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Kalvelage J, Rabus R. Multifaceted Dinoflagellates and the Marine Model Prorocentrum cordatum. Microb Physiol 2024; 34:197-242. [PMID: 39047710 DOI: 10.1159/000540520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 07/20/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Dinoflagellates are a monophyletic group within the taxon Alveolata, which comprises unicellular eukaryotes. Dinoflagellates have long been studied for their organismic and morphologic diversity as well as striking cellular features. They have a main size range of 10-100 µm, a complex "cell covering", exceptionally large genomes (∼1-250 Gbp with a mean of 50,000 protein-encoding genes) spread over a variable number of highly condensed chromosomes, and perform a closed mitosis with extranuclear spindles (dinomitosis). Photosynthetic, marine, and free-living Prorocentrum cordatum is a ubiquitously occurring, bloom-forming dinoflagellate, and an emerging model system, particularly with respect to systems biology. SUMMARY Focused ion beam/scanning electron microscopy (FIB/SEM) analysis of P. cordatum recently revealed (i) a flattened nucleus with unusual structural features and a total of 62 tightly packed chromosomes, (ii) a single, barrel-shaped chloroplast devoid of grana and harboring multiple starch granules, (iii) a single, highly reticular mitochondrion, and (iv) multiple phosphate and lipid storage bodies. Comprehensive proteomics of subcellular fractions suggested (i) major basic nuclear proteins to participate in chromosome condensation, (ii) composition of nuclear pores to differ from standard knowledge, (iii) photosystems I and II, chloroplast complex I, and chlorophyll a-b binding light-harvesting complex to form a large megacomplex (>1.5 MDa), and (iv) an extraordinary richness in pigment-binding proteins. Systems biology-level investigation of heat stress response demonstrated a concerted down-regulation of CO2-concentrating mechanisms, CO2-fixation, central metabolism, and monomer biosynthesis, which agrees with reduced growth yields. KEY MESSAGES FIB/SEM analysis revealed new insights into the remarkable subcellular architecture of P. cordatum, complemented by proteogenomic unraveling of novel nuclear structures and a photosynthetic megacomplex. These recent findings are put in the wider context of current understanding of dinoflagellates.
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Affiliation(s)
- Jana Kalvelage
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Ralf Rabus
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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Gottschling M, Wietkamp S, Bantle A, Tillmann U. Oxytoxaceae are prorocentralean rather than peridinialean dinophytes and taxonomic clarification of heterotrophic Oxytoxum lohmannii (≡ "Amphidinium" crassum) by epitypification. Sci Rep 2024; 14:6689. [PMID: 38509105 PMCID: PMC10954643 DOI: 10.1038/s41598-024-56848-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 03/12/2024] [Indexed: 03/22/2024] Open
Abstract
During evolution of Dinophyceae, size reduction of the episome has occurred in several lineages (including unarmoured Amphidiniales and armoured Prorocentrales). One such species is Amphidinium crassum, whose taxonomic identity is elusive though showing morphological similarities with Oxytoxaceae (currently placed in armoured Peridiniales). Plankton samples were taken at the type locality of A. crassum in Kiel Bight (Baltic Sea) in order to establish monoclonal strains. The protist material was examined in detail using light and electron microscopy, and a long (2984 bp) ribosomal RNA sequence gained was part of a taxon sample comprising 206 specimen vouchers and representing the known molecular diversity of Dinophyceae. Cells of A. crassum were ovoid and exhibited a plate pattern po, 4', 1a, 6'', 5c, 4s, 5''', 1''''. In the molecular phylogeny, the species seemed to belong neither to Amphidiniales nor to Peridiniales but to Prorocentrales and clustered with other representatives of Oxytoxaceae. The morphological diversity of Prorocentrales appears thus expanded, and the group may include a number of previously unrecognised representatives unusually having five postcingular and only a single antapical plate. The taxonomic identity of A. crassum is clarified by epitypification, and the species notably exhibits both an apical pore and an additional epithecal pore.
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Affiliation(s)
- Marc Gottschling
- Department Biologie-Systematik, Biodiversität und Evolution der Pflanzen, GeoBio-Center, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80 638, München, Germany
| | - Stephan Wietkamp
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27 570, Bremerhaven, Germany
| | - Alexis Bantle
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27 570, Bremerhaven, Germany
| | - Urban Tillmann
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27 570, Bremerhaven, Germany.
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Park E, Cooney E, Heng Phua Y, Horiguchi T, Husnik F, Keeling P, Wakeman K, Leander B. Phylogenomics shows that novel tapeworm-like traits of haplozoan parasites evolved from within the Peridiniales (Dinoflagellata). Mol Phylogenet Evol 2023:107859. [PMID: 37329929 DOI: 10.1016/j.ympev.2023.107859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/08/2023] [Accepted: 06/10/2023] [Indexed: 06/19/2023]
Abstract
Haplozoans are intestinal parasites of marine annelids with bizarre traits, including a differentiated and dynamic trophozoite stage that resembles the scolex and strobila of tapeworms. Described originally as "Mesozoa", comparative ultrastructural data and molecular phylogenetic analyses have shown that haplozoans are aberrant dinoflagellates; however, these data failed to resolve the phylogenetic position of haplozoans within this diverse group of protists. Several hypotheses for the phylogenetic position of haplozoans have been proposed: (1) within the Gymnodiniales based on tabulation patterns on the trophozoites, (2) within the Blastodiniales based on the parasitic life cycle, and (3) part of a new lineage of dinoflagellates that reflects the highly modified morphology. Here, we demonstrate the phylogenetic position of haplozoans by using three single-trophozoite transcriptomes representing two species: Haplozoon axiothellae and two isolates of H. pugnus collected from the Northwestern and Northeastern Pacific Ocean. Unexpectedly, our phylogenomic analysis of 241 genes showed that these parasites are unambiguously nested within the Peridiniales, a clade of single-celled flagellates that is well represented in marine phytoplankton communities around the world. Although the intestinal trophozoites of Haplozoon species do not show any peridinioid characteristics, we suspect that uncharacterized life cycle stages may reflect their evolutionary history within the Peridiniales.
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Affiliation(s)
- Eunji Park
- Department of Botany, University of British Columbia, Vancouver, Canada; Department of Zoology, University of British Columbia, Vancouver, Canada; Hakai Institute, British Columbia, Canada.
| | - Elizabeth Cooney
- Department of Botany, University of British Columbia, Vancouver, Canada; Hakai Institute, British Columbia, Canada
| | - Yong Heng Phua
- Okinawa Institute of Science and Technology, Okinawa, Japan
| | | | - Filip Husnik
- Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Patrick Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Kevin Wakeman
- Institute for the Advancement of Higher Education, Hokkaido University, Sapporo, Japan; Graduate School of Science, Hokkaido University, Sapporo, Japan
| | - Brian Leander
- Department of Botany, University of British Columbia, Vancouver, Canada; Department of Zoology, University of British Columbia, Vancouver, Canada
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Tillmann U, Wietkamp S, Kretschmann J, Chacón J, Gottschling M. Spatial fragmentation in the distribution of diatom endosymbionts from the taxonomically clarified dinophyte Kryptoperidinium triquetrum (= Kryptoperidinium foliaceum, Peridiniales). Sci Rep 2023; 13:8593. [PMID: 37237053 DOI: 10.1038/s41598-023-32949-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 04/05/2023] [Indexed: 05/28/2023] Open
Abstract
Among the photosynthetically active dinophytes, the Kryptoperidiniaceae are unique in having a diatom as endosymbiont instead of the widely present peridinin chloroplast. Phylogenetically, it is unresolved at present how the endosymbionts are inherited, and the taxonomic identities of two iconic dinophyte names, Kryptoperidinium foliaceum and Kryptoperidinium triquetrum, are also unclear. Multiple strains were newly established from the type locality in the German Baltic Sea off Wismar and inspected using microscopy as well as molecular sequence diagnostics of both host and endosymbiont. All strains were bi-nucleate, shared the same plate formula (i.e., po, X, 4', 2a, 7'', 5c, 7s, 5''', 2'''') and exhibited a narrow and characteristically L-shaped precingular plate 7''. Within the molecular phylogeny of Bacillariaceae, endosymbionts were scattered over the tree in a highly polyphyletic pattern, even if they were gained from different strains of a single species, namely K. triquetrum. Notably, endosymbionts from the Baltic Sea show molecular sequences distinct from the Atlantic and the Mediterranean Sea, which is the first report of such a spatial fragmentation in a planktonic species of dinophytes. The two names K. foliaceum and K. triquetrum are taxonomically clarified by epitypification, with K. triquetrum having priority over its synonym K. foliaceum. Our study underlines the need of stable taxonomy for central questions in evolutionary biology.
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Affiliation(s)
- Urban Tillmann
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27 570, Bremerhaven, Germany
| | - Stephan Wietkamp
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27 570, Bremerhaven, Germany
| | - Juliane Kretschmann
- Department Biologie, Systematics, Biodiversity & Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80 638, Munich, Germany
| | - Juliana Chacón
- Department Biologie, Systematics, Biodiversity & Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80 638, Munich, Germany
| | - Marc Gottschling
- Department Biologie, Systematics, Biodiversity & Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80 638, Munich, Germany.
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Cooney EC, Leander BS, Keeling PJ. Phylogenomics shows unique traits in Noctilucales are derived rather than ancestral. PNAS NEXUS 2022; 1:pgac202. [PMID: 36714854 PMCID: PMC9802342 DOI: 10.1093/pnasnexus/pgac202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/19/2022] [Indexed: 02/01/2023]
Abstract
Dinoflagellates are a diverse protist group possessing many unique traits. These include (but are not limited to) expansive genomes packaged into permanently condensed chromosomes, photosynthetic or cryptic plastids acquired vertically or horizontally in serial endosymbioses, and a ruffle-like transverse flagellum attached along its length to the cell. When reconstructing character evolution, early branching lineages with unusual features that distinguish them from the rest of the group have proven useful for inferring ancestral states. The Noctilucales are one such lineage, possessing relaxed chromosomes in some life stages and a trailing, thread-like transverse flagellum. However, most of the cellular and molecular data for the entire group come from a single cultured species, Noctiluca scintillans, and because its phylogenetic position is unresolved it remains unclear if these traits are ancestral or derived. Here, we use single cell transcriptomics to characterize three diverse Noctilucales genera: Spatulodinium, Kofoidinium, and a new lineage, Fabadinium gen. nov. We also provide transcriptomes for undescribed species in Amphidinium and Abediniales, critical taxa for clarifying the phylogenetic position of Noctilucales. Phylogenomic analyses suggests that the Noctilucales are sister to Amphidinium rather than an independent branch outside the core dinoflagellates. This topology is consistent with observations of shared characteristics between some members of Noctilucales and Amphidinium and provides the most compelling evidence to date that the unusual traits within this group are derived rather than ancestral. We also confirm that Spatulodinium plastids are photosynthetic and of ancestral origin, and show that all non-photosynthetic Noctilucales retain plastid genes indicating a cryptic organelle.
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Affiliation(s)
| | - Brian S Leander
- Department of Botany, University of British Columbia, British Columbia, Vancouver V6T 1Z4, Canada,Department of Zoology, University of British Columbia, British Columbia, Vancouver V6T 1Z4, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, British Columbia, Vancouver V6T 1Z4, Canada
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Morphologic and phylogenic characterization of two bloom-forming planktonic Prorocentrum (Dinophyceae) species and their potential distribution in the China Sea. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ott BM, Litaker RW, Holland WC, Delwiche CF. Using RDNA sequences to define dinoflagellate species. PLoS One 2022; 17:e0264143. [PMID: 35213572 PMCID: PMC8880924 DOI: 10.1371/journal.pone.0264143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/03/2022] [Indexed: 11/18/2022] Open
Abstract
Dinoflagellate species are traditionally defined using morphological characters, but molecular evidence accumulated over the past several decades indicates many morphologically-based descriptions are inaccurate. This recognition led to an increasing reliance on DNA sequence data, particularly rDNA gene segments, in defining species. The validity of this approach assumes the divergence in rDNA or other selected genes parallels speciation events. Another concern is whether single gene rDNA phylogenies by themselves are adequate for delineating species or if multigene phylogenies are required instead. Currently, few studies have directly assessed the relative utility of multigene versus rDNA-based phylogenies for distinguishing species. To address this, the current study examined D1-D3 and ITS/5.8S rDNA gene regions, a multi-gene phylogeny, and morphological characters in Gambierdiscus and other related dinoflagellate genera to determine if they produce congruent phylogenies and identify the same species. Data for the analyses were obtained from previous sequencing efforts and publicly available dinoflagellate transcriptomic libraries as well from the additional nine well-characterized Gambierdiscus species transcriptomic libraries generated in this study. The D1-D3 and ITS/5.8S phylogenies successfully identified the described Gambierdiscus and Alexandrium species. Additionally, the data showed that the D1-D3 and multigene phylogenies were equally capable of identifying the same species. The multigene phylogenies, however, showed different relationships among species and are likely to prove more accurate at determining phylogenetic relationships above the species level. These data indicated that D1-D3 and ITS/5.8S rDNA region phylogenies are generally successful for identifying species of Gambierdiscus, and likely those of other dinoflagellates. To assess how broadly general this finding is likely to be, rDNA molecular phylogenies from over 473 manuscripts representing 232 genera and 863 described species of dinoflagellates were reviewed. Results showed the D1-D3 rDNA and ITS phylogenies in combination are capable of identifying 97% of dinoflagellate species including all the species belonging to the genera Alexandrium, Ostreopsis and Gambierdiscus, although it should be noted that multi-gene phylogenies are preferred for inferring relationships among these species. A protocol is presented for determining when D1-D3, confirmed by ITS/5.8S rDNA sequence data, would take precedence over morphological features when describing new dinoflagellate species. This protocol addresses situations such as: a) when a new species is both morphologically and molecularly distinct from other known species; b) when a new species and closely related species are morphologically indistinguishable, but genetically distinct; and c) how to handle potentially cryptic species and cases where morphotypes are clearly distinct but have the same rDNA sequence. The protocol also addresses other molecular, morphological, and genetic approaches required to resolve species boundaries in the small minority of species where the D1-D3/ITS region phylogenies fail.
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Affiliation(s)
- Brittany M. Ott
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), University of Maryland—College Park, College Park, MD, United States of America
- Cell Biology and Molecular Genetics, University of Maryland—College Park, College Park, MD, United States of America
- * E-mail: (BMO); (RWL)
| | - R. Wayne Litaker
- CSS, Inc. Under Contract to National Oceanic and Atmospheric Administration (NOAA), National Ocean Service, National Centers for Coastal Ocean Science, Beaufort Laboratory, Beaufort, North Carolina, United States of America
- * E-mail: (BMO); (RWL)
| | - William C. Holland
- National Oceanic and Atmospheric Administration, National Ocean Service, National Centers for Coastal Ocean Science, Beaufort Laboratory, Beaufort, North Carolina, United States of America
| | - Charles F. Delwiche
- Cell Biology and Molecular Genetics, University of Maryland—College Park, College Park, MD, United States of America
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Expression Patterns of the Heat Shock Protein 90 (Hsp90) Gene Suggest Its Possible Involvement in Maintaining the Dormancy of Dinoflagellate Resting Cysts. Int J Mol Sci 2021; 22:ijms222011054. [PMID: 34681714 PMCID: PMC8538777 DOI: 10.3390/ijms222011054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 11/21/2022] Open
Abstract
Heat shock protein 90 (Hsp90) is a highly conserved molecular chaperone functioning in cellular structural folding and conformational integrity maintenance and thus plays vital roles in a variety of biological processes. However, many aspects of these functions and processes remain to be fully elucidated, particularly for non-model organisms. Dinoflagellates are a group of eukaryotes that are exceedingly important in primary production and are responsible for the most harmful algal blooms (HABs) in aquatic ecosystems. The success of dinoflagellates in dominating the plankton community is undoubtedly pertinent to their remarkable adaptive strategies, characteristic of resting cyst production and broad tolerance to stresses of temperature and others. Therefore, this study was conducted to examine the putative roles of Hsp90 in the acclimation to temperature stress and life stage alterations of dinoflagellates. Firstly, we isolated the full-length cDNA of an Hsp90 gene (StHsp90) via RACE from the cosmopolitan HAB species Scrippsiella trochoidea and tracked its transcriptions in response to varied scenarios via real-time qPCR. The results indicated that StHsp90 displayed significant mRNA augment patterns, escalating during 180-min treatments, when the cells were exposed to elevated and lowered temperatures. Secondly, we observed prominently elevated StHsp90 transcriptions in the cysts that were stored at the cold and dark conditions compared to those in newly formed resting cysts and vegetative cells. Finally, and perhaps most importantly, we identified 29 entries of Hsp90-encoding genes with complete coding regions from a dinoflagellate-specific environmental cDNA library generated from marine sediment assemblages. The observed active transcription of these genes in sediment-buried resting cysts was fully supported by the qPCR results for the cold-stored resting cysts of S. trochoidea. Hsp90s expressions in both laboratory-raised and field-collected cysts collectively highlighted the possible involvement and engagement of Hsp90 chaperones in the resting stage persistence of dinoflagellates.
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Graeff JE, Leblond JD. Sterol Composition of the Peridinioid Dinoflagellate Zooxanthella nutricula, A Symbiont of Polycystine Radiolarians. Protist 2021; 172:125817. [PMID: 34198015 DOI: 10.1016/j.protis.2021.125817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 10/21/2022]
Abstract
Some dinoflagellates, such as Symbiodinium, are able to form symbiotic relationships with larger marine organisms. An important aspect of dinoflagellate symbiosis involves the exchange of lipids, namely sterols, from the symbiont to the host. Much research has explored the lipid biochemistry of the symbiotic relationship between cnidarians and Symbiodinium dinoflagellates. However, no research has addressed the sterol biochemistry of the symbiosis between radiolarians and dinoflagellates such as Zooxanthella nutricula. To this end, we have provided the first sterol characterization of Z. nutricula isolated from a spumellarian polycystine radiolarian. Fifteen sterols and one steroidal ketone were observed where the major sterol identified was C27 22-dehydrocholesterol, which does not tend to be a dominant sterol among dinoflagellates, including closely related peridinioid species in the genus Heterocapsa. However, C30 dinosterol and dinostanol were major sterols in both Z. nutricula and Heterocapsa spp., thus indicating common sterols between closely related taxa. Major sterols of the distantly related genus Symbiodinium, a symbiont of foraminifera and cnidarians, have included C27 cholesterol and C30 gorgosterol, whereas in Z. nutricula these sterols were minor and absent, respectively. Our results indicate potentially different sterol pools available to cnidarian and radiolarian symbiont hosts during their respective relationships with symbiotic dinoflagellates.
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Affiliation(s)
- Jori E Graeff
- Ecology and Evolution Group, Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Jeffrey D Leblond
- Ecology and Evolution Group, Department of Biology, Middle Tennessee State University, Murfreesboro, TN 37132, USA.
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10
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Tillmann U, Bantle A, Krock B, Elbrächter M, Gottschling M. Recommendations for epitypification of dinophytes exemplified by Lingulodinium polyedra and molecular phylogenetics of the Gonyaulacales based on curated rRNA sequence data. HARMFUL ALGAE 2021; 104:101956. [PMID: 34023073 DOI: 10.1016/j.hal.2020.101956] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/26/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
Gonyaulacales include a considerable number of harmful algae and to understand their origin and rise, knowledge of the evolutionary relationships is necessary. Many scientific names of protists introduced prior to the availability of DNA analytics are ambiguous and impede communication about biological species and their traits in the microbial world. Strains of Lingulodinium polyedra were established from its type locality in the Kiel Fjord (Germany) to clarify its taxonomy. Moreover, the phylogeny of Gonyaulacales was inferred based on 329 rRNA sequence accessions compiled in a curated sequence data base, with as much as possible type material equivalents included. Gonyaulacales were monophyletic and segregated into seven lineages at high systematic level, of which †Lingulodiniaceae constituted the first branch of the Gonyaulacales. Their type species had a plate formula APC (Po, X, cp), 3', 3a, 6'' 6c, 6s, 6''', 2'''' and is taxonomically clarified by epitypification. Recommendations for this important taxonomic tool are provided, with a focus on microorganisms. Most gonyaulacalean taxa established at generic rank are monophyletic, with Alexandrium, Coolia and Gonyaulax as notable exceptions. From an evolutionary perspective, gonyaulacalean dinophytes with quinqueform hypotheca are monophyletic and derive from a paraphyletic group showing the sexiform configuration.
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Affiliation(s)
- Urban Tillmann
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, D - 27 570 Bremerhaven, Germany
| | - Alexis Bantle
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, D - 27 570 Bremerhaven, Germany
| | - Bernd Krock
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, D - 27 570 Bremerhaven, Germany
| | - Malte Elbrächter
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Sylt, Hafenstr. 43, D - 25 992 List/Sylt, Germany
| | - Marc Gottschling
- Department Biologie, Systematische Botanik und Mykologie, GeoBio-Center, Ludwig-Maximilians-Universität München, Menzinger Str. 67, D - 80 638 München, Germany.
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11
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Cusick KD, Widder EA. Bioluminescence and toxicity as driving factors in harmful algal blooms: Ecological functions and genetic variability. HARMFUL ALGAE 2020; 98:101850. [PMID: 33129462 DOI: 10.1016/j.hal.2020.101850] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 06/11/2023]
Abstract
Dinoflagellates are an ecologically important group of marine microbial eukaryotes with a remarkable array of adaptive strategies. It is ironic that two of the traits for which dinoflagellates are best known, toxin production and bioluminescence, are rarely linked when considering the ecological significance of either. Although dinoflagellate species that form some of the most widespread and frequent harmful algal blooms (HABs) are bioluminescent, the molecular and eco-evolutionary associations between these two traits has received little attention. Here, the major themes of biochemistry and genetics, ecological functions, signaling mechanisms, and evolution are addressed, with parallels and connections drawn between the two. Of the 17 major classes of dinoflagellate toxins, only two are produced by bioluminescent species: saxitoxin (STX) and yessotoxin. Of these, STX has been extensively studied, including the identification of the STX biosynthetic genes. While numerous theories have been put forward as to the eco-evolutionary roles of both bioluminescence and toxicity, a general consensus is that both function as grazing deterrents. Thus, both bioluminescence and toxicity may aid in HAB initiation as they alleviate grazing pressure on the HAB species. A large gap in our understanding is the genetic variability among natural bloom populations, as both toxic and non-toxic strains have been isolated from the same geographic location. The same applies to bioluminescence, as there exist both bioluminescent and non-bioluminescent strains of the same species. Recent evidence demonstrating that blooms are not monoclonal events necessitates a greater level of understanding as to the genetic variability of these traits among sub-populations as well as the mechanisms by which cells acquire or lose the trait, as sequence analysis of STX+ and STX- species indicate the key gene required for toxicity is lost rather than gained. While the extent of genetic variability for both bioluminescence and toxicity among natural HAB sub-populations remains unknown, it is an area that needs to be explored in order to gain greater insights into the molecular mechanisms and environmental parameters driving HAB evolution.
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Affiliation(s)
- Kathleen D Cusick
- University of Maryland Baltimore County, Department of Biological Sciences, 1000 Hilltop Circle, Baltimore, MD 21250, United States.
| | - Edith A Widder
- Ocean Research and Conservation Association, 1420 Seaway Dr, Fort Pierce, FL 34949, United States.
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Mertens KN, Adachi M, Anderson DM, Band-Schmidt CJ, Bravo I, Brosnahan ML, Bolch CJS, Calado AJ, Carbonell-Moore MC, Chomérat N, Elbrächter M, Figueroa RI, Fraga S, Gárate-Lizárraga I, Garcés E, Gu H, Hallegraeff G, Hess P, Hoppenrath M, Horiguchi T, Iwataki M, John U, Kremp A, Larsen J, Leaw CP, Li Z, Lim PT, Litaker W, MacKenzie L, Masseret E, Matsuoka K, Moestrup Ø, Montresor M, Nagai S, Nézan E, Nishimura T, Okolodkov YB, Orlova TY, Reñé A, Sampedro N, Satta CT, Shin HH, Siano R, Smith KF, Steidinger K, Takano Y, Tillmann U, Wolny J, Yamaguchi A, Murray S. Morphological and phylogenetic data do not support the split of Alexandrium into four genera. HARMFUL ALGAE 2020; 98:101902. [PMID: 33129459 DOI: 10.1016/j.hal.2020.101902] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 09/02/2020] [Accepted: 09/09/2020] [Indexed: 06/11/2023]
Abstract
A recently published study analyzed the phylogenetic relationship between the genera Centrodinium and Alexandrium, confirming an earlier publication showing the genus Alexandrium as paraphyletic. This most recent manuscript retained the genus Alexandrium, introduced a new genus Episemicolon, resurrected two genera, Gessnerium and Protogonyaulax, and stated that: "The polyphyly [sic] of Alexandrium is solved with the split into four genera". However, these reintroduced taxa were not based on monophyletic groups. Therefore this work, if accepted, would result in replacing a single paraphyletic taxon with several non-monophyletic ones. The morphological data presented for genus characterization also do not convincingly support taxa delimitations. The combination of weak molecular phylogenetics and the lack of diagnostic traits (i.e., autapomorphies) render the applicability of the concept of limited use. The proposal to split the genus Alexandrium on the basis of our current knowledge is rejected herein. The aim here is not to present an alternative analysis and revision, but to maintain Alexandrium. A better constructed and more phylogenetically accurate revision can and should wait until more complete evidence becomes available and there is a strong reason to revise the genus Alexandrium. The reasons are explained in detail by a review of the available molecular and morphological data for species of the genera Alexandrium and Centrodinium. In addition, cyst morphology and chemotaxonomy are discussed, and the need for integrative taxonomy is highlighted.
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Affiliation(s)
- Kenneth Neil Mertens
- Ifremer, LER BO, Station de Biologie Marine, Place de la Croix, BP40537, F-29185 Concarneau Cedex, France.
| | - Masao Adachi
- Laboratory of Aquatic Environmental Science (LAQUES), Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi 783-8502, Japan
| | | | - Christine J Band-Schmidt
- Departamento de Plancton y Ecología Marina, Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas (IPN-CICIMAR), La Paz, B.C.S. 23096, Mexico
| | - Isabel Bravo
- Instituto Español de Oceanografía (IEO), Subida a Radio Faro 50, 36390 Vigo, Spain
| | | | - Christopher J S Bolch
- Institute for Marine & Antarctic Studies, University of Tasmania, Locked Bag 1370, Launceston TAS 7250, Australia
| | - António J Calado
- Department of Biology and GeoBioTec Research Unit, University of Aveiro, P-3810-193 Aveiro, Portugal
| | - M Consuelo Carbonell-Moore
- Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331-2902, USA
| | - Nicolas Chomérat
- Ifremer, LER BO, Station de Biologie Marine, Place de la Croix, BP40537, F-29185 Concarneau Cedex, France
| | - Malte Elbrächter
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung Sylt, Hafenstr. 43, 25992 List/Sylt, Germany
| | - Rosa Isabel Figueroa
- Instituto Español de Oceanografía (IEO), Subida a Radio Faro 50, 36390 Vigo, Spain
| | | | - Ismael Gárate-Lizárraga
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, Apartado Postal 592, Col. Centro, La Paz, B.C.S. 23000, Mexico
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografía, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Haifeng Gu
- Third Institute of Oceanography, Ministry of Natural Resources, Xiamen 361005, China
| | - Gustaaf Hallegraeff
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 129, Hobart, Tasmania 7001, Australia
| | - Philipp Hess
- Ifremer, DYNECO, Laboratoire Phycotoxines, Rue de l'Ile d'Yeu, 44311 Nantes, France
| | - Mona Hoppenrath
- Senckenberg am Meer, German Center for Marine Biodiversity Research, Wilhelmshaven, Germany
| | - Takeo Horiguchi
- Department of Biological Sciences, Faculty of Science, Hokkaido University, North 10, West 8, Sapporo 060-0810, Hokkaido, Japan
| | - Mitsunori Iwataki
- Asian Natural Environmental Science Center, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | - Uwe John
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Anke Kremp
- Leibniz Institut für Ostseeforschung Warnemünde, Seestr. 15, 18119 Rostock, Germany
| | - Jacob Larsen
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100 Copenhagen Ø, Denmark
| | - Chui Pin Leaw
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Zhun Li
- Biological Resource Center/Korean Collection for Type Cultures (KCTC), Korea Research Institute of Bioscience and Biotechnology, Jeongeup 56212, Republic of Korea
| | - Po Teen Lim
- Bachok Marine Research Station, Institute of Ocean and Earth Sciences, University of Malaya, 16310 Bachok, Kelantan, Malaysia
| | - Wayne Litaker
- CSS Inc. Under contract to NOS/NOAA, Center for Coastal Fisheries and Habitat Research, 101 Pivers Island Road, Beaufort, NC 28516, USA
| | - Lincoln MacKenzie
- Coastal & Freshwater Group, Cawthron Institute, Private Bag 2, 98 Halifax Street East, Nelson 7042, New Zealand
| | - Estelle Masseret
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Kazumi Matsuoka
- C/O Institute for East China Sea Research, Nagasaki University, 1551-7 Taira-machi, Nagasaki 851-2213, Japan
| | - Øjvind Moestrup
- Marine Biological Section, Department of Biology, University of Copenhagen, Universitetsparken 4, DK-2100 Copenhagen Ø, Denmark
| | - Marina Montresor
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Satoshi Nagai
- National Research Institute of Fisheries Science, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Elisabeth Nézan
- Ifremer, LER BO, Station de Biologie Marine, Place de la Croix, BP40537, F-29185 Concarneau Cedex, France; National Museum of Natural History, DGD-REVE, Station de Biologie Marine de Concarneau, Place de la Croix, 29900 Concarneau, France
| | - Tomohiro Nishimura
- Coastal & Freshwater Group, Cawthron Institute, Private Bag 2, 98 Halifax Street East, Nelson 7042, New Zealand
| | - Yuri B Okolodkov
- Universidad Veracruzana, Instituto de Ciencias Marinas y Pesquerías, Laboratorio de Botánica Marina y Planctología, Calle Mar Mediterráneo No. 314, Fracc. Costa Verde, C.P. 94294 Boca del Río, Veracruz, Mexico
| | - Tatiana Yu Orlova
- A.V. Zhirmunsky National Scientific Center of Marine Biology of the Far Eastern Branch of the Russian Academy of Sciences, Palchevskogo Street, 17, Vladivostok 690041, Russia
| | - Albert Reñé
- Departament de Biologia Marina i Oceanografía, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Nagore Sampedro
- Departament de Biologia Marina i Oceanografía, Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Spain
| | - Cecilia Teodora Satta
- Dipartimento di Architettura, Design e Urbanistica, University of Sassari, Via Piandanna 4, 07100 Sassari, Italy
| | - Hyeon Ho Shin
- Library of Marine Samples, Korea Institute of Ocean Science and Technology, Geoje, Republic of Korea
| | | | - Kirsty F Smith
- Coastal & Freshwater Group, Cawthron Institute, Private Bag 2, 98 Halifax Street East, Nelson 7042, New Zealand
| | - Karen Steidinger
- Florida Fish and Wildlife Conservation Commission Fish and Wildlife Research Institute, 100 8th Avenue SE St. Petersburg, FL 33701, USA
| | | | - Urban Tillmann
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Jennifer Wolny
- Maryland Department of Natural Resources, 1919 Lincoln Drive Annapolis, MD 21401 USA
| | - Aika Yamaguchi
- Department of Biological Sciences, Faculty of Science, Hokkaido University, North 10, West 8, Sapporo 060-0810, Hokkaido, Japan
| | - Shauna Murray
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW 2007, Australia
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13
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Chacón J, Gottschling M. Dawn of the dinophytes: A first attempt to date origin and diversification of harmful algae. HARMFUL ALGAE 2020; 97:101871. [PMID: 32732051 DOI: 10.1016/j.hal.2020.101871] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 07/01/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
Unicellular dinophytes include a considerable number of harmful algae and potent producers of toxins. The dinophyte fossil record is one of the richest among protists and indicates a geologically old origin of the group dating back to the Triassic. Besides of these records, very few molecular dating studies of dinophytes have been published to date, precluding an understanding of the diversification history of these organisms. In the present study, we used first appearances in the fossil record for the best-represented dinophyte lineages, namely Gonyaulacales and Peridiniales, to calibrate a molecular phylogeny. It is inferred from ribosomal RNA sequence data covering a representative taxon sampling of all currently recognised lineages. Dinophytes may have started diversifying during main tectonic events of the supercontinent Pangaea, witnessing and surviving some of the biggest mass extinction events on Earth. Groups including harmful dinophytes originated at different points in time, but they all predate the Cretaceous-Paleogene boundary. Our chronogram provides a first time frame and may stimulate studies in future bringing molecular phylogenetics of dinophytes and their impressive fossil record together in more detail.
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Affiliation(s)
- Juliana Chacón
- Department Biologie, Systematische Botanik und Mykologie, GeoBio-Center, Ludwig-Maximilians-Universität München, Menzinger Str. 67, München D - 80 638, Germany
| | - Marc Gottschling
- Department Biologie, Systematische Botanik und Mykologie, GeoBio-Center, Ludwig-Maximilians-Universität München, Menzinger Str. 67, München D - 80 638, Germany.
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14
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Fajardo C, De Donato M, Rodulfo H, Martinez-Rodriguez G, Costas B, Mancera JM, Fernandez-Acero FJ. New Perspectives Related to the Bioluminescent System in Dinoflagellates: Pyrocystis lunula, a Case Study. Int J Mol Sci 2020; 21:E1784. [PMID: 32150894 PMCID: PMC7084563 DOI: 10.3390/ijms21051784] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/19/2020] [Accepted: 03/03/2020] [Indexed: 11/22/2022] Open
Abstract
Pyrocystis lunula is considered a model organism due to its bioluminescence capacity linked to circadian rhythms. The mechanisms underlying the bioluminescent phenomenon have been well characterized in dinoflagellates; however, there are still some aspects that remain an enigma. Such is the case of the presence and diversity of the luciferin-binding protein (LBP), as well as the synthesis process of luciferin. Here we carry out a review of the literature in relation to the molecular players responsible for bioluminescence in dinoflagellates, with particular interest in P. lunula. We also carried out a phylogenetic analysis of the conservation of protein sequence, structure and evolutionary pattern of these key players. The basic structure of the luciferase (LCF) is quite conserved among the sequences reported to date for dinoflagellate species, but not in the case of the LBP, which has proven to be more variable in terms of sequence and structure. In the case of luciferin, its synthesis has been shown to be complex process with more than one metabolic pathway involved. The glutathione S-transferase (GST) and the P630 or blue compound, seem to be involved in this process. In the same way, various hypotheses regarding the role of bioluminescence in dinoflagellates are exposed.
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Affiliation(s)
- Carlos Fajardo
- Microbiology Laboratory, Institute of Viticulture and Agri-food Research (IVAGRO), Environmental and Marine Sciences Faculty. University of Cadiz (UCA), 11510 Puerto Real, Spain;
| | - Marcos De Donato
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, 76130 Queretaro, Mexico; (M.D.D.); (H.R.)
| | - Hectorina Rodulfo
- Tecnologico de Monterrey, Escuela de Ingenieria y Ciencias, 76130 Queretaro, Mexico; (M.D.D.); (H.R.)
| | - Gonzalo Martinez-Rodriguez
- Institute of Marine Sciences of Andalusia (ICMAN), Department of Marine Biology and Aquaculture, Spanish National Research Council (CSIC), 11519 Puerto Real, Spain;
| | - Benjamin Costas
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto (CIIMAR), 4450-208 Matosinhos, Portugal;
- Institute of Biomedical Sciences Abel Salazar (ICBAS-UP), University of Porto, 4050-313 Porto, Portugal
| | - Juan Miguel Mancera
- Faculty of Marine and Environmental Sciences, Biology Department, University of Cadiz (UCA), 11510 Puerto Real, Spain;
| | - Francisco Javier Fernandez-Acero
- Microbiology Laboratory, Institute of Viticulture and Agri-food Research (IVAGRO), Environmental and Marine Sciences Faculty. University of Cadiz (UCA), 11510 Puerto Real, Spain;
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15
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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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16
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Žerdoner Čalasan A, Kretschmann J, Gottschling M. They are young, and they are many: dating freshwater lineages in unicellular dinophytes. Environ Microbiol 2019; 21:4125-4135. [DOI: 10.1111/1462-2920.14766] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 07/24/2019] [Accepted: 07/29/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Anže Žerdoner Čalasan
- Department Biologie/Chemie, Botanik Universität Osnabrück Barbarastr. 11, 49076 Osnabrück Germany
- Department Biologie Systematische Botanik und Mykologie, GeoBio‐Center, Ludwig‐Maximilians‐Universität München Menzinger Street. 67, 80638 Munich Germany
| | - Juliane Kretschmann
- Department Biologie Systematische Botanik und Mykologie, GeoBio‐Center, Ludwig‐Maximilians‐Universität München Menzinger Street. 67, 80638 Munich Germany
| | - Marc Gottschling
- Department Biologie Systematische Botanik und Mykologie, GeoBio‐Center, Ludwig‐Maximilians‐Universität München Menzinger Street. 67, 80638 Munich Germany
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17
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Tillmann U, Edvardsen B, Krock B, Smith KF, Paterson RF, Voß D. Diversity, distribution, and azaspiracids of Amphidomataceae (Dinophyceae) along the Norwegian coast. HARMFUL ALGAE 2018; 80:15-34. [PMID: 30502808 DOI: 10.1016/j.hal.2018.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 08/27/2018] [Accepted: 08/30/2018] [Indexed: 06/09/2023]
Abstract
Azaspiracids (AZA) are a group of lipophilic polyether compounds which have been implicated in shellfish poisoning incidents around Europe. They are produced by a few species of the dinophycean genera Azadinium and Amphidoma (Amphidomataceae). The presence of AZA toxins in Norway is well documented, but knowledge of the distribution and diversity of Azadinium and other Amphidomataceae along the Norwegian coast is rather limited and poorly documented. On a research survey along the Norwegian coast in 2015 from the Skagerrak in the South to Trondheimsfjorden in the North, plankton samples from 67 stations were analysed for the presence of Azadinium and Amphidoma and their respective AZA by on-board live microscopy, real-time PCR assays specific for Amphidomataceae, and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Microscopy using live samples and positive real-time PCR assays using a general family probe and two species specific probes revealed the presence of Amphidomataceae distributed throughout the sampling area. Overall abundance was low, however, and was in agreement with a lack of detectable AZA in plankton samples. Single cell isolation and morphological and molecular characterisation of established strains revealed the presence of 7 amphidomatacean species (Azadiniun spinosum, Az. poporum, Az. obesum, Az. dalianense, Az. trinitatum, Az. polongum, Amphidoma languida) in the area. Azaspiracids were produced by the known AZA producing species Az. spinosum, Az. poporum and Am. languida only. LC-MS/MS analysis further revealed that Norwegian strains produce previously unreported AZA for Norway (AZA-11 by Az. spinosum, AZA-37 by Az. poporum, AZA-38 and AZA-39 by Am. languida), and also four novel compounds (AZA-50, -51 by Az. spinosum, AZA-52, -53 by Am. languida), whose structural properties are described and which now can be included in existing analytical protocols. A maximum likelihood analysis of concatenated rDNA regions (SSU, ITS1-ITS2, partial LSU) showed that the strains of Az. spinosum fell in two well supported clades, where most but not all new Norwegian strains formed the new Ribotype B. Ribotype differentiation was supported by a minor morphological difference with respect to the presence/absence of a rim around the pore plate, and was consistently reflected by different AZA profiles. Strains of Az. spinosum from ribotype A produce AZA-1, -2 and -33, whereas the new strains of ribotype B produce mainly AZA-11 and AZA-51. Significant sequence differences between both Az. spinosum ribotypes underline the need to redesign the currently used qPCR probes in order to detect all AZA producing Az. spinosum. The results generally underline the conclusion that for the Norwegian coast area it is important that amphidomatacean species are taken into account in future studies and monitoring programs.
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Affiliation(s)
- Urban Tillmann
- Alfred Wegener Institute, Am Handelshafen 12, D-27570 Bremerhaven, Germany.
| | - Bente Edvardsen
- University of Oslo, Department of Biosciences, Section for Aquatic Biology and Toxicology, P.O. Box 1066 Blindern, 0316 Oslo, Norway
| | - Bernd Krock
- Alfred Wegener Institute, Am Handelshafen 12, D-27570 Bremerhaven, Germany
| | - Kirsty F Smith
- Cawthron Institute, Privat Bag 2, Nelson 7042, New Zealand
| | - Ruth F Paterson
- Scottish Association for Marine Science, Scotland, PA37 1QA, United Kingdom
| | - Daniela Voß
- Institut für Chemie und Biologie des Meeres (ICBM), Carl von Ossietzky Universität Oldenburg, Schleusenstraße 1, D-26382 Wilhelmshaven, Germany
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18
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Annenkova NV, Ahrén D, Logares R, Kremp A, Rengefors K. Delineating closely related dinoflagellate lineages using phylotranscriptomics. JOURNAL OF PHYCOLOGY 2018; 54:571-576. [PMID: 29676790 DOI: 10.1111/jpy.12748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 04/05/2018] [Indexed: 06/08/2023]
Abstract
Recently radiated dinoflagellates Apocalathium aciculiferum (collected in Lake Erken, Sweden), Apocalathium malmogiense (Baltic Sea) and Apocalathium aff. malmogiense (Highway Lake, Antarctica) represent a lineage with an unresolved phylogeny. We determined their phylogenetic relationships using phylotranscriptomics based on 792 amino acid sequences. Our results showed that A. aciculiferum diverged from the other two closely related lineages, consistent with their different morphologies in cell size, relative cell length and presence of spines. We hypothesized that A. aff. malmogiense and A. malmogiense, which inhabit different hemispheres, are evolutionarily more closely related because they diverged from a marine common ancestor, adapting to a wide salinity range, while A. aciculiferum colonized a freshwater habitat, by acquiring adaptations to this environment, in particular, salinity intolerance. We show that phylotranscriptomics can resolve the phylogeny of recently diverged protists. This has broad relevance, given that many phytoplankton species are morphologically very similar, and single genes sometimes lack the information to determine species' relationships.
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Affiliation(s)
- Nataliia V Annenkova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences 3, Ulan-Batorskaya St., 664033, Irkutsk, Russia
| | - Dag Ahrén
- Microbial Ecology Group, Department of Biology, Lund University, Ecology Building, SE-223 62, Lund, Sweden
- Bioinformatics Infrastructures for Life Sciences (BILS), Department of Biology, Lund University, Ecology Building, SE-223 62, Lund, Sweden
| | - Ramiro Logares
- Department of Marine Biology and Oceanography, Institute of Marine Science (ICM)-Consejo Superior de Investigaciones Científicas (CSIC), Passeig Marítim de la Barceloneta 37-49, E08003, Barcelona, Spain
| | - Anke Kremp
- Marine Research Centre, Finnish Environment Institute, Erik Palmenin aukio 1, 00560, Helsinki, Finland
| | - Karin Rengefors
- Aquatic Ecology, Department of Biology, Lund University, Ecology Building, SE-223 62, Lund, Sweden
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19
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Kigundu G, Cooper JL, Smith SME. H v 1 Proton Channels in Dinoflagellates: Not Just for Bioluminescence? J Eukaryot Microbiol 2018; 65:928-933. [PMID: 29698585 PMCID: PMC7167071 DOI: 10.1111/jeu.12627] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/11/2018] [Accepted: 04/15/2018] [Indexed: 01/08/2023]
Abstract
Bioluminescence in dinoflagellates is controlled by HV1 proton channels. Database searches of dinoflagellate transcriptomes and genomes yielded hits with sequence features diagnostic of all confirmed HV1, and show that HV1 is widely distributed in the dinoflagellate phylogeny including the basal species Oxyrrhis marina. Multiple sequence alignments followed by phylogenetic analysis revealed three major subfamilies of HV1 that do not correlate with presence of theca, autotrophy, geographic location, or bioluminescence. These data suggest that most dinoflagellates express a HV1 which has a function separate from bioluminescence. Sequence evidence also suggests that dinoflagellates can contain more than one HV1 gene.
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Affiliation(s)
- Gabriel Kigundu
- Department of Molecular and Cellular Biology, Kennesaw State University, 370 Paulding Avenue MD 1202, Kennesaw, Georgia, 30144
| | - Jennifer L Cooper
- Department of Molecular and Cellular Biology, Kennesaw State University, 370 Paulding Avenue MD 1202, Kennesaw, Georgia, 30144
| | - Susan M E Smith
- Department of Molecular and Cellular Biology, Kennesaw State University, 370 Paulding Avenue MD 1202, Kennesaw, Georgia, 30144
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20
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Meng A, Corre E, Probert I, Gutierrez-Rodriguez A, Siano R, Annamale A, Alberti A, Da Silva C, Wincker P, Le Crom S, Not F, Bittner L. Analysis of the genomic basis of functional diversity in dinoflagellates using a transcriptome-based sequence similarity network. Mol Ecol 2018; 27:2365-2380. [PMID: 29624751 DOI: 10.1111/mec.14579] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 02/23/2018] [Accepted: 03/21/2018] [Indexed: 02/06/2023]
Abstract
Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core-predicted proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated with functional traits. With respect to toxicity, sequences homologous to those of proteins found in species with toxicity potential (e.g., sxtA4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of, respectively, the toxic and symbiotic species represented in our analyses. Of these, 56% and 57%, respectively (i.e., 25,393 and 52,193 pCDs), completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization.
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Affiliation(s)
- Arnaud Meng
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles Guyane, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), Paris, France
| | - Erwan Corre
- CNRS, UPMC, FR2424, ABiMS, Station Biologique, Roscoff, France
| | - Ian Probert
- UPMC-CNRS, FR2424, Roscoff Culture Collection, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | | | - Raffaele Siano
- Ifremer - Centre de Brest, DYNECO PELAGOS, Plouzané, France
| | - Anita Annamale
- CEA - Institut de Génomique, GENOSCOPE, Evry, France.,CNRS, UMR8030, Evry, France.,Université d'Evry Val d'Essonne, Evry, France
| | - Adriana Alberti
- CEA - Institut de Génomique, GENOSCOPE, Evry, France.,CNRS, UMR8030, Evry, France.,Université d'Evry Val d'Essonne, Evry, France
| | - Corinne Da Silva
- CEA - Institut de Génomique, GENOSCOPE, Evry, France.,CNRS, UMR8030, Evry, France.,Université d'Evry Val d'Essonne, Evry, France
| | - Patrick Wincker
- CEA - Institut de Génomique, GENOSCOPE, Evry, France.,CNRS, UMR8030, Evry, France.,Université d'Evry Val d'Essonne, Evry, France
| | - Stéphane Le Crom
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles Guyane, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), Paris, France
| | - Fabrice Not
- CNRS, UMR 7144, Station Biologique de Roscoff, Place Georges Teissier, Roscoff, France
| | - Lucie Bittner
- Sorbonne Universités, UPMC Univ Paris 06, Univ Antilles Guyane, Univ Nice Sophia Antipolis, CNRS, Evolution Paris Seine - Institut de Biologie Paris Seine (EPS - IBPS), Paris, France
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21
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Mordret S, Piredda R, Vaulot D, Montresor M, Kooistra WHCF, Sarno D. dinoref: A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene. Mol Ecol Resour 2018; 18:974-987. [PMID: 29603631 DOI: 10.1111/1755-0998.12781] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/15/2018] [Accepted: 02/24/2018] [Indexed: 01/28/2023]
Abstract
Dinoflagellates are a heterogeneous group of protists present in all aquatic ecosystems where they occupy various ecological niches. They play a major role as primary producers, but many species are mixotrophic or heterotrophic. Environmental metabarcoding based on high-throughput sequencing is increasingly applied to assess diversity and abundance of planktonic organisms, and reference databases are definitely needed to taxonomically assign the huge number of sequences. We provide an updated 18S rRNA reference database of dinoflagellates: dinoref. Sequences were downloaded from genbank and filtered based on stringent quality criteria. All sequences were taxonomically curated, classified taking into account classical morphotaxonomic studies and molecular phylogenies, and linked to a series of metadata. dinoref includes 1,671 sequences representing 149 genera and 422 species. The taxonomic assignation of 468 sequences was revised. The largest number of sequences belongs to Gonyaulacales and Suessiales that include toxic and symbiotic species. dinoref provides an opportunity to test the level of taxonomic resolution of different 18S barcode markers based on a large number of sequences and species. As an example, when only the V4 region is considered, 374 of the 422 species included in dinoref can still be unambiguously identified. Clustering the V4 sequences at 98% similarity, a threshold that is commonly applied in metabarcoding studies, resulted in a considerable underestimation of species diversity.
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Affiliation(s)
- Solenn Mordret
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Roberta Piredda
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Daniel Vaulot
- Sorbonne Université, CNRS, UMR Adaptation et Diversité en Milieu Marin, Station Biologique, Roscoff, France
| | - Marina Montresor
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | | | - Diana Sarno
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
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22
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Vader A, Laughinghouse HD, Griffiths C, Jakobsen KS, Gabrielsen TM. Proton-pumping rhodopsins are abundantly expressed by microbial eukaryotes in a high-Arctic fjord. Environ Microbiol 2018; 20:890-902. [PMID: 29266690 DOI: 10.1111/1462-2920.14035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 11/21/2017] [Accepted: 12/18/2017] [Indexed: 01/07/2023]
Abstract
Proton-pumping rhodopsins provide an alternative pathway to photosynthesis by which solar energy can enter the marine food web. Rhodopsin genes are widely found in marine bacteria, also in the Arctic, and were recently reported from several eukaryotic lineages. So far, little is known about rhodopsin expression in Arctic eukaryotes. In this study, we used metatranscriptomics and 18S rDNA tag sequencing to examine the mid-summer function and composition of marine protists (size 0.45-10 µm) in the high-Arctic Billefjorden (Spitsbergen), especially focussing on the expression of microbial proton-pumping rhodopsins. Rhodopsin transcripts were highly abundant, at a level similar to that of genes involved in photosynthesis. Phylogenetic analyses placed the environmental rhodopsins within disparate eukaryotic lineages, including dinoflagellates, stramenopiles, haptophytes and cryptophytes. Sequence comparison indicated the presence of several functional types, including xanthorhodopsins and a eukaryotic clade of proteorhodopsin. Transcripts belonging to the proteorhodopsin clade were also abundant in published metatranscriptomes from other oceanic regions, suggesting a global distribution. The diversity and abundance of rhodopsins show that these light-driven proton pumps play an important role in Arctic microbial eukaryotes. Understanding this role is imperative to predicting the future of the Arctic marine ecosystem faced by a changing light climate due to diminishing sea-ice.
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Affiliation(s)
- Anna Vader
- University Centre in Svalbard, Longyearbyen, Norway
| | | | | | - Kjetill S Jakobsen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Norway
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23
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Cavalier-Smith T. Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences. PROTOPLASMA 2018; 255:297-357. [PMID: 28875267 PMCID: PMC5756292 DOI: 10.1007/s00709-017-1147-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/18/2017] [Indexed: 05/18/2023]
Abstract
In 1981 I established kingdom Chromista, distinguished from Plantae because of its more complex chloroplast-associated membrane topology and rigid tubular multipartite ciliary hairs. Plantae originated by converting a cyanobacterium to chloroplasts with Toc/Tic translocons; most evolved cell walls early, thereby losing phagotrophy. Chromists originated by enslaving a phagocytosed red alga, surrounding plastids by two extra membranes, placing them within the endomembrane system, necessitating novel protein import machineries. Early chromists retained phagotrophy, remaining naked and repeatedly reverted to heterotrophy by losing chloroplasts. Therefore, Chromista include secondary phagoheterotrophs (notably ciliates, many dinoflagellates, Opalozoa, Rhizaria, heliozoans) or walled osmotrophs (Pseudofungi, Labyrinthulea), formerly considered protozoa or fungi respectively, plus endoparasites (e.g. Sporozoa) and all chromophyte algae (other dinoflagellates, chromeroids, ochrophytes, haptophytes, cryptophytes). I discuss their origin, evolutionary diversification, and reasons for making chromists one kingdom despite highly divergent cytoskeletons and trophic modes, including improved explanations for periplastid/chloroplast protein targeting, derlin evolution, and ciliary/cytoskeletal diversification. I conjecture that transit-peptide-receptor-mediated 'endocytosis' from periplastid membranes generates periplastid vesicles that fuse with the arguably derlin-translocon-containing periplastid reticulum (putative red algal trans-Golgi network homologue; present in all chromophytes except dinoflagellates). I explain chromist origin from ancestral corticates and neokaryotes, reappraising tertiary symbiogenesis; a chromist cytoskeletal synapomorphy, a bypassing microtubule band dextral to both centrioles, favoured multiple axopodial origins. I revise chromist higher classification by transferring rhizarian subphylum Endomyxa from Cercozoa to Retaria; establishing retarian subphylum Ectoreta for Foraminifera plus Radiozoa, apicomonad subclasses, new dinozoan classes Myzodinea (grouping Colpovora gen. n., Psammosa), Endodinea, Sulcodinea, and subclass Karlodinia; and ranking heterokont Gyrista as phylum not superphylum.
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24
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Price DC, Bhattacharya D. Robust Dinoflagellata phylogeny inferred from public transcriptome databases. JOURNAL OF PHYCOLOGY 2017; 53:725-729. [PMID: 28273342 DOI: 10.1111/jpy.12529] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 02/24/2017] [Indexed: 05/13/2023]
Abstract
Dinoflagellates are dominant members of the plankton and play key roles in ocean ecosystems as primary producers, predators, parasites, coral photobionts, and causative agents of algal blooms that produce toxins harmful to humans and commercial fisheries. These unicellular protists exhibit remarkable trophic and morphological diversity and include species with some of the largest reported nuclear genomes. Despite their high ecological and economic importance, comprehensive genome (or transcriptome) based dinoflagellate trees of life are few in number. To address this issue, we used recently generated public sequencing data, including from the Moore Microbial Eukaryote Transcriptome Sequencing Project, to identify dinoflagellate-specific ortholog groups. These orthologs were combined to create a broadly sampled and highly resolved phylogeny of dinoflagellates. Our results emphasize the scope and utility of public sequencing databases in creating broad and robust phylogenies for large and complex taxonomic lineages, while also providing unique insights into the evolution of thecate dinoflagellates.
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Affiliation(s)
- Dana C Price
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey, 08901, USA
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, New Jersey, 08901, USA
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25
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Kohli GS, Campbell K, John U, Smith KF, Fraga S, Rhodes LL, Murray SA. Role of Modular Polyketide Synthases in the Production of Polyether Ladder Compounds in Ciguatoxin-Producing Gambierdiscus polynesiensis and G. excentricus (Dinophyceae). J Eukaryot Microbiol 2017; 64:691-706. [PMID: 28211202 DOI: 10.1111/jeu.12405] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 01/31/2017] [Accepted: 02/03/2017] [Indexed: 11/28/2022]
Abstract
Gambierdiscus, a benthic dinoflagellate, produces ciguatoxins that cause the human illness Ciguatera. Ciguatoxins are polyether ladder compounds that have a polyketide origin, indicating that polyketide synthases (PKS) are involved in their production. We sequenced transcriptomes of Gambierdiscus excentricus and Gambierdiscus polynesiensis and found 264 contigs encoding single domain ketoacyl synthases (KS; G. excentricus: 106, G. polynesiensis: 143) and ketoreductases (KR; G. excentricus: 7, G. polynesiensis: 8) with sequence similarity to type I PKSs, as reported in other dinoflagellates. In addition, 24 contigs (G. excentricus: 3, G. polynesiensis: 21) encoding multiple PKS domains (forming typical type I PKSs modules) were found. The proposed structure produced by one of these megasynthases resembles a partial carbon backbone of a polyether ladder compound. Seventeen contigs encoding single domain KS, KR, s-malonyltransacylase, dehydratase and enoyl reductase with sequence similarity to type II fatty acid synthases (FAS) in plants were found. Type I PKS and type II FAS genes were distinguished based on the arrangement of domains on the contigs and their sequence similarity and phylogenetic clustering with known PKS/FAS genes in other organisms. This differentiation of PKS and FAS pathways in Gambierdiscus is important, as it will facilitate approaches to investigating toxin biosynthesis pathways in dinoflagellates.
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Affiliation(s)
- Gurjeet S Kohli
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 689528, Singapore
| | - Katrina Campbell
- Institute for Global Food Security, School of Biological Sciences, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, United Kingdom
| | - Uwe John
- Alfred-Wegener-Institute Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, 27515, Germany.,Helmholtz Institute for Functional Marine Biodiversity, University of Oldenburg, Oldenburg, 26111, Germany
| | - Kirsty F Smith
- Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
| | - Santiago Fraga
- Instituto Español de Oceanografía, Centro Oceanográfico de Vigo, Subida a Radio Faro 50, Vigo, 36390, Spain
| | - Lesley L Rhodes
- Cawthron Institute, 98 Halifax Street East, Nelson, 7010, New Zealand
| | - Shauna A Murray
- Climate Change Cluster, University of Technology Sydney, Ultimo, NSW, 2007, Australia
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26
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Luo Z, Zhang H, Krock B, Lu S, Yang W, Gu H. Morphology, molecular phylogeny and okadaic acid production of epibenthic Prorocentrum (Dinophyceae) species from the northern South China Sea. ALGAL RES 2017. [DOI: 10.1016/j.algal.2016.11.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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27
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Rodriguez JD, Haq S, Bachvaroff T, Nowak KF, Nowak SJ, Morgan D, Cherny VV, Sapp MM, Bernstein S, Bolt A, DeCoursey TE, Place AR, Smith SME. Identification of a vacuolar proton channel that triggers the bioluminescent flash in dinoflagellates. PLoS One 2017; 12:e0171594. [PMID: 28178296 PMCID: PMC5298346 DOI: 10.1371/journal.pone.0171594] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 01/23/2017] [Indexed: 11/19/2022] Open
Abstract
In 1972, J. Woodland Hastings and colleagues predicted the existence of a proton selective channel (HV1) that opens in response to depolarizing voltage across the vacuole membrane of bioluminescent dinoflagellates and conducts protons into specialized luminescence compartments (scintillons), thereby causing a pH drop that triggers light emission. HV1 channels were subsequently identified and demonstrated to have important functions in a multitude of eukaryotic cells. Here we report a predicted protein from Lingulodinium polyedrum that displays hallmark properties of bona fide HV1, including time-dependent opening with depolarization, perfect proton selectivity, and characteristic ΔpH dependent gating. Western blotting and fluorescence confocal microscopy of isolated L. polyedrum scintillons immunostained with antibody to LpHV1 confirm LpHV1's predicted organellar location. Proteomics analysis demonstrates that isolated scintillon preparations contain peptides that map to LpHV1. Finally, Zn2+ inhibits both LpHV1 proton current and the acid-induced flash in isolated scintillons. These results implicate LpHV1 as the voltage gated proton channel that triggers bioluminescence in L. polyedrum, confirming Hastings' hypothesis. The same channel likely mediates the action potential that communicates the signal along the tonoplast to the scintillon.
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Affiliation(s)
- Juan D. Rodriguez
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Saddef Haq
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Tsvetan Bachvaroff
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Kristine F. Nowak
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Scott J. Nowak
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Deri Morgan
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, Illinois, United States of America
| | - Vladimir V. Cherny
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, Illinois, United States of America
| | - Maredith M. Sapp
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Steven Bernstein
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Andrew Bolt
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia, United States of America
| | - Thomas E. DeCoursey
- Department of Molecular Biophysics and Physiology, Rush University, Chicago, Illinois, United States of America
| | - Allen R. Place
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Susan M. E. Smith
- Department of Molecular and Cellular Biology, Kennesaw State University, Kennesaw, Georgia, United States of America
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28
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Jang SH, Jeong HJ, Chon JK, Lee SY. De novo assembly and characterization of the transcriptome of the newly described dinoflagellate Ansanella granifera: Spotlight on flagellum-associated genes. Mar Genomics 2017; 33:47-55. [PMID: 28111206 DOI: 10.1016/j.margen.2017.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/11/2017] [Accepted: 01/11/2017] [Indexed: 11/15/2022]
Abstract
Many dinoflagellates are known to cause red tides and often outgrow non-motile diatoms and motile small flagellates through active vertical migration between well-lit surface and eutrophic deep waters and/or by locating and ingesting prey cells. Their flagella play important roles in these two critical behaviors. However, the structural and functional genes of dinoflagellate flagella are very little known. Thus, a de novo assembly and characterization of the transcriptome of the fast-swimming dinoflagellate Ansanella granifera were conducted and its flagellum genes were compared with those of other dinoflagellates, motile small flagellates, and non-motile protist species. Based on assembled data using Trinity/CLC combined strategy, 83,652 transcripts of A. granifera were identified. The assembled consensus sequences were annotated to the NCBI non-redundant (nr), InterProScan, Gene Ontology (GO), and KEGG pathway analyses. Moreover, 71 structural and 35 functional flagellum-associated genes expressed were identified. The number of expressed flagellar structural and functional genes of A. granifera was not markedly different from those of other dinoflagellates or motile small flagellates, but much greater than those of non-motile species. Furthermore, in both phylogenetic trees based on the outer dynein arm (ODA1, ODA9, and DLC1) and inner dynein arm (IDA4, IDA7, and BOP5) flagellum genes of dinoflagellates, the problem of the long-branch attraction artifacts of Oxyrrhis marina which has been reported in the phylogenetic trees based on ribosomal DNA was removed. Moreover, in both phylogenetic trees based on the ODA and IDA flagellum genes, the species in the order Peridiniales or Gymnodiniales were revealed to belong to a big clade of each order. Therefore, the phylogenetic tree based on the flagellum genes is likely to give a clue to resolve the problem of separation in a big clade of a dinoflagellate order which has also been reported in the phylogenetic trees based on ribosomal DNA.
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Affiliation(s)
- Se Hyeon Jang
- School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Hae Jin Jeong
- School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea; Advanced Institutes of Convergence Technology, Suwon, Gyeonggi-do 16229, Republic of Korea.
| | - Jae Kyung Chon
- Department of Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Yeon Lee
- School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
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29
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Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics. Proc Natl Acad Sci U S A 2016; 114:E171-E180. [PMID: 28028238 DOI: 10.1073/pnas.1614842114] [Citation(s) in RCA: 130] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dinoflagellates are key species in marine environments, but they remain poorly understood in part because of their large, complex genomes, unique molecular biology, and unresolved in-group relationships. We created a taxonomically representative dataset of dinoflagellate transcriptomes and used this to infer a strongly supported phylogeny to map major morphological and molecular transitions in dinoflagellate evolution. Our results show an early-branching position of Noctiluca, monophyly of thecate (plate-bearing) dinoflagellates, and paraphyly of athecate ones. This represents unambiguous phylogenetic evidence for a single origin of the group's cellulosic theca, which we show coincided with a radiation of cellulases implicated in cell division. By integrating dinoflagellate molecular, fossil, and biogeochemical evidence, we propose a revised model for the evolution of thecal tabulations and suggest that the late acquisition of dinosterol in the group is inconsistent with dinoflagellates being the source of this biomarker in pre-Mesozoic strata. Three distantly related, fundamentally nonphotosynthetic dinoflagellates, Noctiluca, Oxyrrhis, and Dinophysis, contain cryptic plastidial metabolisms and lack alternative cytosolic pathways, suggesting that all free-living dinoflagellates are metabolically dependent on plastids. This finding led us to propose general mechanisms of dependency on plastid organelles in eukaryotes that have lost photosynthesis; it also suggests that the evolutionary origin of bioluminescence in nonphotosynthetic dinoflagellates may be linked to plastidic tetrapyrrole biosynthesis. Finally, we use our phylogenetic framework to show that dinoflagellate nuclei have recruited DNA-binding proteins in three distinct evolutionary waves, which included two independent acquisitions of bacterial histone-like proteins.
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30
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Kohli GS, John U, Van Dolah FM, Murray SA. Evolutionary distinctiveness of fatty acid and polyketide synthesis in eukaryotes. ISME JOURNAL 2016; 10:1877-90. [PMID: 26784357 PMCID: PMC5029157 DOI: 10.1038/ismej.2015.263] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 11/18/2015] [Accepted: 12/07/2015] [Indexed: 11/09/2022]
Abstract
Fatty acids, which are essential cell membrane constituents and fuel storage molecules, are thought to share a common evolutionary origin with polyketide toxins in eukaryotes. While fatty acids are primary metabolic products, polyketide toxins are secondary metabolites that are involved in ecologically relevant processes, such as chemical defence, and produce the adverse effects of harmful algal blooms. Selection pressures on such compounds may be different, resulting in differing evolutionary histories. Surprisingly, some studies of dinoflagellates have suggested that the same enzymes may catalyse these processes. Here we show the presence and evolutionary distinctiveness of genes encoding six key enzymes essential for fatty acid production in 13 eukaryotic lineages for which no previous sequence data were available (alveolates: dinoflagellates, Vitrella, Chromera; stramenopiles: bolidophytes, chrysophytes, pelagophytes, raphidophytes, dictyochophytes, pinguiophytes, xanthophytes; Rhizaria: chlorarachniophytes, haplosporida; euglenids) and 8 other lineages (apicomplexans, bacillariophytes, synurophytes, cryptophytes, haptophytes, chlorophyceans, prasinophytes, trebouxiophytes). The phylogeny of fatty acid synthase genes reflects the evolutionary history of the organism, indicating selection to maintain conserved functionality. In contrast, polyketide synthase gene families are highly expanded in dinoflagellates and haptophytes, suggesting relaxed constraints in their evolutionary history, while completely absent from some protist lineages. This demonstrates a vast potential for the production of bioactive polyketide compounds in some lineages of microbial eukaryotes, indicating that the evolution of these compounds may have played an important role in their ecological success.
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Affiliation(s)
- Gurjeet S Kohli
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia.,Sydney Institute of Marine Sciences, Mosman, New South Wales, Australia
| | - Uwe John
- Alfred-Wegener-Institute Helmholtz Center for Polar and Marine Research, Bremerhaven, Germany
| | - Frances M Van Dolah
- Marine Biotoxins Program, National Oceanic and Atmospheric Administration Center for Coastal and Environmental Health and Biomolecular Research, Charleston, SC, USA
| | - Shauna A Murray
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia.,Sydney Institute of Marine Sciences, Mosman, New South Wales, Australia
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31
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Abstract
Histone proteins and the nucleosomal organization of chromatin are near-universal eukaroytic features, with the exception of dinoflagellates. Previous studies have suggested that histones do not play a major role in the packaging of dinoflagellate genomes, although several genomic and transcriptomic surveys have detected a full set of core histone genes. Here, transcriptomic and genomic sequence data from multiple dinoflagellate lineages are analyzed, and the diversity of histone proteins and their variants characterized, with particular focus on their potential post-translational modifications and the conservation of the histone code. In addition, the set of putative epigenetic mark readers and writers, chromatin remodelers and histone chaperones are examined. Dinoflagellates clearly express the most derived set of histones among all autonomous eukaryote nuclei, consistent with a combination of relaxation of sequence constraints imposed by the histone code and the presence of numerous specialized histone variants. The histone code itself appears to have diverged significantly in some of its components, yet others are conserved, implying conservation of the associated biochemical processes. Specifically, and with major implications for the function of histones in dinoflagellates, the results presented here strongly suggest that transcription through nucleosomal arrays happens in dinoflagellates. Finally, the plausible roles of histones in dinoflagellate nuclei are discussed.
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32
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Taxonomic Clarification of the Unusual Dinophyte Gymnodinium limneticum W ołosz . (Gymnodiniaceae) from the Tatra Mountains. Protist 2015; 166:621-37. [DOI: 10.1016/j.protis.2015.09.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 08/21/2015] [Accepted: 09/11/2015] [Indexed: 11/15/2022]
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33
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Le Bescot N, Mahé F, Audic S, Dimier C, Garet MJ, Poulain J, Wincker P, de Vargas C, Siano R. Global patterns of pelagic dinoflagellate diversity across protist size classes unveiled by metabarcoding. Environ Microbiol 2015; 18:609-26. [DOI: 10.1111/1462-2920.13039] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 08/25/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Noan Le Bescot
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
| | - Frédéric Mahé
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
- Department of Ecology; Technische Universität Kaiserslautern; Erwin-Schrödinger Str. 14 D-67663 Kaiserslautern Germany
| | - Stéphane Audic
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
| | - Céline Dimier
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
| | - Marie-José Garet
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
| | - Julie Poulain
- Centre National de Séquençage; CEA-Institut de Génomique, GENOSCOPE; Evry Cedex France
| | - Patrick Wincker
- Centre National de Séquençage; CEA-Institut de Génomique, GENOSCOPE; Evry Cedex France
- Université d'Evry, UMR 8030; rue Gaston Crémieux CP5706 91057 Evry Cedex France
- Centre National de la Recherche Scientifique (CNRS), UMR 8030; rue Gaston Crémieux CP5706 91057 Evry Cedex France
| | - Colomban de Vargas
- EPEP - Evolution of Protists and Pelagic Ecosystems; Centre National de la Recherche Scientifique (CNRS) UMR 7144 Station Biologique de Roscoff; 29680 Roscoff France
- Station Biologique de Roscoff; Sorbonne Universités, UPMC Univ Paris 06, UMR7144; 29680 Roscoff France
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Craveiro SC, Daugbjerg N, Moestrup Ø, Calado AJ. Fine-structural characterization and phylogeny of Peridinium polonicum, type species of the recently described genus Naiadinium (Dinophyceae). Eur J Protistol 2015; 51:259-79. [DOI: 10.1016/j.ejop.2015.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/08/2015] [Accepted: 05/11/2015] [Indexed: 10/23/2022]
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Murray SA, Diwan R, Orr RJS, Kohli GS, John U. Gene duplication, loss and selection in the evolution of saxitoxin biosynthesis in alveolates. Mol Phylogenet Evol 2015; 92:165-80. [PMID: 26140862 DOI: 10.1016/j.ympev.2015.06.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/01/2015] [Accepted: 06/25/2015] [Indexed: 11/29/2022]
Abstract
A group of marine dinoflagellates (Alveolata, Eukaryota), consisting of ∼10 species of the genus Alexandrium, Gymnodinium catenatum and Pyrodinium bahamense, produce the toxin saxitoxin and its analogues (STX), which can accumulate in shellfish, leading to ecosystem and human health impacts. The genes, sxt, putatively involved in STX biosynthesis, have recently been identified, however, the evolution of these genes within dinoflagellates is not clear. There are two reasons for this: uncertainty over the phylogeny of dinoflagellates; and that the sxt genes of many species of Alexandrium and other dinoflagellate genera are not known. Here, we determined the phylogeny of STX-producing and other dinoflagellates based on a concatenated eight-gene alignment. We determined the presence, diversity and phylogeny of sxtA, domains A1 and A4 and sxtG in 52 strains of Alexandrium, and a further 43 species of dinoflagellates and thirteen other alveolates. We confirmed the presence and high sequence conservation of sxtA, domain A4, in 40 strains (35 Alexandrium, 1 Pyrodinium, 4 Gymnodinium) of 8 species of STX-producing dinoflagellates, and absence from non-producing species. We found three paralogs of sxtA, domain A1, and a widespread distribution of sxtA1 in non-STX producing dinoflagellates, indicating duplication events in the evolution of this gene. One paralog, clade 2, of sxtA1 may be particularly related to STX biosynthesis. Similarly, sxtG appears to be generally restricted to STX-producing species, while three amidinotransferase gene paralogs were found in dinoflagellates. We investigated the role of positive (diversifying) selection following duplication in sxtA1 and sxtG, and found negative selection in clades of sxtG and sxtA1, clade 2, suggesting they were functionally constrained. Significant episodic diversifying selection was found in some strains in clade 3 of sxtA1, a clade that may not be involved in STX biosynthesis, indicating pressure for diversification of function.
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Affiliation(s)
- Shauna A Murray
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia; Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, NSW, Australia.
| | - Rutuja Diwan
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia; Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, NSW, Australia
| | - Russell J S Orr
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Norway
| | - Gurjeet S Kohli
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia
| | - Uwe John
- Section Ecological Chemistry, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
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Reñé A, Camp J, Garcés E. Diversity and Phylogeny of Gymnodiniales (Dinophyceae) from the NW Mediterranean Sea Revealed by a Morphological and Molecular Approach. Protist 2015; 166:234-63. [DOI: 10.1016/j.protis.2015.03.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 02/21/2015] [Accepted: 03/02/2015] [Indexed: 12/01/2022]
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Boopathi T, Faria DG, Cheon JY, Youn SH, Ki JS. Implications of High Molecular Divergence of Nuclear rRNA and Phylogenetic Structure for the Dinoflagellate Prorocentrum (Dinophyceae, Prorocentrales). J Eukaryot Microbiol 2015; 62:519-31. [PMID: 25594436 DOI: 10.1111/jeu.12206] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 12/06/2014] [Accepted: 12/10/2014] [Indexed: 12/01/2022]
Abstract
The small and large nuclear subunit molecular phylogeny of the genus Prorocentrum demonstrated that the species are dichotomized into two clades. These two clades were significantly different (one-factor ANOVA, p < 0.01) with patterns compatible for both small and large subunit Bayesian phylogenetic trees, and for a larger taxon sampled dinoflagellate phylogeny. Evaluation of the molecular divergence levels showed that intraspecies genetic variations were significantly low (t-test, p < 0.05), than those for interspecies variations (> 2.9% and > 26.8% dissimilarity in the small and large subunit [D1/D2], respectively). Based on the calculated molecular divergence, the genus comprises two genetically distinct groups that should be considered as two separate genera, thereby setting the pace for major systematic changes for the genus Prorocentrum sensu Dodge. Moreover, the information presented in this study would be useful for improving species identification, detection of novel clades from environmental samples.
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Affiliation(s)
| | | | - Ju-Yong Cheon
- Department of Life Science, Sangmyung University, Seoul, 110-743, Korea
| | - Seok Hyun Youn
- Fishery and Ocean Information Division, National Fisheries Research & Development Institute, Busan, 619-705, Korea
| | - Jang-Seu Ki
- Department of Life Science, Sangmyung University, Seoul, 110-743, Korea
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Bogus K, Mertens KN, Lauwaert J, Harding IC, Vrielinck H, Zonneveld KAF, Versteegh GJM. Differences in the chemical composition of organic-walled dinoflagellate resting cysts from phototrophic and heterotrophic dinoflagellates. JOURNAL OF PHYCOLOGY 2014; 50:254-266. [PMID: 26988183 DOI: 10.1111/jpy.12170] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 01/12/2014] [Indexed: 06/05/2023]
Abstract
Dinoflagellates constitute a large proportion of the planktonic biomass from marine to freshwater environments. Some species produce a preservable organic-walled resting cyst (dinocyst) during the sexual phase of their life cycle that is an important link between the organisms, the environment in which their parent motile theca grew, and the sedimentary record. Despite their abundance and widespread usage as proxy indicators for environmental conditions, there is a lack of knowledge regarding the dinocyst wall chemical composition. It is likely that numerous factors, including phylogeny and life strategy, determine the cyst wall chemistry. However, the extent to which this composition varies based on inherent (phylogenetic) or variable (ecological) factors has not been studied. To address this, we used micro-Fourier transform infrared spectroscopy to analyze nine cyst species produced by either phototrophic or heterotrophic dinoflagellates from the extant orders Gonyaulacales, Gymnodiniales, and Peridiniales. Based on the presence of characteristic functional groups, two significantly different cyst wall compositions are observed that correspond to the dinoflagellate's nutritional strategy. The dinocyst wall compositions analyzed appeared carbohydrate-based, but the cyst wall produced by phototrophic dinoflagellates suggested a cellulose-like glucan, while heterotrophic forms produced a nitrogen-rich glycan. This constitutes the first empirical evidence nutritional strategy is related to different dinocyst wall chemistries. Our results indicated phylogeny was less important for predicting composition than the nutritional strategy of the dinoflagellate, suggesting potential for cyst wall chemistry to infer past nutritional strategies of extinct taxa preserved in the sedimentary record.
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Affiliation(s)
- Kara Bogus
- Department of Geosciences, University of Bremen, Klagenfurter Strasse, Bremen, 28359, Germany
- MARUM - Center for Marine Environmental Sciences, Leobener Strasse, Bremen, 28334, Germany
| | - Kenneth Neil Mertens
- Research Unit for Palaeontology, Ghent University, Krijgslaan 281/S8, Gent, 9000, Belgium
| | - Johan Lauwaert
- Department of Solid State Sciences, Ghent University, Krijgslaan 281/S1, Gent, 9000, Belgium
| | - Ian C Harding
- Ocean and Earth Science, University of Southampton, National Oceanography Centre, European Way, Southampton, SO14 3ZH, UK
| | - Henk Vrielinck
- Department of Solid State Sciences, Ghent University, Krijgslaan 281/S1, Gent, 9000, Belgium
| | - Karin A F Zonneveld
- MARUM - Center for Marine Environmental Sciences, Leobener Strasse, Bremen, 28334, Germany
| | - Gerard J M Versteegh
- MARUM - Center for Marine Environmental Sciences, Leobener Strasse, Bremen, 28334, Germany
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Kang NS, Jeong HJ, Moestrup Ø, Lee SY, Lim AS, Jang TY, Lee KH, Lee MJ, Jang SH, Potvin E, Lee SK, Noh JH. Gymnodinium smaydae
n. sp., a New Planktonic Phototrophic Dinoflagellate from the Coastal Waters of Western Korea: Morphology and Molecular Characterization. J Eukaryot Microbiol 2014; 61:182-203. [DOI: 10.1111/jeu.12098] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/23/2013] [Accepted: 10/29/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Nam Seon Kang
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul 151-747 Korea
| | - Hae Jin Jeong
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul 151-747 Korea
| | - Øjvind Moestrup
- Biological Institute; Section of Phycology; University of Copenhagen; Universitetsparken 4 DK-2100 Copenhagen K Denmark
| | - Sung Yeon Lee
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul 151-747 Korea
| | - An Suk Lim
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul 151-747 Korea
| | - Tae Young Jang
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul 151-747 Korea
| | - Kyung Ha Lee
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul 151-747 Korea
| | - Moo Joon Lee
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul 151-747 Korea
| | - Se Hyeon Jang
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul 151-747 Korea
| | - Eric Potvin
- School of Earth and Environmental Sciences; College of Natural Sciences; Seoul National University; Seoul 151-747 Korea
| | - Sook Kyung Lee
- KHNP-Central Research Institute; Korea Hydro & Nuclear Power Corporation; 1312-70 Yuseong daero Yuseong-gu Daejeon 305-343 Korea
| | - Jae Hoon Noh
- Marine Resources Research Department; KORDI; Ansan P. O. Box 29 Gyeonggi-do 425-600 Korea
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Kremp A, Tahvanainen P, Litaker W, Krock B, Suikkanen S, Leaw CP, Tomas C. Phylogenetic relationships, morphological variation, and toxin patterns in the Alexandrium ostenfeldii (Dinophyceae) complex: implications for species boundaries and identities. JOURNAL OF PHYCOLOGY 2014; 50:81-100. [PMID: 26988010 DOI: 10.1111/jpy.12134] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Accepted: 09/03/2013] [Indexed: 05/16/2023]
Abstract
Alexandrium ostenfeldii (Paulsen) Balech and Tangen and A. peruvianum (Balech and B.R. Mendiola) Balech and Tangen are morphologically closely related dinoflagellates known to produce potent neurotoxins. Together with Gonyaulax dimorpha Biecheler, they constitute the A. ostenfeldii species complex. Due to the subtle differences in the morphological characters used to differentiate these species, unambiguous species identification has proven problematic. To better understand the species boundaries within the A. ostenfeldii complex we compared rDNA data, morphometric characters and toxin profiles of multiple cultured isolates from different geographic regions. Phylogenetic analysis of rDNA sequences from cultures characterized as A. ostenfeldii or A. peruvianum formed a monophyletic clade consisting of six distinct groups. Each group examined contained strains morphologically identified as either A. ostenfeldii or A. peruvianum. Though key morphological characters were generally found to be highly variable and not consistently distributed, selected plate features and toxin profiles differed significantly among phylogenetic clusters. Additional sequence analyses revealed a lack of compensatory base changes in ITS2 rRNA structure, low to intermediate ITS/5.8S uncorrected genetic distances, and evidence of reticulation. Together these data (criteria currently used for species delineation in dinoflagellates) imply that the A. ostenfeldii complex should be regarded a single genetically structured species until more material and alternative criteria for species delimitation are available. Consequently, we propose that A. peruvianum is a heterotypic synonym of A. ostenfeldii and this taxon name should be discontinued.
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Affiliation(s)
- Anke Kremp
- Finnish Environment Institute, Marine Research Centre, Erik Palménin aukio 1, Helsinki, 00560, Finland
| | - Pia Tahvanainen
- Finnish Environment Institute, Marine Research Centre, Erik Palménin aukio 1, Helsinki, 00560, Finland
- University of Helsinki, Tvärminne Zoological Station, J.A. Palménin tie 260, Hanko, 10900, Finland
| | - Wayne Litaker
- National Oceanic and Atmospheric Administration, National Ocean Service, Center for Coastal Fisheries and Habitat Research, 101 Pivers Island Rd., Beaufort, North Carolina
| | - Bernd Krock
- Alfred Wegener Institute for Polar and Marine Research, Division of Biosciences, Am Handelshafen 12, Bremerhaven, 27570, Germany
| | - Sanna Suikkanen
- Finnish Environment Institute, Marine Research Centre, Erik Palménin aukio 1, Helsinki, 00560, Finland
| | - Chui Pin Leaw
- Institute of Biodiversity and Environmental Conservation, University Malaysia Sarawak, Kota Samarahan, Sarawak, 94300, Malaysia
| | - Carmelo Tomas
- University of North Carolina at Wilmington, Center for Marine Science, Myrtle Grove 2336, Wilmington, North Carolina
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Murray SA, Hoppenrath M, Orr RJS, Bolch C, John U, Diwan R, Yauwenas R, Harwood T, de Salas M, Neilan B, Hallegraeff G. Alexandrium diversaporum sp. nov., a new non-saxitoxin producing species: Phylogeny, morphology and sxtA genes. HARMFUL ALGAE 2014; 31:54-65. [PMID: 28040111 DOI: 10.1016/j.hal.2013.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/16/2013] [Accepted: 09/16/2013] [Indexed: 06/06/2023]
Abstract
Species of the PST producing planktonic marine dinoflagellate genus Alexandrium have been intensively scrutinised, and it is therefore surprising that new taxa can still be found. Here we report a new species, Alexandrium diversaporum nov. sp., isolated from spherical cysts found at two sites in Tasmania, Australia. This species differs in its morphology from all previously reported Alexandrium species, possessing a unique combination of morphological features: the presence of 2 size classes of thecal pores on the cell surface, a medium cell size, the size and shape of the 6″, 1', 2⁗ and Sp plates, the lack of a ventral pore, a lack of anterior and posterior connecting pores, and a lack of chain formation. We determined the relationship of the two strains to other species of Alexandrium based on an alignment of concatenated SSU-ITS1, 5.8S, ITS2 and partial LSU ribosomal RNA sequences, and found A. diversaporum to be a sister group to Alexandrium leei with high support. A. leei shares several morphological features, including the relative size and shapes of the 6″, 1', 2⁗ and Sp plates and the fact that some strains of A. leei have two size classes of thecal pores. We examined A. diversaporum strains for saxitoxin production and found them to be non-toxic. The species lacked sequences for the domain A4 of sxtA, as has been previously found for non-saxitoxin producing species of Alexandrium.
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Affiliation(s)
- Shauna A Murray
- Sydney Institute of Marine Science, Chowder Bay Road, Mosman, NSW, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Mona Hoppenrath
- Senckenberg Research Institute, Senckenberg am Meer, German Center for Marine Biodiversity Research (DZMB), Südstrand 44, D-26382 Wilhelmshaven, Germany
| | - Russell J S Orr
- Microbial Evolution Research Group, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Christopher Bolch
- National Centre for Marine Conservation and Resource Sustainability, Australian Maritime College, University of Tasmania, Locked Bag 1370, Launceston, Tasmania 7250, Australia
| | - Uwe John
- Section Ecological Chemistry, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Rutuja Diwan
- Sydney Institute of Marine Science, Chowder Bay Road, Mosman, NSW, Australia
| | - Rouna Yauwenas
- Sydney Institute of Marine Science, Chowder Bay Road, Mosman, NSW, Australia
| | - Tim Harwood
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Miguel de Salas
- Tasmanian Herbarium, University of Tasmania, Private Bag 4, Hobart, Tasmania 7001, Australia
| | - Brett Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Gustaaf Hallegraeff
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
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Valiadi M, Iglesias-Rodriguez MD. Diversity of the luciferin binding protein gene in bioluminescent dinoflagellates--insights from a new gene in Noctiluca scintillans and sequences from gonyaulacoid genera. J Eukaryot Microbiol 2013; 61:134-45. [PMID: 24373055 DOI: 10.1111/jeu.12091] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 12/10/2013] [Accepted: 10/13/2013] [Indexed: 11/30/2022]
Abstract
Dinoflagellate bioluminescence systems operate with or without a luciferin binding protein, representing two distinct modes of light production. However, the distribution, diversity, and evolution of the luciferin binding protein gene within bioluminescent dinoflagellates are not well known. We used PCR to detect and partially sequence this gene from the heterotrophic dinoflagellate Noctiluca scintillans and a group of ecologically important gonyaulacoid species. We report an additional luciferin binding protein gene in N. scintillans which is not attached to luciferase, further to its typical combined bioluminescence gene. This supports the hypothesis that a profound re-organization of the bioluminescence system has taken place in this organism. We also show that the luciferin binding protein gene is present in the genera Ceratocorys, Gonyaulax, and Protoceratium, and is prevalent in bioluminescent species of Alexandrium. Therefore, this gene is an integral component of the standard molecular bioluminescence machinery in dinoflagellates. Nucleotide sequences showed high within-strain variation among gene copies, revealing a highly diverse gene family comprising multiple gene types in some organisms. Phylogenetic analyses showed that, in some species, the evolution of the luciferin binding protein gene was different from the organism's general phylogenies, highlighting the complex evolutionary history of dinoflagellate bioluminescence systems.
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Affiliation(s)
- Martha Valiadi
- Ocean and Earth Science, University of Southampton, Waterfront Campus, European Way, Southampton, SO14 3ZH, UK
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43
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Kohli GS, Neilan BA, Brown MV, Hoppenrath M, Murray SA. Cobgene pyrosequencing enables characterization of benthic dinoflagellate diversity and biogeography. Environ Microbiol 2013; 16:467-85. [DOI: 10.1111/1462-2920.12275] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 09/01/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Gurjeet S. Kohli
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney New South Wales 2052 Australia
- Plant Functional Biology and Climate Change Cluster (C3); University of Technology Sydney; Sydney New South Wales 2007 Australia
| | - Brett A. Neilan
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney New South Wales 2052 Australia
- Australian Centre for Astrobiology; University of New South Wales; Sydney New South Wales 2052 Australia
| | - Mark V. Brown
- School of Biotechnology and Biomolecular Sciences; University of New South Wales; Sydney New South Wales 2052 Australia
- Australian Centre for Astrobiology; University of New South Wales; Sydney New South Wales 2052 Australia
| | - Mona Hoppenrath
- Senckenberg am Meer; Deutsches Zentrum für Marine Biodiversitätsforschung (DZMB); Wilhelmshaven 32689 Germany
| | - Shauna A. Murray
- Sydney Institute of Marine Sciences; Sydney New South Wales 2088 Australia
- Plant Functional Biology and Climate Change Cluster (C3); University of Technology Sydney; Sydney New South Wales 2007 Australia
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Bachvaroff TR, Gornik SG, Concepcion GT, Waller RF, Mendez GS, Lippmeier JC, Delwiche CF. Dinoflagellate phylogeny revisited: using ribosomal proteins to resolve deep branching dinoflagellate clades. Mol Phylogenet Evol 2013; 70:314-22. [PMID: 24135237 DOI: 10.1016/j.ympev.2013.10.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 09/24/2013] [Accepted: 10/07/2013] [Indexed: 10/26/2022]
Abstract
The alveolates are composed of three major lineages, the ciliates, dinoflagellates, and apicomplexans. Together these 'protist' taxa play key roles in primary production and ecology, as well as in illness of humans and other animals. The interface between the dinoflagellate and apicomplexan clades has been an area of recent discovery, blurring the distinction between these two clades. Moreover, phylogenetic analysis has yet to determine the position of basal dinoflagellate clades hence the deepest branches of the dinoflagellate tree currently remain unresolved. Large-scale mRNA sequencing was applied to 11 species of dinoflagellates, including strains of the syndinean genera Hematodinium and Amoebophrya, parasites of crustaceans and dinoflagellates, respectively, to optimize and update the dinoflagellate tree. From the transcriptome-scale data a total of 73 ribosomal protein-coding genes were selected for phylogeny. After individual gene orthology assessment, the genes were concatenated into a >15,000 amino acid alignment with 76 taxa from dinoflagellates, apicomplexans, ciliates, and the outgroup heterokonts. Overall the tree was well resolved and supported, when the data was subsampled with gblocks or constraint trees were tested with the approximately unbiased test. The deepest branches of the dinoflagellate tree can now be resolved with strong support, and provides a clearer view of the evolution of the distinctive traits of dinoflagellates.
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Affiliation(s)
- Tsvetan R Bachvaroff
- Smithsonian Environmental Research Center, 647 Contees Wharf Rd., Edgewater, MD 21037, United States.
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Valiadi M, Iglesias-Rodriguez D. Understanding Bioluminescence in Dinoflagellates-How Far Have We Come? Microorganisms 2013; 1:3-25. [PMID: 27694761 PMCID: PMC5029497 DOI: 10.3390/microorganisms1010003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 08/20/2013] [Accepted: 08/24/2013] [Indexed: 11/27/2022] Open
Abstract
Some dinoflagellates possess the remarkable genetic, biochemical, and cellular machinery to produce bioluminescence. Bioluminescent species appear to be ubiquitous in surface waters globally and include numerous cosmopolitan and harmful taxa. Nevertheless, bioluminescence remains an enigmatic topic in biology, particularly with regard to the organisms' lifestyle. In this paper, we review the literature on the cellular mechanisms, molecular evolution, diversity, and ecology of bioluminescence in dinoflagellates, highlighting significant discoveries of the last quarter of a century. We identify significant gaps in our knowledge and conflicting information and propose some important research questions that need to be addressed to advance this research field.
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Affiliation(s)
- Martha Valiadi
- Department of Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse, Plӧn 24306, Germany.
| | - Debora Iglesias-Rodriguez
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA.
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46
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A New Clade, Based on Partial LSU rDNA Sequences, of Unarmoured Dinoflagellates. Protist 2013; 164:673-85. [DOI: 10.1016/j.protis.2013.07.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 07/01/2013] [Accepted: 07/04/2013] [Indexed: 11/23/2022]
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47
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Tandem repeats, high copy number and remarkable diel expression rhythm of form II RuBisCO in Prorocentrum donghaiense (Dinophyceae). PLoS One 2013; 8:e71232. [PMID: 23976999 PMCID: PMC3747160 DOI: 10.1371/journal.pone.0071232] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Accepted: 06/27/2013] [Indexed: 11/24/2022] Open
Abstract
Gene structure and expression regulation of form II RuBisCO (rbcII) in dinoflagellates are still poorly understood. Here we isolated this gene (Pdrbc) and investigated its diel expression pattern in a harmful algal bloom forming dinoflagellate Prorocentrum donghaiense. We obtained cDNA sequences with triple tandem repeats of the coding unit (CU); the 5′ region has the sequence of a typical dinoflagellate plastid gene, encoding an N-terminus with two transmembrane regions separated by a plastid transit peptide. The CUs (1,455 bp except 1464 bp in last CU) are connected through a 63 bp spacer. Phylogenetic analysis showed that rbcII CUs within species formed monophyletic clusters, indicative of intraspecific gene duplication or purifying evolution. Using quantitative PCR (qPCR) we estimated 117±40 CUs of Pdrbc in the P. donghaiense genome. Although it is commonly believed that most dinoflagellate genes lack transcriptional regulation, our RT-qPCR analysis on synchronized cultures revealed remarkable diel rhythm of Pdrbc expression, showing significant correlations of transcript abundance with the timing of the dark-to-light transition and cell cycle G2M-phase. When the cultures were shifted to continuous light, Pdrbc expression remained significantly correlated with the G2M-phase. Under continuous darkness the cell cycle was arrested at the G1 phase, and the rhythm of Pdrbc transcription disappeared. Our results suggest that dinoflagellate rbcII 1) undergoes duplication or sequence purification within species, 2) is organized in tandem arrays in most species probably to facilitate efficient translation and import of the encoded enzyme, and 3) is regulated transcriptionally in a cell cycle-dependent fashion at least in some dinoflagellates.
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Orr RJS, Stüken A, Murray SA, Jakobsen KS. Evolution and distribution of saxitoxin biosynthesis in dinoflagellates. Mar Drugs 2013; 11:2814-28. [PMID: 23966031 PMCID: PMC3766867 DOI: 10.3390/md11082814] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 07/04/2013] [Accepted: 07/08/2013] [Indexed: 11/16/2022] Open
Abstract
Numerous species of marine dinoflagellates synthesize the potent environmental neurotoxic alkaloid, saxitoxin, the agent of the human illness, paralytic shellfish poisoning. In addition, certain freshwater species of cyanobacteria also synthesize the same toxic compound, with the biosynthetic pathway and genes responsible being recently reported. Three theories have been postulated to explain the origin of saxitoxin in dinoflagellates: The production of saxitoxin by co-cultured bacteria rather than the dinoflagellates themselves, convergent evolution within both dinoflagellates and bacteria and horizontal gene transfer between dinoflagellates and bacteria. The discovery of cyanobacterial saxitoxin homologs in dinoflagellates has enabled us for the first time to evaluate these theories. Here, we review the distribution of saxitoxin within the dinoflagellates and our knowledge of its genetic basis to determine the likely evolutionary origins of this potent neurotoxin.
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Affiliation(s)
- Russell J. S. Orr
- Microbial Evolution Research Group (MERG), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway; E-Mails: (R.J.S.O.); (A.S.)
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway
| | - Anke Stüken
- Microbial Evolution Research Group (MERG), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway; E-Mails: (R.J.S.O.); (A.S.)
| | - Shauna A. Murray
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology, Sydney, PO Box 123 Broadway, NSW 2007, Australia; E-Mail:
- Sydney Institute of Marine Science, Mosman, NSW 2088, Australia
| | - Kjetill S. Jakobsen
- Microbial Evolution Research Group (MERG), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway; E-Mails: (R.J.S.O.); (A.S.)
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +47-22854602; Fax: +47-22854001
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Gu H, Kirsch M, Zinssmeister C, Soehner S, Meier KJS, Liu T, Gottschling M. Waking the dead: morphological and molecular characterization of extant †Posoniella tricarinelloides (Thoracosphaeraceae, Dinophyceae). Protist 2013; 164:583-97. [PMID: 23850812 DOI: 10.1016/j.protis.2013.06.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 05/07/2013] [Accepted: 06/01/2013] [Indexed: 10/26/2022]
Abstract
The Thoracosphaeraceae are dinophytes that produce calcareous shells during their life history, whose optical crystallography has been the basis for the division into subfamilies. To evaluate the validity of the classification (mainly applied by palaeontologists), living material of phylogenetic key species is necessary albeit frequently difficult to access for contemporary morphological and molecular analyses. We isolated and established five living strains of the rare fossil-taxon †Posoniella tricarinelloides from different sediment samples collected in the South China Sea, Yellow Sea and in the Mediterranean Sea (west coast off Italy). Here, we provide detailed descriptions of its morphology and conducted phylogenetic analyses based on hundreds of accessions and thousands of informative sites on concatenated rRNA datasets. Within the monophyletic Peridiniales, †P. tricarinelloides was reliably nested in the Thoracosphaeraceae and exhibited two distinct morphological types of coccoid cells. The two morphologies of coccoid cells would have been assigned to different taxa at the subfamily level if found separately in fossil samples. Our results thus challenge previous classification concepts within the dinophytes and underline the importance of comparative morphological and molecular studies to better understand the complex biology of unicellular organisms such as †P. tricarinelloides.
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Affiliation(s)
- Haifeng Gu
- Third Institute of Oceanography, State Oceanic Administration, 361005 Xiamen, China
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Gottschling M, McLean TI. New home for tiny symbionts: Dinophytes determined as Zooxanthella are Peridiniales and distantly related to Symbiodinium. Mol Phylogenet Evol 2013; 67:217-22. [DOI: 10.1016/j.ympev.2013.01.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 12/21/2012] [Accepted: 01/07/2013] [Indexed: 11/24/2022]
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