101
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Stephens TG, González-Pech RA, Cheng Y, Mohamed AR, Burt DW, Bhattacharya D, Ragan MA, Chan CX. Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions. BMC Biol 2020; 18:56. [PMID: 32448240 PMCID: PMC7245778 DOI: 10.1186/s12915-020-00782-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 04/20/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Dinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis of aquatic primary production; most taxa are free-living, while some can form symbiotic and parasitic associations with other organisms. However, knowledge of the molecular mechanisms that underpin the adaptation of these organisms to diverse ecological niches is limited by the scarce availability of genomic data, partly due to their large genome sizes estimated up to 250 Gbp. Currently available dinoflagellate genome data are restricted to Symbiodiniaceae (particularly symbionts of reef-building corals) and parasitic lineages, from taxa that have smaller genome size ranges, while genomic information from more diverse free-living species is still lacking. RESULTS Here, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis, isolated from the Arctic and Antarctica. We found that about 68% of the genomes are composed of repetitive sequence, with long terminal repeats likely contributing to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). For each genome, guided using full-length transcriptome data, we predicted > 50,000 high-quality protein-coding genes, of which ~40% are in unidirectional gene clusters and ~25% comprise single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial origin of ice-binding domains in cold-adapted dinoflagellates. CONCLUSIONS Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Because most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light polar environments. These genomes provide a foundational reference for future research on dinoflagellate evolution.
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Affiliation(s)
- Timothy G Stephens
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,Present Address: Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Raúl A González-Pech
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,Present address: Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Yuanyuan Cheng
- UQ Genomics Initiative, The University of Queensland, Brisbane, QLD, 4072, Australia.,Present Address: Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Amin R Mohamed
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Queensland Bioscience Precinct, Brisbane, QLD, 4067, Australia
| | - David W Burt
- UQ Genomics, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia. .,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, 4072, Australia.
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102
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Wu Z, Luo H, Yu L, Lee WH, Li L, Mak YL, Lin S, Lam PKS. Characterizing ciguatoxin (CTX)- and Non-CTX-producing strains of Gambierdiscus balechii using comparative transcriptomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 717:137184. [PMID: 32084685 DOI: 10.1016/j.scitotenv.2020.137184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/28/2020] [Accepted: 02/06/2020] [Indexed: 06/10/2023]
Abstract
Gambierdiscus spp. can produce the polyketide compound, ciguatoxin (CTX), and are hence responsible for ciguatera fish poisoning (CFP). Studying the molecular mechanism that regulates CTX production is crucial for understanding the environmental trigger of CTX as well as for better informing fishery management. Commonly, polyketide synthases are important for polyketide synthesis; however, no gene has been confirmatively assigned to CTX production. Here, suppression subtractive hybridization (SSH) and transcriptome sequencing (RNA-Seq) were used to compare a CTX-producing strain with a non-CTX-producing strain. Using both methods, a total of 52 polyketide synthase (PKS) genes were identified to be up-regulated in the CTX-producing G. balechii, including transcripts encoding single-domain PKSs as well as transcripts encoding multi-domain PKSs. Using reverse transcription quantitative PCR, the expression of these genes in the CTX-producing strain and in nitrogen-limited cultures of the strain was further documented. These data suggest that PKSs are likely involved in polyketide synthesis and potentially in CTX synthesis in this dinoflagellate species. Our study provides the candidate biomarkers for the detection of CTXs or CFP in waters or any other organisms as well as a valuable genomic resource for the research on Gambierdiscus and other dinoflagellates.
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Affiliation(s)
- Zhen Wu
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China; Department of Chemistry, City University of Hong Kong, Hong Kong, China
| | - Hao Luo
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Wai Hin Lee
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China; Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yim Ling Mak
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China; Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China; Department of Marine Sciences, University of Connecticut, Groton, CT, USA.
| | - Paul K S Lam
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China; Department of Chemistry, City University of Hong Kong, Hong Kong, China; Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
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103
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Quek RZB, Jain SS, Neo ML, Rouse GW, Huang D. Transcriptome-based target-enrichment baits for stony corals (Cnidaria: Anthozoa: Scleractinia). Mol Ecol Resour 2020; 20:807-818. [PMID: 32077619 PMCID: PMC7468246 DOI: 10.1111/1755-0998.13150] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 02/01/2020] [Accepted: 02/10/2020] [Indexed: 01/09/2023]
Abstract
Despite the ecological and economic significance of stony corals (Scleractinia), a robust understanding of their phylogeny remains elusive due to patchy taxonomic and genetic sampling, as well as the limited availability of informative markers. To increase the number of genetic loci available for phylogenomic analyses in Scleractinia, we designed 15,919 DNA enrichment baits targeting 605 orthogroups (mean 565 ± SD 366 bp) over 1,139 exon regions. A further 236 and 62 barcoding baits were designed for COI and histone H3 genes respectively for quality and contamination checks. Hybrid capture using these baits was performed on 18 coral species spanning the presently understood scleractinian phylogeny, with two corallimorpharians as outgroup. On average, 74% of all loci targeted were successfully captured for each species. Barcoding baits were matched unambiguously to their respective samples and revealed low levels of cross-contamination in accordance with expectation. We put the data through a series of stringent filtering steps to ensure only scleractinian and phylogenetically informative loci were retained, and the final probe set comprised 13,479 baits, targeting 452 loci (mean 531 ± SD 307 bp) across 865 exon regions. Maximum likelihood, Bayesian and species tree analyses recovered maximally supported, topologically congruent trees consistent with previous phylogenomic reconstructions. The phylogenomic method presented here allows for consistent capture of orthologous loci among divergent coral taxa, facilitating the pooling of data from different studies and increasing the phylogenetic sampling of scleractinians in the future.
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Affiliation(s)
- Randolph Z. B. Quek
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Sudhanshi S. Jain
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
| | - Mei Lin Neo
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Tropical Marine Science InstituteNational University of SingaporeSingaporeSingapore
| | - Greg W. Rouse
- Scripps Institution of OceanographyUniversity of California San DiegoSan DiegoCAUSA
| | - Danwei Huang
- Department of Biological SciencesNational University of SingaporeSingaporeSingapore
- Tropical Marine Science InstituteNational University of SingaporeSingaporeSingapore
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104
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Van Dolah FM, Morey JS, Milne S, Ung A, Anderson PE, Chinain M. Transcriptomic analysis of polyketide synthases in a highly ciguatoxic dinoflagellate, Gambierdiscus polynesiensis and low toxicity Gambierdiscus pacificus, from French Polynesia. PLoS One 2020; 15:e0231400. [PMID: 32294110 PMCID: PMC7159223 DOI: 10.1371/journal.pone.0231400] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 03/23/2020] [Indexed: 11/18/2022] Open
Abstract
Marine dinoflagellates produce a diversity of polyketide toxins that are accumulated in marine food webs and are responsible for a variety of seafood poisonings. Reef-associated dinoflagellates of the genus Gambierdiscus produce toxins responsible for ciguatera poisoning (CP), which causes over 50,000 cases of illness annually worldwide. The biosynthetic machinery for dinoflagellate polyketides remains poorly understood. Recent transcriptomic and genomic sequencing projects have revealed the presence of Type I modular polyketide synthases in dinoflagellates, as well as a plethora of single domain transcripts with Type I sequence homology. The current transcriptome analysis compares polyketide synthase (PKS) gene transcripts expressed in two species of Gambierdiscus from French Polynesia: a highly toxic ciguatoxin producer, G. polynesiensis, versus a non-ciguatoxic species G. pacificus, each assembled from approximately 180 million Illumina 125 nt reads using Trinity, and compares their PKS content with previously published data from other Gambierdiscus species and more distantly related dinoflagellates. Both modular and single-domain PKS transcripts were present. Single domain β-ketoacyl synthase (KS) transcripts were highly amplified in both species (98 in G. polynesiensis, 99 in G. pacificus), with smaller numbers of standalone acyl transferase (AT), ketoacyl reductase (KR), dehydratase (DH), enoyl reductase (ER), and thioesterase (TE) domains. G. polynesiensis expressed both a larger number of multidomain PKSs, and larger numbers of modules per transcript, than the non-ciguatoxic G. pacificus. The largest PKS transcript in G. polynesiensis encoded a 10,516 aa, 7 module protein, predicted to synthesize part of the polyether backbone. Transcripts and gene models representing portions of this PKS are present in other species, suggesting that its function may be performed in those species by multiple interacting proteins. This study contributes to the building consensus that dinoflagellates utilize a combination of Type I modular and single domain PKS proteins, in an as yet undefined manner, to synthesize polyketides.
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Affiliation(s)
- Frances M. Van Dolah
- Marine Genomics Core, Hollings Marine Laboratory, Charleston, SC, United States of America
- * E-mail:
| | - Jeanine S. Morey
- Marine Genomics Core, Hollings Marine Laboratory, Charleston, SC, United States of America
| | - Shard Milne
- Charleston Computational Genomics Group, Department of Computer Science, College of Charleston, Charleston, SC, United States of America
| | - André Ung
- Laboratoire des Biotoxines Marines, Institut Louis Malardé—UMR 241 EIO, Papeete, Tahiti, French Polynesia
| | - Paul E. Anderson
- Charleston Computational Genomics Group, Department of Computer Science, College of Charleston, Charleston, SC, United States of America
| | - Mireille Chinain
- Laboratoire des Biotoxines Marines, Institut Louis Malardé—UMR 241 EIO, Papeete, Tahiti, French Polynesia
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105
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Chakravarti LJ, Buerger P, Levin RA, van Oppen MJH. Gene regulation underpinning increased thermal tolerance in a laboratory-evolved coral photosymbiont. Mol Ecol 2020; 29:1684-1703. [PMID: 32268445 DOI: 10.1111/mec.15432] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 03/07/2020] [Accepted: 03/16/2020] [Indexed: 12/12/2022]
Abstract
Small increases in ocean temperature can disrupt the obligate symbiosis between corals and dinoflagellate microalgae, resulting in coral bleaching. Little is known about the genes that drive the physiological and bleaching response of algal symbionts to elevated temperature. Moreover, many studies to-date have compared highly divergent strains, making it challenging to accredit specific genes to contrasting traits. Here, we compare transcriptional responses at ambient (27°C) and bleaching-relevant (31°C) temperatures in a monoclonal, wild-type (WT) strain of Symbiodiniaceae to those of a selected-strain (SS), derived from the same monoclonal culture and experimentally evolved to elevated temperature over 80 generations (2.5 years). Thousands of genes were differentially expressed at a log fold-change of >8 between the WT and SS over a 35 days temperature treatment period. At 31°C, WT cells exhibited a temporally unstable transcriptomic response upregulating genes involved in the universal stress response such as molecular chaperoning, protein repair, protein degradation and DNA repair. Comparatively, SS cells exhibited a temporally stable transcriptomic response and downregulated many stress response genes that were upregulated by the WT. Among the most highly upregulated genes in the SS at 31°C were algal transcription factors and a gene probably of bacterial origin that encodes a type II secretion system protein, suggesting interactions with bacteria may contribute to the increased thermal tolerance of the SS. Genes and functional pathways conferring thermal tolerance in the SS could be targeted in future genetic engineering experiments designed to develop thermally resilient algal symbionts for use in coral restoration and conservation.
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Affiliation(s)
- Leela J Chakravarti
- Australian Institute of Marine Science, Townsville MC, Qld, Australia.,AIMS@JCU, Australian Institute of Marine Science, College of Marine and Environmental Sciences, James Cook University, Townsville, Qld, Australia.,College of Marine and Environmental Sciences, James Cook University, Townsville, Qld, Australia.,Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, Qld, Australia
| | - Patrick Buerger
- CSIRO, Land & Water, Canberra, ACT, Australia.,School of BioSciences, University of Melbourne, Parkville, Vic, Australia
| | | | - Madeleine J H van Oppen
- Australian Institute of Marine Science, Townsville MC, Qld, Australia.,School of BioSciences, University of Melbourne, Parkville, Vic, Australia
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106
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Camp EF, Kahlke T, Nitschke MR, Varkey D, Fisher NL, Fujise L, Goyen S, Hughes DJ, Lawson CA, Ros M, Woodcock S, Xiao K, Leggat W, Suggett DJ. Revealing changes in the microbiome of Symbiodiniaceae under thermal stress. Environ Microbiol 2020; 22:1294-1309. [DOI: 10.1111/1462-2920.14935] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 01/08/2020] [Accepted: 01/27/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Emma F. Camp
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Tim Kahlke
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Matthew R. Nitschke
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
- School of Biological SciencesVictoria University of Wellington Wellington New Zealand
| | - Deepa Varkey
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
- Department of Molecular SciencesMacquarie University Sydney NSW 2109 Australia
| | - Nerissa L. Fisher
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Lisa Fujise
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Samantha Goyen
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - David J. Hughes
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Caitlin A. Lawson
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Mickael Ros
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Stephen Woodcock
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - Kun Xiao
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
| | - William Leggat
- School of Environmental and Life SciencesUniversity of Newcastle Ourimbah NSW 2308 Australia
| | - David J. Suggett
- Climate Change ClusterUniversity of Technology Sydney Broadway NSW 2007 Australia
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107
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van der Burg CA, Pavasovic A, Gilding EK, Pelzer ES, Surm JM, Smith HL, Walsh TP, Prentis PJ. The Rapid Regenerative Response of a Model Sea Anemone Species Exaiptasia pallida Is Characterised by Tissue Plasticity and Highly Coordinated Cell Communication. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:285-307. [PMID: 32016679 DOI: 10.1007/s10126-020-09951-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 01/20/2020] [Indexed: 06/10/2023]
Abstract
Regeneration of a limb or tissue can be achieved through multiple different pathways and mechanisms. The sea anemone Exaiptasia pallida has been observed to have excellent regenerative proficiency, but this has not yet been described transcriptionally. In this study, we examined the genetic expression changes during a regenerative timecourse and reported key genes involved in regeneration and wound healing. We found that the major response was an early (within the first 8 h) upregulation of genes involved in cellular movement and cell communication, which likely contribute to a high level of tissue plasticity resulting in the rapid regeneration response observed in this species. We find the immune system was only transcriptionally active in the first 8 h post-amputation and conclude, in accordance with previous literature, that the immune system and regeneration have an inverse relationship. Fifty-nine genes (3.8% of total) differentially expressed during regeneration were identified as having no orthologues in other species, indicating that regeneration in E. pallida may rely on the activation of species-specific novel genes. Additionally, taxonomically restricted novel genes, including species-specific novels, and highly conserved genes were identified throughout the regenerative timecourse, showing that both may work in concert to achieve complete regeneration.
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Affiliation(s)
- Chloé A van der Burg
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, 4059, Australia.
| | - Ana Pavasovic
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, 4059, Australia
| | - Edward K Gilding
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, 4067, Australia
| | - Elise S Pelzer
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, 4059, Australia
| | - Joachim M Surm
- Department of Ecology, Evolution and Behavior, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Hayden L Smith
- Earth, Environment and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Institute for Future Environments, Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Terence P Walsh
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, QLD, 4059, Australia
| | - Peter J Prentis
- Earth, Environment and Biological Sciences, Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- Institute for Future Environments, Science and Engineering Faculty, Queensland University of Technology, Brisbane, QLD, 4000, Australia
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108
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Alves Monteiro HJ, Brahmi C, Mayfield AB, Vidal-Dupiol J, Lapeyre B, Le Luyer J. Molecular mechanisms of acclimation to long-term elevated temperature exposure in marine symbioses. GLOBAL CHANGE BIOLOGY 2020; 26:1271-1284. [PMID: 31692206 DOI: 10.1111/gcb.14907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 10/02/2019] [Indexed: 06/10/2023]
Abstract
Seawater temperature rise in French Polynesia has repeatedly resulted in the bleaching of corals and giant clams. Because giant clams possess distinctive ectosymbiotic features, they represent a unique and powerful model for comparing molecular pathways involved in (a) maintenance of symbiosis and (b) acquisition of thermotolerance among coral reef organisms. Herein, we explored the physiological and transcriptomic responses of the clam hosts and their photosynthetically active symbionts over a 65 day experiment in which clams were exposed to either normal or environmentally relevant elevated seawater temperatures. Additionally, we used metabarcoding data coupled with in situ sampling/survey data to explore the relative importance of holobiont adaptation (i.e., a symbiont community shift) versus acclimation (i.e., physiological changes at the molecular level) in the clams' responses to environmental change. We finally compared transcriptomic data to publicly available genomic datasets for Symbiodiniaceae dinoflagellates (both cultured and in hospite with the coral Pocillopora damicornis) to better tease apart the responses of both hosts and specific symbiont genotypes in this mutualistic association. Gene module preservation analysis revealed that the function of the symbionts' photosystem II was impaired at high temperature, and this response was also found across all holobionts and Symbiodiniaceae lineages examined. Similarly, epigenetic modulation appeared to be a key response mechanism for symbionts in hospite with giant clams exposed to high temperatures, and such modulation was able to distinguish thermotolerant from thermosensitive Cladocopium goreaui ecotypes; epigenetic processes may, then, represent a promising research avenue for those interested in coral reef conservation in this era of changing global climate.
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Affiliation(s)
| | - Chloé Brahmi
- Université de la Polynésie Française, UMR Ecosystèmes Insulaires Océaniens, Ifremer, ILM, IRD, Tahiti, Polynésie Française
| | - Anderson B Mayfield
- National Museum of Marine Biology and Aquarium, Checheng, Taiwan
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA
| | | | - Bruno Lapeyre
- EPHE-CNRS-UPVD, USR3278-CRIOBE, Labex CORAIL, Moorea, Polynésie Française
| | - Jérémy Le Luyer
- IFREMER, UMR Ecosystèmes Insulaires Océaniens, UPF, ILM, IRD, Tahiti, Polynésie Française
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109
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Presence-absence polymorphisms of single-copy genes in the stony coral Acropora digitifera. BMC Genomics 2020; 21:158. [PMID: 32054446 PMCID: PMC7020367 DOI: 10.1186/s12864-020-6566-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 02/07/2020] [Indexed: 12/15/2022] Open
Abstract
Background Despite the importance of characterizing genetic variation among coral individuals for understanding phenotypic variation, the correlation between coral genomic diversity and phenotypic expression is still poorly understood. Results In this study, we detected a high frequency of genes showing presence–absence polymorphisms (PAPs) for single-copy genes in Acropora digitifera. Among 10,455 single-copy genes, 516 (5%) exhibited PAPs, including 32 transposable element (TE)-related genes. Five hundred sixteen genes exhibited a homozygous absence in one (102) or more than one (414) individuals (n = 33), indicating that most of the absent alleles were not rare variants. Among genes showing PAPs (PAP genes), roughly half were expressed in adults and/or larvae, and the PAP status was associated with differential expression among individuals. Although 85% of PAP genes were uncharacterized or had ambiguous annotations, 70% of these genes were specifically distributed in cnidarian lineages in eumetazoa, suggesting that these genes have functional roles related to traits related to cnidarians or the family Acroporidae or the genus Acropora. Indeed, four of these genes encoded toxins that are usually components of venom in cnidarian-specific cnidocytes. At least 17% of A. digitifera PAP genes were also PAPs in A. tenuis, the basal lineage in the genus Acropora, indicating that PAPs were shared among species in Acropora. Conclusions Expression differences caused by a high frequency of PAP genes may be a novel genomic feature in the genus Acropora; these findings will contribute to improve our understanding of correlation between genetic and phenotypic variation in corals.
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110
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Insights on the genetic repertoire of the coral Mussismilia braziliensis endosymbiont Symbiodinium. Symbiosis 2020. [DOI: 10.1007/s13199-020-00664-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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111
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Akbar MA, Mohd Yusof NY, Tahir NI, Ahmad A, Usup G, Sahrani FK, Bunawan H. Biosynthesis of Saxitoxin in Marine Dinoflagellates: An Omics Perspective. Mar Drugs 2020; 18:md18020103. [PMID: 32033403 PMCID: PMC7073992 DOI: 10.3390/md18020103] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/09/2020] [Accepted: 01/09/2020] [Indexed: 02/07/2023] Open
Abstract
Saxitoxin is an alkaloid neurotoxin originally isolated from the clam Saxidomus giganteus in 1957. This group of neurotoxins is produced by several species of freshwater cyanobacteria and marine dinoflagellates. The saxitoxin biosynthesis pathway was described for the first time in the 1980s and, since then, it was studied in more than seven cyanobacterial genera, comprising 26 genes that form a cluster ranging from 25.7 kb to 35 kb in sequence length. Due to the complexity of the genomic landscape, saxitoxin biosynthesis in dinoflagellates remains unknown. In order to reveal and understand the dynamics of the activity in such impressive unicellular organisms with a complex genome, a strategy that can carefully engage them in a systems view is necessary. Advances in omics technology (the collective tools of biological sciences) facilitated high-throughput studies of the genome, transcriptome, proteome, and metabolome of dinoflagellates. The omics approach was utilized to address saxitoxin-producing dinoflagellates in response to environmental stresses to improve understanding of dinoflagellates gene–environment interactions. Therefore, in this review, the progress in understanding dinoflagellate saxitoxin biosynthesis using an omics approach is emphasized. Further potential applications of metabolomics and genomics to unravel novel insights into saxitoxin biosynthesis in dinoflagellates are also reviewed.
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Affiliation(s)
- Muhamad Afiq Akbar
- School of Bioscience and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia;
| | - Nurul Yuziana Mohd Yusof
- Department of Earth Science and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (N.Y.M.Y.); (F.K.S.)
| | - Noor Idayu Tahir
- Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia;
| | - Asmat Ahmad
- University College Sabah Foundation, Jalan Sanzac, Kota Kinabalu 88100, Sabah, Malaysia; (A.A.); (G.U.)
| | - Gires Usup
- University College Sabah Foundation, Jalan Sanzac, Kota Kinabalu 88100, Sabah, Malaysia; (A.A.); (G.U.)
| | - Fathul Karim Sahrani
- Department of Earth Science and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (N.Y.M.Y.); (F.K.S.)
| | - Hamidun Bunawan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia
- Correspondence: ; Tel.: +60-389-214-546
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112
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Chen Y, González‐Pech RA, Stephens TG, Bhattacharya D, Chan CX. Evidence That Inconsistent Gene Prediction Can Mislead Analysis of Dinoflagellate Genomes. JOURNAL OF PHYCOLOGY 2020; 56:6-10. [PMID: 31713873 PMCID: PMC7065002 DOI: 10.1111/jpy.12947] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/04/2019] [Indexed: 05/05/2023]
Abstract
Comparative algal genomics often relies on predicted genes from de novo assembled genomes. However, the artifacts introduced by different gene-prediction approaches, and their impact on comparative genomic analysis remain poorly understood. Here, using available genome data from six dinoflagellate species in the Symbiodiniaceae, we identified methodological biases in the published genes that were predicted using different approaches and putative contaminant sequences in the published genome assemblies. We developed and applied a comprehensive customized workflow to predict genes from these genomes. The observed variation among predicted genes resulting from our workflow agreed with current understanding of phylogenetic relationships among these taxa, whereas the variation among the previously published genes was largely biased by the distinct approaches used in each instance. Importantly, these biases affect the inference of homologous gene families and synteny among genomes, thus impacting biological interpretation of these data. Our results demonstrate that a consistent gene-prediction approach is critical for comparative analysis of dinoflagellate genomes.
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Affiliation(s)
- Yibi Chen
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneQueensland4072Australia
- School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQueensland4072Australia
| | - Raúl A. González‐Pech
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneQueensland4072Australia
| | - Timothy G. Stephens
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneQueensland4072Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and MicrobiologyRutgers UniversityNew BrunswickNew Jersey08901USA
| | - Cheong Xin Chan
- Institute for Molecular BioscienceThe University of QueenslandBrisbaneQueensland4072Australia
- School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQueensland4072Australia
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113
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A Zeaxanthin-Producing Bacterium Isolated from the Algal Phycosphere Protects Coral Endosymbionts from Environmental Stress. mBio 2020; 11:mBio.01019-19. [PMID: 31964724 PMCID: PMC6974559 DOI: 10.1128/mbio.01019-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Occupying less than 1% of the seas, coral reefs are estimated to harbor ∼25% of all marine species. However, the destruction of coral reefs has intensified in the face of global climate changes, such as rising seawater temperatures, which induce the overproduction of reactive oxygen species harmful to corals. Although reef-building corals form complex consortia with bacteria and photosynthetic endosymbiotic algae of the family Symbiodiniaceae, the functional roles of coral-associated bacteria remain largely elusive. By manipulating the Symbiodiniaceae bacterial community, we demonstrated that a bacterium that produces an antioxidant carotenoid could mitigate thermal and light stresses in cultured Symbiodiniaceae isolated from a reef-building coral. Therefore, this study illuminates the unexplored roles of coral-associated bacteria under stressful conditions. Reef-building corals form a complex consortium with photosynthetic algae in the family Symbiodiniaceae and bacteria, collectively termed the coral holobiont. These bacteria are hypothesized to be involved in the stress resistance of the coral holobiont, but their functional roles remain largely elusive. Here, we show that cultured Symbiodiniaceae algae isolated from the reef-building coral Galaxea fascicularis are associated with novel bacteria affiliated with the family Flavobacteriaceae. Antibiotic treatment eliminated the bacteria from cultured Symbiodiniaceae, resulting in a decreased maximum quantum yield of PSII (variable fluorescence divided by maximum fluorescence [Fv/Fm]) and an increased production of reactive oxygen species (ROS) under thermal and light stresses. We then isolated this bacterial strain, named GF1. GF1 inoculation in the antibiotic-treated Symbiodiniaceae cultures restored the Fv/Fm and reduced the ROS production. Furthermore, we found that GF1 produces the carotenoid zeaxanthin, which possesses potent antioxidant activity. Zeaxanthin supplementation to cultured Symbiodiniaceae ameliorated the Fv/Fm and ROS production, suggesting that GF1 mitigates thermal and light stresses in cultured Symbiodiniaceae via zeaxanthin production. These findings could advance our understanding of the roles of bacteria in Symbiodiniaceae and the coral holobiont, thereby contributing to the development of novel approaches toward coral protection through the use of symbiotic bacteria and their metabolites.
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114
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Sprecher BN, Zhang H, Lin S. Nuclear Gene Transformation in the Dinoflagellate Oxyrrhis marina. Microorganisms 2020; 8:E126. [PMID: 31963386 PMCID: PMC7022241 DOI: 10.3390/microorganisms8010126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 11/16/2022] Open
Abstract
The lack of a robust gene transformation tool that allows proper expression of foreign genes and functional testing for the vast number of nuclear genes in dinoflagellates has greatly hampered our understanding of the fundamental biology in this ecologically important and evolutionarily unique lineage of microeukaryotes. Here, we report the development of a dinoflagellate expression vector containing various DNA elements from phylogenetically separate dinoflagellate lineages, an electroporation protocol, and successful expression of introduced genes in an early branching dinoflagellate, Oxyrrhis marina. This protocol, involving the use of Lonza's Nucleofector and a codon-optimized antibiotic resistance gene, has been successfully used to produce consistent results in several independent experiments for O. marina. It is anticipated that this protocol will be adaptable for other dinoflagellates and will allow characterization of many novel dinoflagellate genes.
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Affiliation(s)
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Rd, Groton, CT 06340, USA;
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, 1080 Shennecossett Rd, Groton, CT 06340, USA;
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115
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Li T, Yu L, Song B, Song Y, Li L, Lin X, Lin S. Genome Improvement and Core Gene Set Refinement of Fugacium kawagutii. Microorganisms 2020; 8:microorganisms8010102. [PMID: 31940756 PMCID: PMC7023079 DOI: 10.3390/microorganisms8010102] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/01/2020] [Accepted: 01/08/2020] [Indexed: 01/15/2023] Open
Abstract
Cataloging an accurate functional gene set for the Symbiodiniaceae species is crucial for addressing biological questions of dinoflagellate symbiosis with corals and other invertebrates. To improve the gene models of Fugacium kawagutii, we conducted high-throughput chromosome conformation capture (Hi-C) for the genome and Illumina combined with PacBio sequencing for the transcriptome to achieve a new genome assembly and gene prediction. A 0.937-Gbp assembly of F. kawagutii were obtained, with a N50 > 13 Mbp and the longest scaffold of 121 Mbp capped with telomere motif at both ends. Gene annotation produced 45,192 protein-coding genes, among which, 11,984 are new compared to previous versions of the genome. The newly identified genes are mainly enriched in 38 KEGG pathways including N-Glycan biosynthesis, mRNA surveillance pathway, cell cycle, autophagy, mitophagy, and fatty acid synthesis, which are important for symbiosis, nutrition, and reproduction. The newly identified genes also included those encoding O-methyltransferase (O-MT), 3-dehydroquinate synthase, homologous-pairing protein 2-like (HOP2) and meiosis protein 2 (MEI2), which function in mycosporine-like amino acids (MAAs) biosynthesis and sexual reproduction, respectively. The improved version of the gene set (Fugka_Geneset _V3) raised transcriptomic read mapping rate from 33% to 54% and BUSCO match from 29% to 55%. Further differential gene expression analysis yielded a set of stably expressed genes under variable trace metal conditions, of which 115 with annotated functions have recently been found to be stably expressed under three other conditions, thus further developing the "core gene set" of F. kawagutii. This improved genome will prove useful for future Symbiodiniaceae transcriptomic, gene structure, and gene expression studies, and the refined "core gene set" will be a valuable resource from which to develop reference genes for gene expression studies.
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Affiliation(s)
- Tangcheng Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (T.L.); (L.Y.); (L.L.)
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (T.L.); (L.Y.); (L.L.)
| | - Bo Song
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
| | - Yue Song
- BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China;
| | - Ling Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (T.L.); (L.Y.); (L.L.)
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (T.L.); (L.Y.); (L.L.)
- Correspondence: (X.L.); (S.L.)
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China; (T.L.); (L.Y.); (L.L.)
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao 266237, China
- Correspondence: (X.L.); (S.L.)
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116
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Xiang T, Lehnert E, Jinkerson RE, Clowez S, Kim RG, DeNofrio JC, Pringle JR, Grossman AR. Symbiont population control by host-symbiont metabolic interaction in Symbiodiniaceae-cnidarian associations. Nat Commun 2020; 11:108. [PMID: 31913264 PMCID: PMC6949306 DOI: 10.1038/s41467-019-13963-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/11/2019] [Indexed: 01/28/2023] Open
Abstract
In cnidarian-Symbiodiniaceae symbioses, algal endosymbiont population control within the host is needed to sustain a symbiotic relationship. However, the molecular mechanisms that underlie such population control are unclear. Here we show that a cnidarian host uses nitrogen limitation as a primary mechanism to control endosymbiont populations. Nitrogen acquisition and assimilation transcripts become elevated in symbiotic Breviolum minutum algae as they reach high-densities within the sea anemone host Exaiptasia pallida. These same transcripts increase in free-living algae deprived of nitrogen. Symbiotic algae also have an elevated carbon-to-nitrogen ratio and shift metabolism towards scavenging nitrogen from purines relative to free-living algae. Exaiptasia glutamine synthetase and glutamate synthase transcripts concomitantly increase with the algal endosymbiont population, suggesting an increased ability of the host to assimilate ammonium. These results suggest algal growth and replication in hospite is controlled by access to nitrogen, which becomes limiting for the algae as their population within the host increases. The relationship between the coral animal and symbiotic algae is essential to coral health, and researchers are turning to Exaiptasia, a model cnidarian system, to study this relationship mechanistically. Here the authors find that endosymbiotic algae become limited by nitrogen at high population densities and provide the host with high levels of fixed carbon.
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Affiliation(s)
- Tingting Xiang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA. .,Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA.
| | - Erik Lehnert
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Robert E Jinkerson
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, 92521, USA
| | - Sophie Clowez
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Rick G Kim
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Jan C DeNofrio
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - John R Pringle
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
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117
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Yu L, Li T, Li L, Lin X, Li H, Liu C, Guo C, Lin S. SAGER: a database of Symbiodiniaceae and Algal Genomic Resource. Database (Oxford) 2020; 2020:baaa051. [PMID: 32621601 PMCID: PMC7334889 DOI: 10.1093/database/baaa051] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 11/19/2022]
Abstract
Symbiodiniaceae dinoflagellates are essential endosymbionts of reef building corals and some other invertebrates. Information of their genome structure and function is critical for understanding coral symbiosis and bleaching. With the rapid development of sequencing technology, genome draft assemblies of several Symbiodiniaceae species and diverse marine algal genomes have become publicly available but spread in multiple separate locations. Here, we present a Symbiodiniaceae and Algal Genomic Resource Database (SAGER), a user-friendly online repository for integrating existing genomic data of Symbiodiniaceae species and diverse marine algal gene sets from MMETSP and PhyloDB databases. Relevant algal data are included to facilitate comparative analyses. The database is freely accessible at http://sampgr.org.cn. It provides comprehensive tools for studying gene function, expression and comparative genomics, including search tools to identify gene information from Symbiodiniaceae species, and BLAST tool to find orthologs from marine algae and protists. Moreover, SAGER integrates transcriptome datasets derived from diverse culture conditions of corresponding Symbiodiniaceae species. SAGER was developed with the capacity to incorporate future Symbiodiniaceae and algal genome and transcriptome data, and will serve as an open-access and sustained platform providing genomic and molecular tools that can be conveniently used to study Symbiodiniaceae and other marine algae. Database URL: http://sampgr.org.cn.
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Affiliation(s)
- Liying Yu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Tangcheng Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Hongfei Li
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Chichi Liu
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Chentao Guo
- State Key Laboratory of Marine Environmental Science and College of Ocean and Earth Sciences, Xiamen University, Xiamen 361102, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science and 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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118
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Maor‐Landaw K, van Oppen MJH, McFadden GI. Symbiotic lifestyle triggers drastic changes in the gene expression of the algal endosymbiont Breviolum minutum (Symbiodiniaceae). Ecol Evol 2020; 10:451-466. [PMID: 31993121 PMCID: PMC6972872 DOI: 10.1002/ece3.5910] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/25/2019] [Accepted: 11/18/2019] [Indexed: 01/13/2023] Open
Abstract
Coral-dinoflagellate symbiosis underpins the evolutionary success of corals reefs. Successful exchange of molecules between the cnidarian host and the Symbiodiniaceae algae enables the mutualistic partnership. The algae translocate photosynthate to their host in exchange for nutrients and shelter. The photosynthate must traverse multiple membranes, most likely facilitated by transporters. Here, we compared gene expression profiles of cultured, free-living Breviolum minutum with those of the homologous symbionts freshly isolated from the sea anemone Exaiptasia diaphana, a widely used model for coral hosts. Additionally, we assessed expression levels of a list of candidate host transporters of interest in anemones with and without symbionts. Our transcriptome analyses highlight the distinctive nature of the two algal life stages, with many gene expression level changes correlating to the different morphologies, cell cycles, and metabolisms adopted in hospite versus free-living. Morphogenesis-related genes that likely underpin the metamorphosis process observed when symbionts enter a host cell were up-regulated. Conversely, many down-regulated genes appear to be indicative of the protective and confined nature of the symbiosome. Our results emphasize the significance of transmembrane transport to the symbiosis, and in particular of ammonium and sugar transport. Further, we pinpoint and characterize candidate transporters-predicted to be localized variously to the algal plasma membrane, the host plasma membrane, and the symbiosome membrane-that likely serve pivotal roles in the interchange of material during symbiosis. Our study provides new insights that expand our understanding of the molecular exchanges that underpin the cnidarian-algal symbiotic relationship.
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Affiliation(s)
- Keren Maor‐Landaw
- School of BioSciencesThe University of MelbourneMelbourneVic.Australia
| | - Madeleine J. H. van Oppen
- School of BioSciencesThe University of MelbourneMelbourneVic.Australia
- Australian Institute of Marine ScienceTownsvilleQldAustralia
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119
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Genome-Wide Analysis of Cell Cycle-Regulating Genes in the Symbiotic Dinoflagellate Breviolum minutum. G3-GENES GENOMES GENETICS 2019; 9:3843-3853. [PMID: 31551286 PMCID: PMC6829154 DOI: 10.1534/g3.119.400363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
A delicate relationship exists between reef-building corals and their photosynthetic endosymbionts. Unfortunately, this relationship can be disrupted, with corals expelling these algae when temperatures rise even marginally above the average summer maximum. Interestingly, several studies indicate that failure of corals to regulate symbiont cell divisions at high temperatures may underlie this disruption; increased proliferation of symbionts may stress host cells by over-production of reactive oxygen species or by disrupting the flow of nutrients. This needs to be further investigated, so to begin deciphering the molecular mechanisms controlling the cell cycle in these organisms, we used a computational approach to identify putative cell cycle-regulating genes in the genome of the dinoflagellate Breviolum minutum. This species is important as an endosymbiont of Aiptasia pallida—an anemone that is used as a model for studying coral biology. We then correlated expression of these putative cell cycle genes with cell cycle phase in diurnally growing B. minutum in culture. This approach allowed us to identify a cyclin/cyclin-dependent kinase pair that may function in the G1/S transition—a likely point for coral cells to exert control over algal cell divisions.
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120
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Liu C, Cheng SH, Lin S. Illuminating the dark depths inside coral. Cell Microbiol 2019; 22:e13122. [PMID: 31634977 DOI: 10.1111/cmi.13122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/23/2019] [Accepted: 09/09/2019] [Indexed: 11/27/2022]
Abstract
The ability to observe in situ 3D distribution and dynamics of endosymbionts in corals is crucial for gaining a mechanistic understanding of coral bleaching and reef degradation. Here, we report the development of a tissue clearing (TC) coupled with light sheet fluorescence microscopy (LSFM) method for 3D imaging of the coral holobiont at single-cell resolution. The initial applications have demonstrated the ability of this technique to provide high spatial resolution quantitative information of endosymbiont abundance and distribution within corals. With specific fluorescent probes or assays, TC-LSFM also revealed spatial distribution and dynamics of physiological conditions (such as cell proliferation, apoptosis, and hypoxia response) in both corals and their endosymbionts. This tool is highly promising for in situ and in-depth data acquisition to illuminate coral symbiosis and health conditions in the changing marine environment, providing fundamental information for coral reef conservation and restoration.
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Affiliation(s)
- Chichi Liu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Shuk Han Cheng
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Department of Marine Sciences, University of Connecticut, Groton, Connecticut
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121
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Fajardo C, Amil-Ruiz F, Fuentes-Almagro C, De Donato M, Martinez-Rodriguez G, Escobar-Niño A, Carrasco R, Mancera JM, Fernandez-Acero FJ. An “omic” approach to Pyrocystis lunula: New insights related with this bioluminescent dinoflagellate. J Proteomics 2019; 209:103502. [DOI: 10.1016/j.jprot.2019.103502] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 01/10/2023]
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122
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A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nat Microbiol 2019; 4:2090-2100. [DOI: 10.1038/s41564-019-0532-4] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 07/05/2019] [Indexed: 11/09/2022]
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123
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González-Pech RA, Bhattacharya D, Ragan MA, Chan CX. Genome Evolution of Coral Reef Symbionts as Intracellular Residents. Trends Ecol Evol 2019; 34:799-806. [DOI: 10.1016/j.tree.2019.04.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/10/2019] [Accepted: 04/15/2019] [Indexed: 02/07/2023]
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124
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Wang X, Niu X, Chen Y, Sun Z, Han A, Lou X, Ge J, Li X, Yang Y, Jian J, Gonçalves RJ, Guan W. Transcriptome sequencing of a toxic dinoflagellate, Karenia mikimotoi subjected to stress from solar ultraviolet radiation. HARMFUL ALGAE 2019; 88:101640. [PMID: 31582153 DOI: 10.1016/j.hal.2019.101640] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
Solar ultraviolet radiation (UVR) is a stress factor in aquatic environments and may act directly or indirectly on orgnisms in the upper layers of the water column. However, UVR effects are usually species-specific and difficult to extrapolate. Here we use the HAB-forming, toxic dinoflagellate Karenia mikimotoi (which was found to be relatively resistant in previous studies) to investigate its transcriptional responses to a one-week UVR exposure. For this, batch cultures of K. mikimotoi were grown with and without UVR, and their transcriptomes (generated via RNAseq technology) were compared. RNA-seq generated 45.31 million reads, which were further assembled to 202600 unigenes (>300bp). Among these, ca. 61% were annotated with NCBI, NR, GO, KOG, PFAM, Swiss-Prot, and KEGG database. Transcriptomic analysis revealed 722 differentially expressed unigenes (DEGs, defined as being within a |log2 fold change| ≥ 2 and padj < 0.05) responding to solar UVR, which were only 0.36% of all unigenes. 716 unigenes were down-regulated, and only 6 unigenes were up-regulated in the UVR compared to non-UVR treatment. KEGG pathway further analysis revealed DEGs were involved in the different pathway; genes involved in the ribosome, endocytosis and steroid biosynthesis pathways were highly down-regulated, but this was not the case for those involved in the energy metabolisms (including photosynthesis, oxidative phosphorylation) which may contribute to the sustainable growth observed in UVR treatment. The up-regulated expression of both zinc-finger proteins (ZFPs) and ribosomal protein L11 (RPL11) may be one of the acclimated mechanisms against UVR. In addition, this work identified down-regulated genes involved in fatty acid degradation and the hydrophobic branched chain amino acids (e.g., Valine, leucine, and isoleucine), which act as structural components of cell membranes modulating lipid homeostasis or turnover. In conclusion, the present study suggests that the toxic dinoflagellate K. mikimotoi has limited transcriptomic regulation but confirms that it appears as a tolerant species in response to solar UVR. These findings expand current knowledge of gene expression in HAB-forming species in response to natural environment factors such as solar radiation.
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Affiliation(s)
- Xinjie Wang
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China; Marine Biology Institute, Shantou University, Shantou, Guangdong 515063 China
| | - Xiaoqin Niu
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Yiji Chen
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Zhewei Sun
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Axiang Han
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Xiayuan Lou
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Jingke Ge
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Xuanwen Li
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Yuqian Yang
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China
| | - Jianbo Jian
- Marine Biology Institute, Shantou University, Shantou, Guangdong 515063 China
| | - Rodrigo J Gonçalves
- Laboratorio de Oceanografía Biológica (LOBio), Centro para el Estudio de Sistemas Marinos (CESIMAR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). U9120ACD, Puerto Madryn, Argentina
| | - Wanchun Guan
- Department of Marine Biotechnology, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang 325035 China.
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125
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Omics Analysis for Dinoflagellates Biology Research. Microorganisms 2019; 7:microorganisms7090288. [PMID: 31450827 PMCID: PMC6780300 DOI: 10.3390/microorganisms7090288] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 01/13/2023] Open
Abstract
Dinoflagellates are important primary producers for marine ecosystems and are also responsible for certain essential components in human foods. However, they are also notorious for their ability to form harmful algal blooms, and cause shellfish poisoning. Although much work has been devoted to dinoflagellates in recent decades, our understanding of them at a molecular level is still limited owing to some of their challenging biological properties, such as large genome size, permanently condensed liquid-crystalline chromosomes, and the 10-fold lower ratio of protein to DNA than other eukaryotic species. In recent years, omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics, have been applied to the study of marine dinoflagellates and have uncovered many new physiological and metabolic characteristics of dinoflagellates. In this article, we review recent application of omics technologies in revealing some of the unusual features of dinoflagellate genomes and molecular mechanisms relevant to their biology, including the mechanism of harmful algal bloom formations, toxin biosynthesis, symbiosis, lipid biosynthesis, as well as species identification and evolution. We also discuss the challenges and provide prospective further study directions and applications of dinoflagellates.
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126
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Wang H, Kim H, Lim WA, Ki JS. Molecular cloning and oxidative-stress responses of a novel manganese superoxide dismutase (MnSOD) gene in the dinoflagellate Prorocentrum minimum. Mol Biol Rep 2019; 46:5955-5966. [PMID: 31407247 DOI: 10.1007/s11033-019-05029-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/07/2019] [Indexed: 10/26/2022]
Abstract
Dinoflagellate algae are microeukaryotes that have distinct genomes and gene regulation systems, making them an interesting model for studying protist evolution and genomics. In the present study, we discovered a novel manganese superoxide dismutase (PmMnSOD) gene from the marine dinoflagellate Prorocentrum minimum, examined its molecular characteristics, and evaluated its transcriptional responses to the oxidative stress-inducing contaminants, CuSO4 and NaOCl. Its cDNA was 1238 bp and contained a dinoflagellate spliced leader sequence, a 906 bp open reading frame (301 amino acids), and a poly (A) tail. The gene was coded on the nuclear genome with one 174 bp intron; signal peptide analysis showed that it might be localized to the mitochondria. Real-time PCR analysis revealed an increase in gene expression of MnSOD and SOD activity when P. minimum cells were separately exposed to CuSO4 and NaOCl. In addition, both contaminants considerably decreased chlorophyll autofluorescence, and increased intracellular reactive oxygen species. These results suggest that dinoflagellate MnSOD may be involved in protecting cells against oxidative damage.
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Affiliation(s)
- Hui Wang
- Department of Biotechnology, Sangmyung University, Seoul, 03016, South Korea
| | - Hansol Kim
- Department of Biotechnology, Sangmyung University, Seoul, 03016, South Korea
| | - Weol-Ae Lim
- Ocean Climate and Ecology Research Division, National Institute of Fisheries Science (NIFS), Busan, 46083, South Korea
| | - Jang-Seu Ki
- Department of Biotechnology, Sangmyung University, Seoul, 03016, South Korea.
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127
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Morse D. A Transcriptome-based Perspective of Meiosis in Dinoflagellates. Protist 2019; 170:397-403. [DOI: 10.1016/j.protis.2019.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/19/2019] [Accepted: 06/21/2019] [Indexed: 01/31/2023]
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128
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Jiang J, Lu Y. Metabolite profiling of Breviolum minutum in response to acidification. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2019; 213:105215. [PMID: 31200330 DOI: 10.1016/j.aquatox.2019.05.017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
Coral reefs are in significant decline globally due to climate change and environmental pollution. The ocean is becoming more acidic due to rising atmospheric pCO2, and ocean acidification is considered a major threat to coral reefs. However, little is known about the exact mechanism by which acidification impacts coral symbiosis. As an important component of the symbiotic association, to explore the responses of symbionts could greatly enhance our understanding of this issue. The present work aimed to identify metabolomic changes of Breviolum minutum in acidification (low pH) condition, and investigate the underlying mechanisms responsible. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was applied to determine metabolite profiles after exposure to ambient and acidic conditions. We analysed the resulting metabolite data, and acidification appeared to have little effect on photosynthetic parameters, but it inhibited growth. Marked alterations in metabolite pools were observed in response to acidification that may be important in acclimation to climate change. Acidification may affect the biosynthesis of amino acids and proteins, and thereby inhibit the growth of B. minutum. Metabolites identified using this approach provide targets for future analyses aimed at understanding the responses of Symbiodiniaceae to environmental disturbance.
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Affiliation(s)
- Jiaoyun Jiang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou 570228, Hainan, China; College of Life Sciences, Guangxi Normal University, Guilin 541004, Guangxi, China.
| | - Yandu Lu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou 570228, Hainan, China.
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129
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Verma A, Barua A, Ruvindy R, Savela H, Ajani PA, Murray SA. The Genetic Basis of Toxin Biosynthesis in Dinoflagellates. Microorganisms 2019; 7:E222. [PMID: 31362398 PMCID: PMC6722697 DOI: 10.3390/microorganisms7080222] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 02/07/2023] Open
Abstract
In marine ecosystems, dinoflagellates can become highly abundant and even dominant at times, despite their comparatively slow growth rates. One factor that may play a role in their ecological success is the production of complex secondary metabolite compounds that can have anti-predator, allelopathic, or other toxic effects on marine organisms, and also cause seafood poisoning in humans. Our knowledge about the genes involved in toxin biosynthesis in dinoflagellates is currently limited due to the complex genomic features of these organisms. Most recently, the sequencing of dinoflagellate transcriptomes has provided us with valuable insights into the biosynthesis of polyketide and alkaloid-based toxin molecules in dinoflagellate species. This review synthesizes the recent progress that has been made in understanding the evolution, biosynthetic pathways, and gene regulation in dinoflagellates with the aid of transcriptomic and other molecular genetic tools, and provides a pathway for future studies of dinoflagellates in this exciting omics era.
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Affiliation(s)
- Arjun Verma
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia.
| | - Abanti Barua
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
- Department of Microbiology, Noakhali Science and Technology University, Chittagong 3814, Bangladesh
| | - Rendy Ruvindy
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
| | - Henna Savela
- Finnish Environment Institute, Marine Research Centre, 00790 Helsinki, Finland
| | - Penelope A Ajani
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
| | - Shauna A Murray
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
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130
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Cunha RL, Forsman ZH, Belderok R, Knapp ISS, Castilho R, Toonen RJ. Rare coral under the genomic microscope: timing and relationships among Hawaiian Montipora. BMC Evol Biol 2019; 19:153. [PMID: 31340762 PMCID: PMC6657087 DOI: 10.1186/s12862-019-1476-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 07/11/2019] [Indexed: 11/10/2022] Open
Abstract
Background Evolutionary patterns of scleractinian (stony) corals are difficult to infer given the existence of few diagnostic characters and pervasive phenotypic plasticity. A previous study of Hawaiian Montipora (Scleractinia: Acroporidae) based on five partial mitochondrial and two nuclear genes revealed the existence of a species complex, grouping one of the rarest known species (M. dilatata, which is listed as Endangered by the International Union for Conservation of Nature - IUCN) with widespread corals of very different colony growth forms (M. flabellata and M. cf. turgescens). These previous results could result from a lack of resolution due to a limited number of markers, compositional heterogeneity or reflect biological processes such as incomplete lineage sorting (ILS) or introgression. Results All 13 mitochondrial protein-coding genes from 55 scleractinians (14 lineages from this study) were used to evaluate if a recent origin of the M. dilatata species complex or rate heterogeneity could be compromising phylogenetic inference. Rate heterogeneity detected in the mitochondrial data set seems to have no significant impacts on the phylogenies but clearly affects age estimates. Dating analyses show different estimations for the speciation of M. dilatata species complex depending on whether taking compositional heterogeneity into account (0.8 [0.05–2.6] Myr) or assuming rate homogeneity (0.4 [0.14–0.75] Myr). Genomic data also provided evidence of introgression among all analysed samples of the complex. RADseq data indicated that M. capitata colour morphs may have a genetic basis. Conclusions Despite the volume of data (over 60,000 SNPs), phylogenetic relationships within the M. dilatata species complex remain unresolved most likely due to a recent origin and ongoing introgression. Species delimitation with genomic data is not concordant with the current taxonomy, which does not reflect the true diversity of this group. Nominal species within the complex are either undergoing a speciation process or represent ecomorphs exhibiting phenotypic polymorphisms. Electronic supplementary material The online version of this article (10.1186/s12862-019-1476-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Regina L Cunha
- University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal. .,Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
| | - Zac H Forsman
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Roy Belderok
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Ingrid S S Knapp
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
| | - Rita Castilho
- University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.,Centre of Marine Sciences, CCMAR, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Robert J Toonen
- Hawai'i Institute of Marine Biology, University of Hawai'i at Mānoa, Kāne'ohe, HI, 96744, USA
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Ishii Y, Maruyama S, Takahashi H, Aihara Y, Yamaguchi T, Yamaguchi K, Shigenobu S, Kawata M, Ueno N, Minagawa J. Global Shifts in Gene Expression Profiles Accompanied with Environmental Changes in Cnidarian-Dinoflagellate Endosymbiosis. G3 (BETHESDA, MD.) 2019; 9:2337-2347. [PMID: 31097480 PMCID: PMC6643889 DOI: 10.1534/g3.118.201012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 05/15/2019] [Indexed: 12/13/2022]
Abstract
Stable endosymbiotic relationships between cnidarian animals and dinoflagellate algae are vital for sustaining coral reef ecosystems. Recent studies have shown that elevated seawater temperatures can cause the collapse of their endosymbiosis, known as 'bleaching', and result in mass mortality. However, the molecular interplay between temperature responses and symbiotic states still remains unclear. To identify candidate genes relevant to the symbiotic stability, we performed transcriptomic analyses under multiple conditions using the symbiotic and apo-symbiotic (symbiont free) Exaiptasia diaphana, an emerging model sea anemone. Gene expression patterns showed that large parts of differentially expressed genes in response to heat stress were specific to the symbiotic state, suggesting that the host sea anemone could react to environmental changes in a symbiotic state-dependent manner. Comparative analysis of expression profiles under multiple conditions highlighted candidate genes potentially important in the symbiotic state transition under heat-induced bleaching. Many of these genes were functionally associated with carbohydrate and protein metabolisms in lysosomes. Symbiont algal genes differentially expressed in hospite encode proteins related to heat shock response, calcium signaling, organellar protein transport, and sugar metabolism. Our data suggest that heat stress alters gene expression in both the hosts and symbionts. In particular, heat stress may affect the lysosome-mediated degradation and transportation of substrates such as carbohydrates through the symbiosome (phagosome-derived organelle harboring symbiont) membrane, which potentially might attenuate the stability of symbiosis and lead to bleaching-associated symbiotic state transition.
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Affiliation(s)
- Yuu Ishii
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | | | - Hiroki Takahashi
- Division of Morphogenesis, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Yusuke Aihara
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Takeshi Yamaguchi
- Division of Morphogenesis, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Katsushi Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Shuji Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Masakado Kawata
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Naoto Ueno
- Division of Morphogenesis, National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
| | - Jun Minagawa
- Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi, Japan
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Aichi, Japan
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132
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Li C, Wong JTY. DNA Damage Response Pathways in Dinoflagellates. Microorganisms 2019; 7:microorganisms7070191. [PMID: 31284474 PMCID: PMC6680887 DOI: 10.3390/microorganisms7070191] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/29/2019] [Accepted: 07/01/2019] [Indexed: 12/17/2022] Open
Abstract
Dinoflagellates are a general group of phytoplankton, ubiquitous in aquatic environments. Most dinoflagellates are non-obligate autotrophs, subjected to potential physical and chemical DNA-damaging agents, including UV irradiation, in the euphotic zone. Delay of cell cycles by irradiation, as part of DNA damage responses (DDRs), could potentially lead to growth inhibition, contributing to major errors in the estimation of primary productivity and interpretations of photo-inhibition. Their liquid crystalline chromosomes (LCCs) have large amount of abnormal bases, restricted placement of coding sequences at the chromosomes periphery, and tandem repeat-encoded genes. These chromosome characteristics, their large genome sizes, as well as the lack of architectural nucleosomes, likely contribute to possible differential responses to DNA damage agents. In this study, we sought potential dinoflagellate orthologues of eukaryotic DNA damage repair pathways, and the linking pathway with cell-cycle control in three dinoflagellate species. It appeared that major orthologues in photoreactivation, base excision repair, nucleotide excision repair, mismatch repair, double-strand break repair and homologous recombination repair are well represented in dinoflagellate genomes. Future studies should address possible differential DNA damage responses of dinoflagellates over other planktonic groups, especially in relation to possible shift of life-cycle transitions in responses to UV irradiation. This may have a potential role in the persistence of dinoflagellate red tides with the advent of climatic change.
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Affiliation(s)
- Chongping Li
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, China.
- Division of Life Science, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, China.
| | - Joseph Tin Yum Wong
- Division of Life Science, The Hong Kong University of Science and Technology, Clearwater Bay, Kowloon, Hong Kong, China.
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133
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Riaz S, Niaz Z, Khan S, Liu Y, Sui Z. Detection, characterization and expression dynamics of histone proteins in the dinoflagellate Alexandrium pacificum during growth regulation. HARMFUL ALGAE 2019; 87:101630. [PMID: 31349883 DOI: 10.1016/j.hal.2019.101630] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/29/2019] [Accepted: 06/10/2019] [Indexed: 06/10/2023]
Abstract
Histones are the most abundant proteins associated with eukaryotic nuclear DNA. The exception is dinoflagellates, which have histone protein expression that is mostly reported to be below detectable levels. In this study, we investigated the presence of histone proteins and their functions in the dinoflagellate, Alexandrium pacificum. Histone protein sequences were analyzed, focusing on phylogenetic analysis and histone code. Histone expression was analyzed during the cell cycle and under nutritionally enhanced conditions using quantitative-PCR and western blots. Acid-soluble proteins were subjected to mass spectrometry analysis. To our knowledge, this is the first report of immunological detection of histone proteins (H2B and H4) in any dinoflagellate species. Absolute quantification of histone transcript in activily dividing cells revealed significant transcription in cells. The stable expression of histones during the cell cycle suggested that the histone genes in A. pacificum belonged to a replication-independent class and appeared to have a limited role in DNA packaging. The conservation of numerous post-translationally modified residues of multiple histone variants and differential expression of histones under nutritionally enhanced conditions suggested their functional significance in dinoflagellates. However, we detected histone H2B protein only via mass spectrometry. Histone-like protein was identified as most abundant acid-soluble protein of the cells.
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Affiliation(s)
- Sadaf Riaz
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Department of Microbiology, University of Central Punjab, Lahore, Pakistan
| | - Zeeshan Niaz
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Department of Microbiology, Hazara University, Mansehra, Pakistan
| | - Sohrab Khan
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China; Department of Microbiology, Hazara University, Mansehra, Pakistan
| | - Yuan Liu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
| | - Zhenghong Sui
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
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134
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Fugacium Spliced Leader Genes Identified from Stranded RNA-Seq Datasets. Microorganisms 2019; 7:microorganisms7060171. [PMID: 31212635 PMCID: PMC6616646 DOI: 10.3390/microorganisms7060171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 05/27/2019] [Accepted: 06/05/2019] [Indexed: 01/10/2023] Open
Abstract
Trans-splicing mechanisms have been documented in many lineages that are widely distributed phylogenetically, including dinoflagellates. The spliced leader (SL) sequence itself is conserved in dinoflagellates, although its gene sequences and arrangements have diversified within or across different species. In this study, we present 18 Fugacium kawagutii SL genes identified from stranded RNA-seq reads. These genes typically have a single SL but can contain several partial SLs with lengths ranging from 103 to 292 bp. Unexpectedly, we find the SL gene transcripts contain sequences upstream of the canonical SL, suggesting that generation of mature transcripts will require additional modifications following trans-splicing. We have also identified 13 SL-like genes whose expression levels and length are comparable to Dino-SL genes. Lastly, introns in these genes were identified and a new site for Sm-protein binding was proposed. Overall, this study provides a strategy for fast identification of SL genes and identifies new sequences of F. kawagutii SL genes to supplement our understanding of trans-splicing.
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135
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Urbarova I, Forêt S, Dahl M, Emblem Å, Milazzo M, Hall-Spencer JM, Johansen SD. Ocean acidification at a coastal CO2 vent induces expression of stress-related transcripts and transposable elements in the sea anemone Anemonia viridis. PLoS One 2019; 14:e0210358. [PMID: 31067218 PMCID: PMC6505742 DOI: 10.1371/journal.pone.0210358] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 04/05/2019] [Indexed: 12/17/2022] Open
Abstract
Ocean acidification threatens to disrupt interactions between organisms throughout marine ecosystems. The diversity of reef-building organisms decreases as seawater CO2 increases along natural gradients, yet soft-bodied animals, such as sea anemones, are often resilient. We sequenced the polyA-enriched transcriptome of adult sea anemone Anemonia viridis and its dinoflagellate symbiont sampled along a natural CO2 gradient in Italy to assess stress levels in these organisms. We found that about 1.4% of the anemone transcripts, but only ~0.5% of the Symbiodinium sp. transcripts were differentially expressed. Processes enriched at high seawater CO2 were mainly linked to cellular stress, including significant up-regulation of protective cellular functions and deregulation of metabolic pathways. Transposable elements were differentially expressed at high seawater CO2, with an extreme up-regulation (> 100-fold) of the BEL-family of long terminal repeat retrotransposons. Seawater acidified by CO2 generated a significant stress reaction in A. viridis, but no bleaching was observed and Symbiodinium sp. appeared to be less affected. These observed changes indicate the mechanisms by which A. viridis acclimate to survive chronic exposure to ocean acidification conditions. We conclude that many organisms that are common in acidified conditions may nevertheless incur costs due to hypercapnia and/or lowered carbonate saturation states.
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Affiliation(s)
- Ilona Urbarova
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
- * E-mail: (IU); (SDJ)
| | - Sylvain Forêt
- Evolution, Ecology and Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Mikael Dahl
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Åse Emblem
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Marco Milazzo
- Department of Earth and Marine Sciences, University of Palermo, Palermo, Italy
| | - Jason M. Hall-Spencer
- School of Biological and Marine Science, University of Plymouth, Plymouth, United Kingdom
- Shimoda Marine Research Center, University of Tsukuba, Shimoda City, Shizuoka, Japan
| | - Steinar D. Johansen
- Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
- Genomics Research Group, Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- * E-mail: (IU); (SDJ)
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Abstract
Over 100 whole-genome sequences from algae are published or soon to be published. The rapidly increasing availability of these fundamental resources is changing how we understand one of the most diverse, complex, and understudied groups of photosynthetic eukaryotes. Genome sequences provide a window into the functional potential of individual algae, with phylogenomics and functional genomics as tools for contextualizing and transferring knowledge from reference organisms into less well-characterized systems. Remarkably, over half of the proteins encoded by algal genomes are of unknown function, highlighting the volume of functional capabilities yet to be discovered. In this review, we provide an overview of publicly available algal genomes, their associated protein inventories, and their quality, with a summary of the statuses of protein function understanding and predictions.
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Affiliation(s)
| | - Sabeeha S Merchant
- Departments of Plant and Microbial Biology and Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
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137
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Rivera-García L, Rivera-Vicéns RE, Veglia AJ, Schizas NV. De novo transcriptome assembly of the digitate morphotype of Briareum asbestinum (Octocorallia: Alcyonacea) from the southwest shelf of Puerto Rico. Mar Genomics 2019; 47:100676. [PMID: 31005610 DOI: 10.1016/j.margen.2019.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Revised: 04/04/2019] [Accepted: 04/04/2019] [Indexed: 11/19/2022]
Abstract
Octocorals have now become the most visually dominant metazoan benthic taxa of most Caribbean reefs, following the precipitous decline of scleractinian corals. Yet taxonomic issues because of their extensive phenotypic plasticity are still abound. Briareum asbestinum one of the iconic octocorals of the shallow Caribbean coral reefs exhibits a biform morphology, the digitate and the encrusting one. The taxonomic status of each form has not been clarified, yet. Until recently, there were few genetic resources for non-model metazoans, however, affordable high-throughput DNA sequencing has removed this hindrance. We present the first transcriptome of the digitate form of Briareum asbestinum from southwest Puerto Rico. We used paired-end sequencing (Illumina NextSeq 500), with a total yield of 159,754,702 raw reads. De novo assembly was performed utilizing a multi-assembler approach generating 371,554 biologically true, non-redundant transcripts. Open reading frame analysis identified 102,839 putative ORFs of which 78,607 were with annotations. BUSCO analysis indicated a total of 96.4% complete orthologous genes from the metazoan dataset. The assembly presented here serves as an important new genomic reference for the Briareum genus that will facilitate future population and phylogenetic studies aiming to better understand the molecular basis of phenotypic plasticity exhibited throughout the genus.
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Affiliation(s)
- Liajay Rivera-García
- Department of Marine Sciences, University of Puerto Rico at Mayagüez, PO Box 9000, Mayagüez, PR 00681, USA
| | - Ramón E Rivera-Vicéns
- Department of Marine Sciences, University of Puerto Rico at Mayagüez, PO Box 9000, Mayagüez, PR 00681, USA; Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Alex J Veglia
- Department of Marine Sciences, University of Puerto Rico at Mayagüez, PO Box 9000, Mayagüez, PR 00681, USA
| | - Nikolaos V Schizas
- Department of Marine Sciences, University of Puerto Rico at Mayagüez, PO Box 9000, Mayagüez, PR 00681, USA.
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138
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Chan WS, Kwok ACM, Wong JTY. Knockdown of Dinoflagellate Cellulose Synthase CesA1 Resulted in Malformed Intracellular Cellulosic Thecal Plates and Severely Impeded Cyst-to-Swarmer Transition. Front Microbiol 2019; 10:546. [PMID: 30941114 PMCID: PMC6433935 DOI: 10.3389/fmicb.2019.00546] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/04/2019] [Indexed: 11/13/2022] Open
Abstract
Cellulose synthesis (CS) is conducted by membrane-bound cellulose synthase complexes (CSCs), containing cellulose synthases (CesA), that are either arranged in hexagonal structures in higher plants or in linear arrays in most microbial organisms, including dinoflagellates. Dinoflagellates are a major phytoplankton group having linear-type CSCs and internal cellulosic thecal plates (CTPs) in large cortical vesicles. Immunological study suggested CesA1p were cortically localized to the periphery of CTPs. During cyst-to-swarmer transition (TC–S), synchronized peaks of CesA1 transcription, CesA1p expression, CS and CTP formation occurred in respective order, over 12–16 h, strategically allowing the study of CS regulation and CTP biogenesis. CesA1-knockdown resulted in 40% reduction in CesA1p level and time required for swarmer cells reappearance. CTPs were severely malformed with reduced cellulose content. As CTPs are deposited in internal organelle, the present study demonstrated dinoflagellate CesA1 ortholog was adapted for non-surface deposition; this is different to paradigm of other CesAps which require plasmamembrane for cellulose fiber deposition. This pioneer gene-knockdown study demonstrated the requirement of a gene for dinoflagellate cell wall remodeling and proper TC–S, which are prominent in dinoflagellate life-cycles.
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Affiliation(s)
- Wai Sun Chan
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, Hong Kong
| | - Alvin Chun Man Kwok
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, Hong Kong
| | - Joseph Tin Yum Wong
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, Hong Kong
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139
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Lin S, Yu L, Zhang H. Transcriptomic Responses to Thermal Stress and Varied Phosphorus Conditions in Fugacium kawagutii. Microorganisms 2019; 7:microorganisms7040096. [PMID: 30987028 PMCID: PMC6517890 DOI: 10.3390/microorganisms7040096] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 03/18/2019] [Accepted: 03/30/2019] [Indexed: 01/08/2023] Open
Abstract
Coral reef-associated Symbiodiniaceae live in tropical and oligotrophic environments and are prone to heat and nutrient stress. How their metabolic pathways respond to pulses of warming and phosphorus (P) depletion is underexplored. Here, we conducted RNA-seq analysis to investigate transcriptomic responses to thermal stress, phosphate deprivation, and organic phosphorus (OP) replacement in Fugacium kawagutii. Using dual-algorithm (edgeR and NOIseq) to remedy the problem of no replicates, we conservatively found 357 differentially expressed genes (DEGs) under heat stress, potentially regulating cell wall modulation and the transport of iron, oxygen, and major nutrients. About 396 DEGs were detected under P deprivation and 671 under OP utilization, both mostly up-regulated and potentially involved in photosystem and defensome, despite different KEGG pathway enrichments. Additionally, we identified 221 genes that showed relatively stable expression levels across all conditions (likely core genes), mostly catalytic and binding proteins. This study reveals a wide range of, and in many cases previously unrecognized, molecular mechanisms in F. kawagutii to cope with heat stress and phosphorus-deficiency stress. Their quantitative expression dynamics, however, requires further verification with triplicated experiments, and the data reported here only provide clues for generating testable hypotheses about molecular mechanisms underpinning responses and adaptation in F. kawagutii to temperature and nutrient stresses.
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Affiliation(s)
- Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, Fujian, China.
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
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140
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John U, Lu Y, Wohlrab S, Groth M, Janouškovec J, Kohli GS, Mark FC, Bickmeyer U, Farhat S, Felder M, Frickenhaus S, Guillou L, Keeling PJ, Moustafa A, Porcel BM, Valentin K, Glöckner G. An aerobic eukaryotic parasite with functional mitochondria that likely lacks a mitochondrial genome. SCIENCE ADVANCES 2019; 5:eaav1110. [PMID: 31032404 PMCID: PMC6482013 DOI: 10.1126/sciadv.aav1110] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/07/2019] [Indexed: 05/30/2023]
Abstract
Dinoflagellates are microbial eukaryotes that have exceptionally large nuclear genomes; however, their organelle genomes are small and fragmented and contain fewer genes than those of other eukaryotes. The genus Amoebophrya (Syndiniales) comprises endoparasites with high genetic diversity that can infect other dinoflagellates, such as those forming harmful algal blooms (e.g., Alexandrium). We sequenced the genome (~100 Mb) of Amoebophrya ceratii to investigate the early evolution of genomic characters in dinoflagellates. The A. ceratii genome encodes almost all essential biosynthetic pathways for self-sustaining cellular metabolism, suggesting a limited dependency on its host. Although dinoflagellates are thought to have descended from a photosynthetic ancestor, A. ceratii appears to have completely lost its plastid and nearly all genes of plastid origin. Functional mitochondria persist in all life stages of A. ceratii, but we found no evidence for the presence of a mitochondrial genome. Instead, all mitochondrial proteins appear to be lost or encoded in the A. ceratii nucleus.
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Affiliation(s)
- Uwe John
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Yameng Lu
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Sylke Wohlrab
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB), Oldenburg, Germany
| | - Marco Groth
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstr. 11, Jena, Germany
| | - Jan Janouškovec
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Gurjeet S. Kohli
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Felix C. Mark
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Ulf Bickmeyer
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Sarah Farhat
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Marius Felder
- Leibniz Institute on Aging, Fritz Lipmann Institute, Beutenbergstr. 11, Jena, Germany
| | - Stephan Frickenhaus
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
- Hochschule Bremerhaven, Bremerhaven, Germany
| | - Laure Guillou
- CNRS, UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Place Georges Teissier, CS90074, 29688 Roscoff cedex, France
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 6, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, CS90074, 29688 Roscoff cedex, France
| | - Patrick J. Keeling
- Botany Department, University of British Columbia, Vancouver, BC, Canada
| | - Ahmed Moustafa
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo 11835, Egypt
| | - Betina M. Porcel
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Klaus Valentin
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Gernot Glöckner
- Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
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141
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Ortiz-Matamoros MF, Villanueva MA, Islas-Flores T. Genetic transformation of cell-walled plant and algae cells: delivering DNA through the cell wall. Brief Funct Genomics 2019; 17:26-33. [PMID: 29365068 DOI: 10.1093/bfgp/elx014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Transformation techniques are a fundamental tool for functional genomics studies. These techniques are routinely used in many prokaryotic and eukaryotic organisms, but in eukaryotes that are surrounded by a cell wall, these protocols have proven difficult to successfully deliver heterologous or homologous DNA within their cytoplasm and nucleus. Such cell-walled organisms represent a challenge that requires the development of genetic transformation techniques that are able to overcome their natural barrier, to achieve targeted gene expression. Here, we review the techniques that have been proven successful and applied to these cell-walled eukaryotic organisms. We focus, especially, on plant cells, microalgae, and the latest approaches to mediate DNA uptake by the photosynthetic dinoflagellate Symbiodinium.
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142
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Bayliss SLJ, Scott ZR, Coffroth MA, terHorst CP. Genetic variation in Breviolum antillogorgium, a coral reef symbiont, in response to temperature and nutrients. Ecol Evol 2019; 9:2803-2813. [PMID: 30891218 PMCID: PMC6406013 DOI: 10.1002/ece3.4959] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 12/30/2018] [Accepted: 01/04/2019] [Indexed: 01/01/2023] Open
Abstract
Symbionts within the family Symbiodiniaceae are important on coral reefs because they provide significant amounts of carbon to many different reef species. The breakdown of this mutualism that occurs as a result of increasingly warmer ocean temperatures is a major threat to coral reef ecosystems globally. Recombination during sexual reproduction and high rates of somatic mutation can lead to increased genetic variation within symbiont species, which may provide the fuel for natural selection and adaptation. However, few studies have asked whether such variation in functional traits exists within these symbionts. We used several genotypes of two closely related species, Breviolum antillogorgium and B. minutum, to examine variation of traits related to symbiosis in response to increases in temperature or nitrogen availability in laboratory cultures. We found significant genetic variation within and among symbiont species in chlorophyll content, photosynthetic efficiency, and growth rate. Two genotypes showed decreases in traits in response to increased temperatures predicted by climate change, but one genotype responded positively. Similarly, some genotypes within a species responded positively to high-nitrogen environments, such as those expected within hosts or eutrophication associated with global change, while other genotypes in the same species responded negatively, suggesting context-dependency in the strength of mutualism. Such variation in traits implies that there is potential for natural selection on symbionts in response to temperature and nutrients, which could confer an adaptive advantage to the holobiont.
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Affiliation(s)
- Shannon L. J. Bayliss
- Biology DepartmentCalifornia State UniversityNorthridgeCalifornia
- Department of Ecology and Evolutionary BiologyUniversity of TennesseeKnoxvilleTennessee
| | - Zoë R. Scott
- Biology DepartmentCalifornia State UniversityNorthridgeCalifornia
| | - Mary Alice Coffroth
- Department of Geology and Graduate Program in Evolution, Ecology and BehaviorUniversity at BuffaloBuffaloNew York
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143
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Cuadrado Á, De Bustos A, Figueroa RI. Chromosomal markers in the genus Karenia: Towards an understanding of the evolution of the chromosomes, life cycle patterns and phylogenetic relationships in dinoflagellates. Sci Rep 2019; 9:3072. [PMID: 30816125 PMCID: PMC6395649 DOI: 10.1038/s41598-018-35785-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 11/07/2018] [Indexed: 12/12/2022] Open
Abstract
Dinoflagellates are a group of protists whose genome is unique among eukaryotes in terms of base composition, chromosomal structure and gene expression. Even after decades of research, the structure and behavior of their amazing chromosomes-which without nucleosomes exist in a liquid crystalline state-are still poorly understood. We used flow cytometry and fluorescence in situ hybridization (FISH) to analyze the genome size of three species of the toxic dinoflagellate genus Karenia as well the organization and behavior of the chromosomes in different cell-cycle stages. FISH was also used to study the distribution patterns of ribosomal DNA (45S rDNA), telomeric and microsatellites repeats in order to develop chromosomal markers. The results revealed several novel and important features regarding dinoflagellate chromosomes during mitosis, including their telocentric behavior and radial arrangement along the nuclear envelope. Additionally, using the (AG)10 probe we identified an unusual chromosome in K. selliformis and especially in K. mikimotoi that is characterized by AG repeats along its entire length. This feature was employed to easily differentiate morphologically indistinguishable life-cycle stages. The evolutionary relationship between Karenia species is discussed with respect to differences in both DNA content and the chromosomal distribution patterns of the DNA sequences analyzed.
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Affiliation(s)
- Ángeles Cuadrado
- Universidad de Alcala (UAH), Dpto Biomedicina y Biotecnología, 28805 Alcalá de Henares, Madrid, Spain.
| | - Alfredo De Bustos
- Universidad de Alcala (UAH), Dpto Biomedicina y Biotecnología, 28805 Alcalá de Henares, Madrid, Spain
| | - Rosa I Figueroa
- Instituto Español de Oceanografia (IEO), Subida a Radio Faro 50, 36390, Vigo, Spain.
- Aquatic Ecology, Biology Building, Lund University, 22362, Lund, Sweden.
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144
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Lehane AM, Dennis ASM, Bray KO, Li D, Rajendran E, McCoy JM, McArthur HM, Winterberg M, Rahimi F, Tonkin CJ, Kirk K, van Dooren GG. Characterization of the ATP4 ion pump in Toxoplasma gondii. J Biol Chem 2019; 294:5720-5734. [PMID: 30723156 DOI: 10.1074/jbc.ra118.006706] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/31/2019] [Indexed: 12/22/2022] Open
Abstract
The Plasmodium falciparum ATPase PfATP4 is the target of a diverse range of antimalarial compounds, including the clinical drug candidate cipargamin. PfATP4 was originally annotated as a Ca2+ transporter, but recent evidence suggests that it is a Na+ efflux pump, extruding Na+ in exchange for H+ Here we demonstrate that ATP4 proteins belong to a clade of P-type ATPases that are restricted to apicomplexans and their closest relatives. We employed a variety of genetic and physiological approaches to investigate the ATP4 protein of the apicomplexan Toxoplasma gondii, TgATP4. We show that TgATP4 is a plasma membrane protein. Knockdown of TgATP4 had no effect on resting pH or Ca2+ but rendered parasites unable to regulate their cytosolic Na+ concentration ([Na+]cyt). PfATP4 inhibitors caused an increase in [Na+]cyt and a cytosolic alkalinization in WT but not TgATP4 knockdown parasites. Parasites in which TgATP4 was knocked down or disrupted exhibited a growth defect, attributable to reduced viability of extracellular parasites. Parasites in which TgATP4 had been disrupted showed reduced virulence in mice. These results provide evidence for ATP4 proteins playing a key conserved role in Na+ regulation in apicomplexan parasites.
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Affiliation(s)
- Adele M Lehane
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia,
| | - Adelaide S M Dennis
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Katherine O Bray
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Dongdi Li
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Esther Rajendran
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - James M McCoy
- the Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia, and.,the Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Hillary M McArthur
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Markus Winterberg
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Farid Rahimi
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Christopher J Tonkin
- the Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3052, Australia, and.,the Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kiaran Kirk
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia,
| | - Giel G van Dooren
- From the Research School of Biology, Australian National University, Canberra, ACT 2601, Australia,
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145
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Beedessee G, Hisata K, Roy MC, Van Dolah FM, Satoh N, Shoguchi E. Diversified secondary metabolite biosynthesis gene repertoire revealed in symbiotic dinoflagellates. Sci Rep 2019; 9:1204. [PMID: 30718591 PMCID: PMC6361889 DOI: 10.1038/s41598-018-37792-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/13/2018] [Indexed: 11/09/2022] Open
Abstract
Symbiodiniaceae dinoflagellates possess smaller nuclear genomes than other dinoflagellates and produce structurally specialized, biologically active, secondary metabolites. Till date, little is known about the evolution of secondary metabolism in dinoflagellates as comparative genomic approaches have been hampered by their large genome sizes. Here, we overcome this challenge by combining genomic and metabolomics approaches to investigate how chemical diversity arises in three decoded Symbiodiniaceae genomes (clades A3, B1 and C). Our analyses identify extensive diversification of polyketide synthase and non-ribosomal peptide synthetase genes from two newly decoded genomes of Symbiodinium tridacnidorum (A3) and Cladocopium sp. (C). Phylogenetic analyses indicate that almost all the gene families are derived from lineage-specific gene duplications in all three clades, suggesting divergence for environmental adaptation. Few metabolic pathways are conserved among the three clades and we detect metabolic similarity only in the recently diverged clades, B1 and C. We establish that secondary metabolism protein architecture guides substrate specificity and that gene duplication and domain shuffling have resulted in diversification of secondary metabolism genes.
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Affiliation(s)
- Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Michael C Roy
- Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Frances M Van Dolah
- College of Charleston, School of Sciences and Mathematics, 66 George St., Charleston, South Carolina, 29424, USA
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
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146
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Ryu T, Cho W, Yum S, Woo S. Holobiont transcriptome of colonial scleractinian coral Alveopora japonica. Mar Genomics 2019. [DOI: 10.1016/j.margen.2018.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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147
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Dinoflagellate nucleus contains an extensive endomembrane network, the nuclear net. Sci Rep 2019; 9:839. [PMID: 30696854 PMCID: PMC6351617 DOI: 10.1038/s41598-018-37065-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/28/2018] [Indexed: 12/12/2022] Open
Abstract
Dinoflagellates are some of the most common eukaryotic cells in the ocean, but have very unusual nuclei. Many exhibit a form of closed mitosis (dinomitosis) wherein the nuclear envelope (NE) invaginates to form one or more trans-nuclear tunnels. Rather than contact spindles directly, the chromatids then bind to membrane-based kinetochores on the NE. To better understand these unique mitotic features, we reconstructed the nuclear architecture of Polykrikos kofoidii in 3D using focused ion beam scanning electron microscopy (FIB-SEM) in conjunction with high-pressure freezing, freeze-substitution, TEM, and confocal microscopy. We found that P. kofoidii possessed six nuclear tunnels, which were continuous with a reticulating network of membranes that has thus far gone unnoticed. These membranous extensions interconnect the six tunnels while ramifying throughout the nucleus to form a “nuclear net.” To our knowledge, the nuclear net is the most elaborate endomembrane structure described within a nucleus. Our findings demonstrate the utility of tomographic approaches for detecting 3D membrane networks and show that nuclear complexity has been underestimated in Polykrikos kofoidii and, potentially, in other dinoflagellates.
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148
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Abstract
Reef-building corals cannot survive without symbiotic algae, Symbiodinium, on which they depend for most of their energy. Most coral species gain symbionts from the environment early in life, and possibly after bleaching (i.e., the loss of symbionts in response to stress). However, Symbiodinium density on coral reefs is very low. Although it has long been hypothesized that corals must be able to attract free-living Symbiodinium, such a mechanism has yet to be identified. Here, we use a series of experiments to demonstrate that corals attract Symbiodinium using their endogenous GFP-related green fluorescence, revealing a biological signaling mechanism that underlies the success of this symbioses that is the building block of coral reef ecosystems. Reef-building corals thrive in nutrient-poor marine environments because of an obligate symbiosis with photosynthetic dinoflagellates of the genus Symbiodinium. Symbiosis is established in most corals through the uptake of Symbiodinium from the environment. Corals are sessile for most of their life history, whereas free-living Symbiodinium are motile; hence, a mechanism to attract Symbiodinium would greatly increase the probability of encounter between host and symbiont. Here, we examined whether corals can attract free-living motile Symbiodinium by their green fluorescence, emitted by the excitation of endogenous GFP by purple-blue light. We found that Symbiodinium have positive and negative phototaxis toward weak green and strong purple-blue light, respectively. Under light conditions that cause corals to emit green fluorescence, (e.g., strong blue light), Symbiodinium were attracted toward live coral fragments. Symbiodinium were also attracted toward an artificial green fluorescence dye with similar excitation and emission spectra to coral-GFP. In the field, more Symbiodinium were found in traps painted with a green fluorescence dye than in controls. Our results revealed a biological signaling mechanism between the coral host and its potential symbionts.
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149
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Wong JTY. Architectural Organization of Dinoflagellate Liquid Crystalline Chromosomes. Microorganisms 2019; 7:microorganisms7020027. [PMID: 30678153 PMCID: PMC6406473 DOI: 10.3390/microorganisms7020027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/12/2019] [Accepted: 01/17/2019] [Indexed: 12/12/2022] Open
Abstract
Dinoflagellates have some of the largest genome sizes, but lack architectural nucleosomes. Their liquid crystalline chromosomes (LCCs) are the only non-architectural protein-mediated chromosome packaging systems, having high degrees of DNA superhelicity, liquid crystalline condensation and high levels of chromosomal divalent cations. Recent observations on the reversible decompaction–recompaction of higher-order structures implicated that LCCs are composed of superhelical modules (SPMs) comprising highly supercoiled DNA. Orientated polarizing light photomicrography suggested the presence of three compartments with different packaging DNA density in LCCs. Recent and previous biophysical data suggest that LCCs are composed of: (a) the highly birefringent inner core compartment (i) with a high-density columnar-hexagonal mesophase (CH-m); (b) the lower-density core surface compartment (ii.1) consisting of a spiraling chromonema; (c) the birefringent-negative periphery compartment (ii.2) comprising peripheral chromosomal loops. C(ii.1) and C(ii.2) are in dynamic equilibrium, and can merge into a single compartment during dinomitosis, regulated through multiphasic reversible soft-matter phase transitions.
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Affiliation(s)
- Joseph Tin Yum Wong
- Division of Life Science, Hong Kong University of Life Science, Clearwater Bay, Kowloon, Hong Kong.
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150
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Helmkampf M, Bellinger MR, Frazier M, Takabayashi M. Symbiont type and environmental factors affect transcriptome-wide gene expression in the coral Montipora capitata. Ecol Evol 2019; 9:378-392. [PMID: 30680121 PMCID: PMC6341978 DOI: 10.1002/ece3.4756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/01/2018] [Accepted: 11/02/2018] [Indexed: 12/18/2022] Open
Abstract
Reef-building corals may harbor genetically distinct lineages of endosymbiotic dinoflagellates in the genus Symbiodinium, which have been shown to affect important colony properties, including growth rates and resilience against environmental stress. However, the molecular processes underlying these differences are not well understood. In this study, we used whole transcriptome sequencing (RNA-seq) to assess gene expression differences between 27 samples of the coral Montipora capitata predominantly hosting two different Symbiodinium types in clades C and D. The samples were further characterized by their origin from two field sites on Hawai'i Island with contrasting environmental conditions. We found that transcriptome-wide gene expression profiles clearly separated by field site first, and symbiont clade second. With 273 differentially expressed genes (DEGs, 1.3% of all host transcripts), symbiont clade had a measurable effect on host gene expression, but the effect of field site proved almost an order of magnitude higher (1,957 DEGs, 9.6%). According to SNP analysis, we found moderate evidence for host genetic differentiation between field sites (F ST = 0.046) and among corals harboring alternative symbiont clades (F ST = 0.036), suggesting that site-related gene expression differences are likely due to a combination of local adaptation and acclimatization to environmental factors. The correlation between host gene expression and symbiont clade may be due to several factors, including host genotype or microhabitat selecting for alternative clades, host physiology responding to different symbionts, or direct modulation of host gene expression by Symbiodinium. However, the magnitude of these effects at the level of transcription was unexpectedly small considering the contribution of symbiont type to holobiont phenotype.
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Affiliation(s)
- Martin Helmkampf
- Tropical Conservation Biology and Environmental ScienceUniversity of Hawaiʻi at HiloHiloHawaii
| | - M. Renee Bellinger
- Tropical Conservation Biology and Environmental ScienceUniversity of Hawaiʻi at HiloHiloHawaii
| | - Monika Frazier
- Tropical Conservation Biology and Environmental ScienceUniversity of Hawaiʻi at HiloHiloHawaii
| | - Misaki Takabayashi
- Tropical Conservation Biology and Environmental ScienceUniversity of Hawaiʻi at HiloHiloHawaii
- Okinawa Institute of Science and TechnologyOnna-son, OkinawaJapan
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