Coral Montipora foliosa Reveals the Gene Expression Profile of Coral-Zooxanthellae Holobiont. BIOLOGY 2021; 10:biology10121274. [PMID: 34943189 PMCID: PMC8698432 DOI: 10.3390/biology10121274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/01/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Coral-zooxanthellae holobionts are one of the most productive ecosystems in the ocean. With global warming and ocean acidification, coral ecosystems are facing unprecedented challenges. To save the coral ecosystems, we need to understand the symbiosis of coral-zooxanthellae. Although some Scleractinia (stony corals) transcriptomes have been sequenced, the reliable full-length transcriptome is still lacking due to the short-read length of second-generation sequencing and the uncertainty of the assembly results. Herein, PacBio Sequel II sequencing technology polished with the Illumina RNA-seq platform was used to obtain relatively complete scleractinian coral M. foliosa transcriptome data and to quantify M. foliosa gene expression. A total of 38,365 consensus sequences and 20,751 unique genes were identified. Seven databases were used for the gene function annotation, and 19,972 genes were annotated in at least one database. We found 131 zooxanthellae transcripts and 18,829 M. foliosa transcripts. A total of 6328 lncRNAs, 847 M. foliosa transcription factors (TFs), and 2 zooxanthellae TF were identified. In zooxanthellae we found pathways related to symbiosis, such as photosynthesis and nitrogen metabolism. Pathways related to symbiosis in M. foliosa include oxidative phosphorylation and nitrogen metabolism, etc. We summarized the isoforms and expression level of the symbiont recognition genes. Among the membrane proteins, we found three pathways of glycan biosynthesis, which may be involved in the organic matter storage and monosaccharide stabilization in M. foliosa. Our results provide better material for studying coral symbiosis.
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Affiliation(s)
- Yunqing Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China; (Y.L.); (T.H.); (A.S.); (Z.G.); (N.L.)
| | - Xin Liao
- Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove Research Center, Beihai 536000, China;
| | - Tingyu Han
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China; (Y.L.); (T.H.); (A.S.); (Z.G.); (N.L.)
| | - Ao Su
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China; (Y.L.); (T.H.); (A.S.); (Z.G.); (N.L.)
| | - Zhuojun Guo
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China; (Y.L.); (T.H.); (A.S.); (Z.G.); (N.L.)
| | - Na Lu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China; (Y.L.); (T.H.); (A.S.); (Z.G.); (N.L.)
| | - Chunpeng He
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China; (Y.L.); (T.H.); (A.S.); (Z.G.); (N.L.)
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China; (Y.L.); (T.H.); (A.S.); (Z.G.); (N.L.)
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Lin S, Song B, Morse D. Spatial organization of dinoflagellate genomes: Novel insights and remaining critical questions. JOURNAL OF PHYCOLOGY 2021; 57:1674-1678. [PMID: 34389979 DOI: 10.1111/jpy.13206] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
As is true for many other aspects, genome architecture, evolution, and function in dinoflagellates are enigmatic and, in the meantime, continuous inspiration for scientific quests. Recent third-generation sequencing and Hi-C linkage analyses brought new insights into the spatial organization of symbiodiniacean genomes, revealing the topologically associated domains, discrete gene clusters and their cis and trans orientations, and relationships with transcription. Where do these new findings bring us in dinoflagellate genomics? Here, we aim to place these new results in the backdrop of the long history of research on this topic and in the context of what critical questions remain to be pursued in the future. The new data suggest, pending verification of other complete chromosome assemblies, a potential evolutionary trend in chromosome number decrease and length increase within the Symbiodiniaceae. While questions remain about the mechanics of the three-dimensional chromosome structure and cell cycle-related DNA replication, the mechanisms of gene transcription and genome size evolution, these latest findings set new starting points for further inquiries.
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Affiliation(s)
- Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
| | - Bo Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China
| | - David Morse
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Quebec, H1X 2B2, Canada
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