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Cooney EC, Holt CC, Hehenberger E, Adams JA, Leander BS, Keeling PJ. Investigation of heterotrophs reveals new insights in dinoflagellate evolution. Mol Phylogenet Evol 2024; 196:108086. [PMID: 38677354 DOI: 10.1016/j.ympev.2024.108086] [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: 12/10/2023] [Revised: 04/12/2024] [Accepted: 04/24/2024] [Indexed: 04/29/2024]
Abstract
Dinoflagellates are diverse and ecologically important protists characterized by many morphological and molecular traits that set them apart from other eukaryotes. These features include, but are not limited to, massive genomes organized using bacterially-derived histone-like proteins (HLPs) and dinoflagellate viral nucleoproteins (DVNP) rather than histones, and a complex history of photobiology with many independent losses of photosynthesis, numerous cases of serial secondary and tertiary plastid gains, and the presence of horizontally acquired bacterial rhodopsins and type II RuBisCo. Elucidating how this all evolved depends on knowing the phylogenetic relationships between dinoflagellate lineages. Half of these species are heterotrophic, but existing molecular data is strongly biased toward the photosynthetic dinoflagellates due to their amenability to cultivation and prevalence in culture collections. These biases make it impossible to interpret the evolution of photosynthesis, but may also affect phylogenetic inferences that impact our understanding of character evolution. Here, we address this problem by isolating individual cells from the Salish Sea and using single cell, culture-free transcriptomics to expand molecular data for dinoflagellates to include 27 more heterotrophic taxa, resulting in a roughly balanced representation. Using these data, we performed a comprehensive search for proteins involved in chromatin packaging, plastid function, and photoactivity across all dinoflagellates. These searches reveal that 1) photosynthesis was lost at least 21 times, 2) two known types of HLP were horizontally acquired around the same time rather than sequentially as previously thought; 3) multiple rhodopsins are present across the dinoflagellates, acquired multiple times from different donors; 4) kleptoplastic species have nucleus-encoded genes for proteins targeted to their temporary plastids and they are derived from multiple lineages, and 5) warnowiids are the only heterotrophs that retain a whole photosystem, although some photosynthesis-related electron transport genes are widely retained in heterotrophs, likely as part of the iron-sulfur cluster pathway that persists in non-photosynthetic plastids.
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Affiliation(s)
- Elizabeth C Cooney
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; Hakai Institute, 1747 Hyacinthe Bay Rd., Heriot Bay, BC V0P 1H0, Canada.
| | - Corey C Holt
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; Hakai Institute, 1747 Hyacinthe Bay Rd., Heriot Bay, BC V0P 1H0, Canada.
| | - Elisabeth Hehenberger
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Jayd A Adams
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.
| | - Brian S Leander
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada; Department of Zoology, University of British Columbia, 4200 - 6270, University Blvd., Vancouver, BC V6T 1Z4, Canada.
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver, BC V6T 1Z4, Canada.
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2
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Marinov GK, Chen X, Swaffer MP, Xiang T, Grossman AR, Greenleaf WJ. Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome. Genome Biol 2024; 25:115. [PMID: 38711126 PMCID: PMC11071213 DOI: 10.1186/s13059-024-03261-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 04/28/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND In dinoflagellates, a unique and extremely divergent genomic and nuclear organization has evolved. The highly unusual features of dinoflagellate nuclei and genomes include permanently condensed liquid crystalline chromosomes, primarily packaged by proteins other than histones, genes organized in very long unidirectional gene arrays, a general absence of transcriptional regulation, high abundance of the otherwise very rare DNA modification 5-hydroxymethyluracil (5-hmU), and many others. While most of these fascinating properties are originally identified in the 1970s and 1980s, they have not yet been investigated using modern genomic tools. RESULTS In this work, we address some of the outstanding questions regarding dinoflagellate genome organization by mapping the genome-wide distribution of 5-hmU (using both immunoprecipitation-based and basepair-resolution chemical mapping approaches) and of chromatin accessibility in the genome of the Symbiodiniaceae dinoflagellate Breviolum minutum. We find that the 5-hmU modification is preferentially enriched over certain classes of repetitive elements, often coincides with the boundaries between gene arrays, and is generally correlated with decreased chromatin accessibility, the latter otherwise being largely uniform along the genome. We discuss the potential roles of 5-hmU in the functional organization of dinoflagellate genomes and its relationship to the transcriptional landscape of gene arrays. CONCLUSIONS Our results provide the first window into the 5-hmU and chromatin accessibility landscapes in dinoflagellates.
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Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
| | - Xinyi Chen
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Matthew P Swaffer
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Tingting Xiang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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3
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Wang H, Wu P, Xiong L, Kim HS, Kim JH, Ki JS. Nuclear genome of dinoflagellates: Size variation and insights into evolutionary mechanisms. Eur J Protistol 2024; 93:126061. [PMID: 38394997 DOI: 10.1016/j.ejop.2024.126061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024]
Abstract
Recent progress in high-throughput sequencing technologies has dramatically increased availability of genome data for prokaryotes and eukaryotes. Dinoflagellates have distinct chromosomes and a huge genome size, which make their genomic analysis complicated. Here, we reviewed the nuclear genomes of core dinoflagellates, focusing on the genome and cell size. Till now, the genome sizes of several dinoflagellates (more than 25) have been measured by certain methods (e.g., flow cytometry), showing a range of 3-250 pg of genomic DNA per cell. In contrast to their relatively small cell size, their genomes are huge (about 1-80 times the human haploid genome). In the present study, we collected the genome and cell size data of dinoflagellates and compared their relationships. We found that dinoflagellate genome size exhibits a positive correlation with cell size. On the other hand, we recognized that the genome size is not correlated with phylogenetic relatedness. These may be caused by genome duplication, increased gene copy number, repetitive non-coding DNA, transposon expansion, horizontal gene transfer, organelle-to-nucleus gene transfer, and/or mRNA reintegration into the genome. Ultimate verification of these factors as potential causative mechanisms would require sequencing of more dinoflagellate genomes in the future.
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Affiliation(s)
- Hui Wang
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China; Department of Life Science, Sangmyung University, Seoul 03016, Republic of Korea
| | - Peiling Wu
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Lu Xiong
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Han-Sol Kim
- Department of Life Science, Sangmyung University, Seoul 03016, Republic of Korea
| | - Jin Ho Kim
- Department of Earth and Marine Science, College of Ocean Sciences, Jeju National University, Jeju 63243, Republic of Korea
| | - Jang-Seu Ki
- Department of Life Science, Sangmyung University, Seoul 03016, Republic of Korea; Department of Biotechnology, Sangmyung University, Seoul 03016, Republic of Korea.
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4
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Novák Vanclová AM, Nef C, Füssy Z, Vancl A, Liu F, Bowler C, Dorrell RG. New plastids, old proteins: repeated endosymbiotic acquisitions in kareniacean dinoflagellates. EMBO Rep 2024; 25:1859-1885. [PMID: 38499810 PMCID: PMC11014865 DOI: 10.1038/s44319-024-00103-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: 11/24/2023] [Revised: 01/19/2024] [Accepted: 02/06/2024] [Indexed: 03/20/2024] Open
Abstract
Dinoflagellates are a diverse group of ecologically significant micro-eukaryotes that can serve as a model system for plastid symbiogenesis due to their susceptibility to plastid loss and replacement via serial endosymbiosis. Kareniaceae harbor fucoxanthin-pigmented plastids instead of the ancestral peridinin-pigmented ones and support them with a diverse range of nucleus-encoded plastid-targeted proteins originating from the haptophyte endosymbiont, dinoflagellate host, and/or lateral gene transfers (LGT). Here, we present predicted plastid proteomes from seven distantly related kareniaceans in three genera (Karenia, Karlodinium, and Takayama) and analyze their evolutionary patterns using automated tree building and sorting. We project a relatively limited ( ~ 10%) haptophyte signal pointing towards a shared origin in the family Chrysochromulinaceae. Our data establish significant variations in the functional distributions of these signals, emphasizing the importance of micro-evolutionary processes in shaping the chimeric proteomes. Analysis of plastid genome sequences recontextualizes these results by a striking finding the extant kareniacean plastids are in fact not all of the same origin, as two of the studied species (Karlodinium armiger, Takayama helix) possess plastids from different haptophyte orders than the rest.
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Affiliation(s)
- Anna Mg Novák Vanclová
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.
- Institute Jacques Monod, Paris, France.
| | - Charlotte Nef
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Zoltán Füssy
- Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Adél Vancl
- Faculty of Mathematics and Physics, Charles University, Prague, Czechia
| | - Fuhai Liu
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Centre de Recherches Interdisciplinaires, Paris, France
- Tsinghua-UC Berkeley Shenzhen Institute, Shenzhen, China
| | - Chris Bowler
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Richard G Dorrell
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
- CNRS Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.
- CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, Sorbonne Université, Paris, France.
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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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Füssy Z, Oborník M. Complex Endosymbioses I: From Primary to Complex Plastids, Serial Endosymbiotic Events. Methods Mol Biol 2024; 2776:21-41. [PMID: 38502496 DOI: 10.1007/978-1-0716-3726-5_2] [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] [Indexed: 03/21/2024]
Abstract
A considerable part of the diversity of eukaryotic phototrophs consists of algae with plastids that evolved from endosymbioses between two eukaryotes. These complex plastids are characterized by a high number of envelope membranes (more than two) and some of them contain a residual nucleus of the endosymbiotic alga called a nucleomorph. Complex plastid-bearing algae are thus chimeric cell assemblies, eukaryotic symbionts living in a eukaryotic host. In contrast, the primary plastids of the Archaeplastida (plants, green algae, red algae, and glaucophytes) possibly evolved from a single endosymbiosis with a cyanobacterium and are surrounded by two membranes. Complex plastids have been acquired several times by unrelated groups of eukaryotic heterotrophic hosts, suggesting that complex plastids are somewhat easier to obtain than primary plastids. Evidence suggests that complex plastids arose twice independently in the green lineage (euglenophytes and chlorarachniophytes) through secondary endosymbiosis, and four times in the red lineage, first through secondary endosymbiosis in cryptophytes, then by higher-order events in stramenopiles, alveolates, and haptophytes. Engulfment of primary and complex plastid-containing algae by eukaryotic hosts (secondary, tertiary, and higher-order endosymbioses) is also responsible for numerous plastid replacements in dinoflagellates. Plastid endosymbiosis is accompanied by massive gene transfer from the endosymbiont to the host nucleus and cell adaptation of both endosymbiotic partners, which is related to the trophic switch to phototrophy and loss of autonomy of the endosymbiont. Such a process is essential for the metabolic integration and division control of the endosymbiont in the host. Although photosynthesis is the main advantage of acquiring plastids, loss of photosynthesis often occurs in algae with complex plastids. This chapter summarizes the essential knowledge of the acquisition, evolution, and function of complex plastids.
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Affiliation(s)
- Zoltán Füssy
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Miroslav Oborník
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
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Miyagishima SY. Taming the perils of photosynthesis by eukaryotes: constraints on endosymbiotic evolution in aquatic ecosystems. Commun Biol 2023; 6:1150. [PMID: 37952050 PMCID: PMC10640588 DOI: 10.1038/s42003-023-05544-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023] Open
Abstract
An ancestral eukaryote acquired photosynthesis by genetically integrating a cyanobacterial endosymbiont as the chloroplast. The chloroplast was then further integrated into many other eukaryotic lineages through secondary endosymbiotic events of unicellular eukaryotic algae. While photosynthesis enables autotrophy, it also generates reactive oxygen species that can cause oxidative stress. To mitigate the stress, photosynthetic eukaryotes employ various mechanisms, including regulating chloroplast light absorption and repairing or removing damaged chloroplasts by sensing light and photosynthetic status. Recent studies have shown that, besides algae and plants with innate chloroplasts, several lineages of numerous unicellular eukaryotes engage in acquired phototrophy by hosting algal endosymbionts or by transiently utilizing chloroplasts sequestrated from algal prey in aquatic ecosystems. In addition, it has become evident that unicellular organisms engaged in acquired phototrophy, as well as those that feed on algae, have also developed mechanisms to cope with photosynthetic oxidative stress. These mechanisms are limited but similar to those employed by algae and plants. Thus, there appear to be constraints on the evolution of those mechanisms, which likely began by incorporating photosynthetic cells before the establishment of chloroplasts by extending preexisting mechanisms to cope with oxidative stress originating from mitochondrial respiration and acquiring new mechanisms.
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Affiliation(s)
- Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
- The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
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Holt CC, Hehenberger E, Tikhonenkov DV, Jacko-Reynolds VKL, Okamoto N, Cooney EC, Irwin NAT, Keeling PJ. Multiple parallel origins of parasitic Marine Alveolates. Nat Commun 2023; 14:7049. [PMID: 37923716 PMCID: PMC10624901 DOI: 10.1038/s41467-023-42807-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/20/2023] [Indexed: 11/06/2023] Open
Abstract
Microbial eukaryotes are important components of marine ecosystems, and the Marine Alveolates (MALVs) are consistently both abundant and diverse in global environmental sequencing surveys. MALVs are dinoflagellates that are thought to be parasites of other protists and animals, but the lack of data beyond ribosomal RNA gene sequences from all but a few described species means much of their biology and evolution remain unknown. Using single-cell transcriptomes from several MALVs and their free-living relatives, we show that MALVs evolved independently from two distinct, free-living ancestors and that their parasitism evolved in parallel. Phylogenomics shows one subgroup (MALV-II and -IV, or Syndiniales) is related to a novel lineage of free-living, eukaryovorous predators, the eleftherids, while the other (MALV-I, or Ichthyodinida) is related to the free-living predator Oxyrrhis and retains proteins targeted to a non-photosynthetic plastid. Reconstructing the evolution of photosynthesis, plastids, and parasitism in early-diverging dinoflagellates shows a number of parallels with the evolution of their apicomplexan sisters. In both groups, similar forms of parasitism evolved multiple times and photosynthesis was lost many times. By contrast, complete loss of the plastid organelle is infrequent and, when this does happen, leaves no residual genes.
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Affiliation(s)
- Corey C Holt
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
- Hakai Institute, Heriot Bay, British Columbia, Canada.
| | - Elisabeth Hehenberger
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
- Institute of Parasitology, Biology Centre Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Denis V Tikhonenkov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
- AquaBioSafe Laboratory, University of Tyumen, Tyumen, Russia
| | | | - Noriko Okamoto
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Elizabeth C Cooney
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Hakai Institute, Heriot Bay, British Columbia, Canada
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Merton College, University of Oxford, Oxford, UK
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.
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Harvey THP. Colonial green algae in the Cambrian plankton. Proc Biol Sci 2023; 290:20231882. [PMID: 37876191 PMCID: PMC10598416 DOI: 10.1098/rspb.2023.1882] [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: 08/20/2023] [Accepted: 09/28/2023] [Indexed: 10/26/2023] Open
Abstract
The fossil record indicates a major turnover in marine phytoplankton across the Ediacaran-Cambrian transition, coincident with the rise of animal-rich ecosystems. However, the diversity, affinities and ecologies of Cambrian phytoplankton are poorly understood, leaving unclear the role of animal interactions and the drivers of diversification. New exceptionally preserved acritarchs (problematic organic-walled microfossils) from the late early Cambrian (around 510 Ma) reveal colonial organization characterized by rings and plates of interconnected, geometrically arranged cells. The assemblage exhibits a wide but gradational variation in cell size, ornamentation and intercell connection, interpreted as representing one or more species with determinate (coenobial) colony formation via cell division, aggregation and growth by cell expansion. An equivalent strategy is known only among green algae, specifically chlorophycean chlorophytes. The fossils differ in detail from modern freshwater examples and apparently represent an earlier convergent radiation in marine settings. Known trade-offs between sinking risk and predator avoidance in colonial phytoplankton point to adaptations triggered by intensifying grazing pressure during a Cambrian metazoan invasion of the water column. The new fossils reveal that not all small acritarchs are unicellular resting cysts, and support an early Palaeozoic prominence of green algal phytoplankton as predicted by molecular biomarkers.
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Affiliation(s)
- Thomas H. P. Harvey
- Centre for Palaeobiology and Biosphere Evolution, School of Geography, Geology and the Environment, University of Leicester, University Road, Leicester LE1 7RH, UK
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10
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Meyvisch P, Mertens KN, Gurdebeke PR, Sandt C, Pospelova V, Vrielinck H, Borondics F, Louwye S. Does dinocyst wall composition really reflect trophic affinity? New evidence from ATR micro-FTIR spectroscopy measurements. JOURNAL OF PHYCOLOGY 2023; 59:1064-1084. [PMID: 37623312 DOI: 10.1111/jpy.13382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/02/2023] [Accepted: 07/21/2023] [Indexed: 08/26/2023]
Abstract
Attenuated total reflection (ATR) microscope Fourier transform infrared (micro-FTIR) spectroscopy was used to investigate the dinosporin composition in the walls of modern, organic-walled dinoflagellate resting cysts (dinocysts). Variable cyst wall compositions were observed, which led to the erection of four spectrochemical groups, some with striking similarities to other resistant biomacromolecules such as sporopollenin and algaenan. Furthermore, possible proxies derivable from the spectrochemical composition of modern and fossil dinocysts were discussed. The color of the dinocyst walls was reflected in the spectral data. When comparing that color with a standard and the results of a series of bleaching experiments with oxidative agents, eumelanin was assigned as a likely pigment contributing to the observed color. Following this assignment, the role of eumelanin as an ultraviolet sunscreen in colored dinocysts was hypothesized, and its implications on the autofluorescence and morphological preservation of dinocysts were further discussed. Unlike what had previously been assumed, it was shown that micro-FTIR data from dinocysts cannot be used to unambiguously infer trophic affinities of their associated cells. Finally, using methods with high spatial resolutions (synchrotron transmission micro-FTIR and optical photothermal infrared spectroscopy), it was shown that dinocyst wall layers are chemically homogenous at the probed scales. This study fills a large knowledge gap in our understanding of the chemical nature of dinocyst walls and has nuanced certain assumptions and interpretations made in the past.
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Affiliation(s)
| | | | | | | | - Vera Pospelova
- Department of Earth and Environmental Sciences, University of Minnesota, Minneapolis, Minnesota, USA
| | - Henk Vrielinck
- Department of Solid-State Sciences, Ghent University, Ghent, Belgium
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11
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Ishida H, John U, Murray SA, Bhattacharya D, Chan CX. Developing model systems for dinoflagellates in the post-genomic era. JOURNAL OF PHYCOLOGY 2023; 59:799-808. [PMID: 37657822 DOI: 10.1111/jpy.13386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 09/03/2023]
Abstract
Dinoflagellates are a diverse group of eukaryotic microbes that are ubiquitous in aquatic environments. Largely photosynthetic, they encompass symbiotic, parasitic, and free-living lineages with a broad spectrum of trophism. Many free-living taxa can produce bioactive secondary metabolites such as biotoxins, some of which cause harmful algal blooms. In contrast, most symbiotic species are crucial for sustaining coral reef health. The year 2023 marked a decade since the first genome data of dinoflagellates became available. The growing genome-scale resources for these taxa are highlighting their remarkable evolutionary and genomic complexities. Here, we discuss the prospect of developing dinoflagellate models using the criteria of accessibility, tractability, resources, research support, and promise. Moving forward in the post-genomic era, we argue for the development of fit-to-purpose models that tailor to specific biological contexts, and that a one-size-fits-all model is inadequate for encapsulating the complex biology, ecology, and evolutionary history of dinoflagellates.
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Affiliation(s)
- Hisatake Ishida
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia
| | - Uwe John
- Alfred-Wegener-Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Shauna A Murray
- School of Life Sciences, University of Technology Sydney, Ultimo, New South Wales, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Cheong Xin Chan
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Queensland, Australia
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12
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Marinov GK, Chen X, Swaffer MP, Xiang T, Grossman AR, Greenleaf WJ. Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558303. [PMID: 37781619 PMCID: PMC10541103 DOI: 10.1101/2023.09.18.558303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
In dinoflagellates, a unique and extremely divergent genomic and nuclear organization has evolved. The highly unusual features of dinoflagellate nuclei and genomes include permanently condensed liquid crystalline chromosomes, primarily packaged by proteins other than histones, genes organized in very long unidirectional gene arrays, a general absence of transcriptional regulation, high abundance of the otherwise very rare DNA modification 5-hydroxymethyluracil (5-hmU), and many others. While most of these fascinating properties were originally identified in the 1970s and 1980s, they have not yet been investigated using modern genomic tools. In this work, we address some of the outstanding questions regarding dinoflagellate genome organization by mapping the genome-wide distribution of 5-hmU (using both immunoprecipitation-based and basepair-resolution chemical mapping approaches) and of chromatin accessibility in the genome of the Symbiodiniaceae dinoflagellate Breviolum minutum. We find that the 5-hmU modification is preferentially enriched over certain classes of repetitive elements, often coincides with the boundaries between gene arrays, and is generally correlated with decreased chromatin accessibility, the latter otherwise being largely uniform along the genome. We discuss the potential roles of 5-hmU in the functional organization of dinoflagellate genomes and its relationship to the transcriptional landscape of gene arrays.
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Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Xinyi Chen
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | | | - Tingting Xiang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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13
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Kalvelage J, Wöhlbrand L, Schoon RA, Zink FM, Correll C, Senkler J, Eubel H, Hoppenrath M, Rhiel E, Braun HP, Winklhofer M, Klingl A, Rabus R. The enigmatic nucleus of the marine dinoflagellate Prorocentrum cordatum. mSphere 2023; 8:e0003823. [PMID: 37358287 PMCID: PMC10449503 DOI: 10.1128/msphere.00038-23] [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: 01/23/2023] [Accepted: 02/20/2023] [Indexed: 06/27/2023] Open
Abstract
The marine, bloom-forming dinoflagellate Prorocentrum cordatum CCMP 1329 (formerly P. minimum) has a genome atypical of eukaryotes, with a large size of ~4.15 Gbp, organized in plentiful, highly condensed chromosomes and packed in a dinoflagellate-specific nucleus (dinokaryon). Here, we apply microscopic and proteogenomic approaches to obtain new insights into this enigmatic nucleus of axenic P. cordatum. High-resolution focused ion beam/scanning electron microscopy analysis of the flattened nucleus revealed highest density of nuclear pores in the vicinity of the nucleolus, a total of 62 tightly packed chromosomes (~0.4-6.7 µm3), and interaction of several chromosomes with the nucleolus and other nuclear structures. A specific procedure for enriching intact nuclei was developed to enable proteomic analyses of soluble and membrane protein-enriched fractions. These were analyzed with geLC and shotgun approaches employing ion-trap and timsTOF (trapped-ion-mobility-spectrometry time-of-flight) mass spectrometers, respectively. This allowed identification of 4,052 proteins (39% of unknown function), out of which 418 were predicted to serve specific nuclear functions; additional 531 proteins of unknown function could be allocated to the nucleus. Compaction of DNA despite very low histone abundance could be accomplished by highly abundant major basic nuclear proteins (HCc2-like). Several nuclear processes including DNA replication/repair and RNA processing/splicing can be fairly well explained on the proteogenomic level. By contrast, transcription and composition of the nuclear pore complex remain largely elusive. One may speculate that the large group of potential nuclear proteins with currently unknown functions may serve yet to be explored functions in nuclear processes differing from those of typical eukaryotic cells. IMPORTANCE Dinoflagellates form a highly diverse group of unicellular microalgae. They provide keystone species for the marine ecosystem and stand out among others by their very large, unusually organized genomes embedded in the nuclei markedly different from other eukaryotic cells. Functional insights into nuclear and other cell biological structures and processes of dinoflagellates have long been hampered by the paucity of available genomic sequences. The here studied cosmopolitan P. cordatum belongs to the harmful algal bloom-forming, marine dinoflagellates and has a recently de novo assembled genome. We present a detailed 3D reconstruction of the P. cordatum nucleus together with comprehensive proteogenomic insights into the protein equipment mastering the broad spectrum of nuclear processes. This study significantly advances our understanding of mechanisms and evolution of the conspicuous dinoflagellate cell biology.
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Affiliation(s)
- Jana Kalvelage
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Lars Wöhlbrand
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Robin-Alexander Schoon
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Fiona-Marine Zink
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Christina Correll
- Plant Development, Botany, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany
| | - Jennifer Senkler
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Holger Eubel
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Mona Hoppenrath
- Marine Biodiversity Research, Institute of Biology and Environmental Sciences (IBU), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), Wilhelmshaven, Germany
| | - Erhard Rhiel
- Planktology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Hans-Peter Braun
- Plant Proteomics, Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Michael Winklhofer
- Sensory Biology of Animals, Institute of Biology and Environmental Sciences (IBU), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
- Research Center Neurosensory Science, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Andreas Klingl
- Plant Development, Botany, Ludwig-Maximilians-Universität München, Planegg, Martinsried, Germany
| | - Ralf Rabus
- General and Molecular Microbiology, Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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14
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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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15
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Veglia AJ, Bistolas KSI, Voolstra CR, Hume BCC, Ruscheweyh HJ, Planes S, Allemand D, Boissin E, Wincker P, Poulain J, Moulin C, Bourdin G, Iwankow G, Romac S, Agostini S, Banaigs B, Boss E, Bowler C, de Vargas C, Douville E, Flores M, Forcioli D, Furla P, Galand PE, Gilson E, Lombard F, Pesant S, Reynaud S, Sunagawa S, Thomas OP, Troublé R, Zoccola D, Correa AMS, Vega Thurber RL. Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes. Commun Biol 2023; 6:566. [PMID: 37264063 DOI: 10.1038/s42003-023-04917-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 04/24/2023] [Indexed: 06/03/2023] Open
Abstract
Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.
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Affiliation(s)
- Alex J Veglia
- BioSciences Department, Rice University, Houston, TX, USA
| | | | | | | | - Hans-Joachim Ruscheweyh
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Denis Allemand
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
- Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/ Tara Oceans-GOSEE, 3 rue Michel-Ange, 75016, Paris, France
| | - Clémentine Moulin
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | | | - Guillaume Iwankow
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Sarah Romac
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Sylvain Agostini
- Shimoda Marine Research Center, University of Tsukuba, 5-10-1, Shimoda, Shizuoka, Japan
| | - Bernard Banaigs
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Laboratoire d'Excellence CORAIL, Université de Perpignan, 52 Avenue Paul Alduy, 66860, Perpignan, Cedex, France
| | - Emmanuel Boss
- School of Marine Sciences, University of Maine, Orono, ME, USA
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, ECOMAP, Roscoff, France
| | - Eric Douville
- Laboratoire des Sciences du Climat et de l'Environnement, LSCE/IPSL, CEA-CNRS-UVSQ, Université Paris-Saclay, F-91191, Gif-sur-Yvette, France
| | - Michel Flores
- Weizmann Institute of Science, Department of Earth and Planetary Sciences, 76100, Rehovot, Israel
| | - Didier Forcioli
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Paola Furla
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Laboratoire International Associé Université Côte d'Azur-Centre Scientifique de Monaco, LIA ROPSE, Monaco, France
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, 66650, Banyuls sur mer, France
| | - Eric Gilson
- Université Côte d'Azur, CNRS, INSERM, IRCAN, Medical School, Nice, France
- Department of Medical Genetics, CHU of Nice, Nice, France
| | - Fabien Lombard
- Sorbonne Université, Institut de la Mer de Villefranche sur mer, Laboratoire d'Océanographie de Villefranche, F-06230, Villefranche-sur-Mer, France
| | - Stéphane Pesant
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stéphanie Reynaud
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
| | - Shinichi Sunagawa
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, Vladimir-Prelog-Weg 4, ETH Zürich, CH-8093, Zürich, Switzerland
| | - Olivier P Thomas
- School of Biological and Chemical Sciences, Ryan Institute, University of Galway, University Road H91 TK33, Galway, Ireland
| | - Romain Troublé
- Fondation Tara Océan, Base Tara, 8 rue de Prague, 75012, Paris, France
| | - Didier Zoccola
- Centre Scientifique de Monaco, 8 Quai Antoine Ier, Monaco, MC-98000, Principality of Monaco
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16
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Alizade A, Jantschke A. Dinoflagellates as sustainable cellulose source: Cultivation, extraction, and characterization. Int J Biol Macromol 2023:125116. [PMID: 37257537 DOI: 10.1016/j.ijbiomac.2023.125116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 04/25/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023]
Abstract
The global demand for manufacturing and consuming biodegradable materials from natural sources has created a great interest in microalgae, such as dinoflagellates. Photosynthetic dinoflagellates are a sustainable source of natural materials such as cellulose as they grow using only sunlight and CO2 at near-neutral pH without any fertilizers. In this paper, the cultivation of two species of dinoflagellates (Peridinium sp. and Prorocentrum micans) is established under lab conditions (up to 20 l), cellulose extraction is optimized, and the resulting material is thoroughly characterized. Dinoflagellate cellulose was extracted at room temperature by sequential treatment with highly concentrated 30 % NaOH and 6 M HCl, followed by bleaching with 10 % H2O2. The overall yield of cellulose is around 73 % (w/w), and roughly 85 % of the original dinoflagellate cellulosic morphology remains intact. Chemical purity, morphology, and porosity of the dinoflagellate-derived cellulose are analysed by different characterization techniques (ICP-OES, SEM, XRD, ATR-FTIR, Raman, NMR, TGA, BET, and GPC). XRD characterization of the extracted cellulose shows characteristic reflexes corresponding to a cellulose II allomorph which is mainly amorphous. This result is further supported by ATR-FTIR, Raman, and NMR spectroscopy. Overall, these results show that the extracted cellulose is a highly porous, lignin-free material that is thermally stable up to 260 °C. Its high degree of purity and porosity make dinoflagellate-derived cellulose a promising, sustainable candidate for the development of functional hybrid materials for biomedical applications.
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Affiliation(s)
- Amina Alizade
- Institute for Geosciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany.
| | - Anne Jantschke
- Institute for Geosciences, Johannes Gutenberg-University Mainz, 55128 Mainz, Germany.
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17
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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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18
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Taniguchi M, Lindsey JS. Absorption and Fluorescence Spectra of Open-chain Tetrapyrrole Pigments–Bilirubins, Biliverdins, Phycobilins, and Synthetic Analogues. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C: PHOTOCHEMISTRY REVIEWS 2023. [DOI: 10.1016/j.jphotochemrev.2023.100585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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19
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Dorrell RG, Kuo A, Füssy Z, Richardson EH, Salamov A, Zarevski N, Freyria NJ, Ibarbalz FM, Jenkins J, Pierella Karlusich JJ, Stecca Steindorff A, Edgar RE, Handley L, Lail K, Lipzen A, Lombard V, McFarlane J, Nef C, Novák Vanclová AM, Peng Y, Plott C, Potvin M, Vieira FRJ, Barry K, de Vargas C, Henrissat B, Pelletier E, Schmutz J, Wincker P, Dacks JB, Bowler C, Grigoriev IV, Lovejoy C. Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae. Life Sci Alliance 2023; 6:6/3/e202201833. [PMID: 36522135 PMCID: PMC9756366 DOI: 10.26508/lsa.202201833] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 11/29/2022] [Accepted: 12/01/2022] [Indexed: 12/23/2022] Open
Abstract
Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.
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Affiliation(s)
- Richard G Dorrell
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zoltan Füssy
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Prague, Czech Republic
| | - Elisabeth H Richardson
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nikola Zarevski
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Nastasia J Freyria
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Federico M Ibarbalz
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Jerry Jenkins
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Juan Jose Pierella Karlusich
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Andrei Stecca Steindorff
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Robyn E Edgar
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Lori Handley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Kathleen Lail
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vincent Lombard
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - John McFarlane
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Charlotte Nef
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Anna Mg Novák Vanclová
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Yi Peng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Marianne Potvin
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
| | - Fabio Rocha Jimenez Vieira
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Colomban de Vargas
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Sorbonne Université, CNRS, Station Biologique de Roscoff, AD2M, UMR 7144, Roscoff, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Eric Pelletier
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Jeremy Schmutz
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Patrick Wincker
- CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France.,Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l'Énergie Atomique, CNRS, Université Évry, Université Paris-Saclay, Évry, France
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta and Department of Biological Sciences, and University of Alberta, Edmonton, Canada
| | - Chris Bowler
- Institut de Biologie de l'ENS, Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.,CNRS Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara Oceans GOSEE, Paris, France
| | - Igor V Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Connie Lovejoy
- Département de Biologie, Institut de Biologie Intégrative des Systèmes, Université Laval, Quebec, Canada
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20
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Kwok ACM, Chan WS, Wong JTY. Dinoflagellate Amphiesmal Dynamics: Cell Wall Deposition with Ecdysis and Cellular Growth. Mar Drugs 2023; 21:md21020070. [PMID: 36827111 PMCID: PMC9959387 DOI: 10.3390/md21020070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 01/24/2023] Open
Abstract
Dinoflagellates are a major aquatic protist group with amphiesma, multiple cortical membranous "cell wall" layers that contain large circum-cortical alveolar sacs (AVs). AVs undergo extensive remodeling during cell- and life-cycle transitions, including ecdysal cysts (ECs) and resting cysts that are important in some harmful algal bloom initiation-termination. AVs are large cortical vesicular compartments, within which are elaborate cellulosic thecal plates (CTPs), in thecate species, and the pellicular layer (PL). AV-CTPs provide cellular mechanical protection and are targets of vesicular transport that are replaced during EC-swarmer cell transition, or with increased deposition during the cellular growth cycle. AV-PL exhibits dynamical-replacement with vesicular trafficking that are orchestrated with amphiesmal chlortetracycline-labeled Ca2+ stores signaling, integrating cellular growth with different modes of cell division cycle/progression. We reviewed the dynamics of amphiesma during different cell division cycle modes and life cycle stages, and its multifaceted regulations, focusing on the regulatory and functional readouts, including the coral-zooxanthellae interactions.
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21
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Jang SH, Na SI, Lee MJ, Yoo YD. Assessing the utility of mitochondrial gene markers in the family Suessiaceae (Dinophyta) with phylogenomic validation. Mol Phylogenet Evol 2022; 177:107625. [PMID: 36064085 DOI: 10.1016/j.ympev.2022.107625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 08/13/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022]
Abstract
The dinoflagellate family Suessiaceae comprises cosmopolitan species distributed across polar and tropical waters in both marine and freshwater ecosystems, encompassing free-living forms, symbionts, and parasites. Recently, species diversity within the family has rapidly expanded, now including a few species reported to cause red tides. Despite their ecological and evolutionary importance, classifying them within Suessiaceae is difficult due to the limitations of the existing molecular markers-the highly conserved small subunit ribosomal gene (SSU rDNA) and the presence of two indel regions of sequence fragments of the large subunit ribosomal gene (LSU rDNA)-resulting in poorly resolved phylogenetic relationships. We assessed mitochondrial cytochrome b (cob) and cytochrome c oxidase 1 (cox1) genes to develop robust molecular markers that can reveal the genetic diversity of the family Suessiaceae. The divergences of cob and cox1 sequences among the species in the family were greater than the SSU rDNA but less than the LSU rDNA and the ITS region. Moreover, the distinctive topology inferred from the mitochondrial genes provided high resolution among the suessiacean species. We examined the validity of the genetic markers using phylogenomics based on 2,023 core proteins. The divergence of the cob phylogeny was most consistent with that of the phylogenomic results. Taken together, the cob gene can be a novel marker reflecting topology at the genome-scale within the family Suessiaceae.
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Affiliation(s)
- Se Hyeon Jang
- Department of Oceanography, Chonnam National University, Gwangju 61186, South Korea.
| | - Seong In Na
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 00826, South Korea
| | - Moo Joon Lee
- Department of Marine Biotechnology, Anyang University, Incheon 23038, South Korea
| | - Yeong Du Yoo
- Department of Marine Biotechnology, College of Ocean Sciences, Kunsan National University, Kunsan 54150, South Korea
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22
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Benites LF, Stephens TG, Bhattacharya D. Multiple waves of viral invasions in Symbiodiniaceae algal genomes. Virus Evol 2022; 8:veac101. [PMID: 36381231 PMCID: PMC9651163 DOI: 10.1093/ve/veac101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/29/2022] [Accepted: 10/25/2022] [Indexed: 08/13/2023] Open
Abstract
Dinoflagellates from the family Symbiodiniaceae are phototrophic marine protists that engage in symbiosis with diverse hosts. Their large and distinct genomes are characterized by pervasive gene duplication and large-scale retroposition events. However, little is known about the role and scale of horizontal gene transfer (HGT) in the evolution of this algal family. In other dinoflagellates, high levels of HGTs have been observed, linked to major genomic transitions, such as the appearance of a viral-acquired nucleoprotein that originated via HGT from a large DNA algal virus. Previous work showed that Symbiodiniaceae from different hosts are actively infected by viral groups, such as giant DNA viruses and ssRNA viruses, that may play an important role in coral health. Latent viral infections may also occur, whereby viruses could persist in the cytoplasm or integrate into the host genome as a provirus. This hypothesis received experimental support; however, the cellular localization of putative latent viruses and their taxonomic affiliation are still unknown. In addition, despite the finding of viral sequences in some genomes of Symbiodiniaceae, viral origin, taxonomic breadth, and metabolic potential have not been explored. To address these questions, we searched for putative viral-derived proteins in thirteen Symbiodiniaceae genomes. We found fifty-nine candidate viral-derived HGTs that gave rise to twelve phylogenies across ten genomes. We also describe the taxonomic affiliation of these virus-related sequences, their structure, and their genomic context. These results lead us to propose a model to explain the origin and fate of Symbiodiniaceae viral acquisitions.
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Affiliation(s)
- L Felipe Benites
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | - Timothy G Stephens
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, 102 Foran Hall, 59 Dudley Road, New Brunswick, NJ 08901-8520, USA
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23
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Lima MS, Hamerski L, Silva TA, da Cruz MLR, Varasteh T, Tschoeke DA, Atella GC, de Souza W, Thompson FL, Thompson CC. Insights on the biochemical and cellular changes induced by heat stress in the Cladocopium isolated from coral Mussismilia braziliensis. Front Microbiol 2022; 13:973980. [PMID: 36299729 PMCID: PMC9590694 DOI: 10.3389/fmicb.2022.973980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/22/2022] [Indexed: 11/13/2022] Open
Abstract
Corals are treatened by global warming. Bleaching is one immediate effect of global warming, resulting from the loss of photosynthetic endosymbiont dinoflagellates. Understanding host-symbiont associations are critical for assessing coral’s habitat requirements and its response to environmental changes. Cladocopium (formerly family Symbiodiniaceae clade C) are dominant endosymbionts in the reef-building coral, Mussismilia braziliensis. This study aimed to investigate the effect of temperature on the biochemical and cellular features of Cladocopium. Heat stress increased oxygen (O2) and decreased proteins, pigments (Chla + Chlc2), hexadecanoic acid- methyl ester, methyl stearate, and octadecenoic acid (Z)- methyl ester molecules. In addition, there was an increase in neutral lipids such as esterified cholesterol and a decrease in free fatty acids that may have been incorporated for the production of lipid droplets. Transmission electron microscopy (TEM) demonstrated that Cladocopium cells subjected to heat stress had thinner cell walls, deformation of chloroplasts, and increased lipid droplets after 3 days at 28°C. These findings indicate that thermal stress negatively affects isolated Cladocopium spp. from Mussismilia host coral.
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Affiliation(s)
- Michele S. Lima
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Lidilhone Hamerski
- Walter Mors Institute of Research on Natural Products, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Tatiana A. Silva
- Laboratory of Celullar Ultrastructure Hertha Meyer, Biophysics Institute Carlos Chagas Filho, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- National Center for Structural Biology and Bioimaging (Cenabio), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Maria Luíza R. da Cruz
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Tooba Varasteh
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Diogo A. Tschoeke
- Biomedical Engineering Program – COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Georgia C. Atella
- Laboratory of Lipids Biochemistry and Lipoprotein, Biochemistry Institute Leopoldo de Meis, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Wanderley de Souza
- Laboratory of Celullar Ultrastructure Hertha Meyer, Biophysics Institute Carlos Chagas Filho, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- National Center for Structural Biology and Bioimaging (Cenabio), Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Fabiano L. Thompson
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Center of Technology-CT2, SAGE-COPPE, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- *Correspondence: Fabiano L. Thompson, ; Cristiane C. Thompson,
| | - Cristiane C. Thompson
- Laboratory of Microbiology, Biology Institute, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- *Correspondence: Fabiano L. Thompson, ; Cristiane C. Thompson,
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24
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Lin S, Yu L, Wu X, Li M, Zhang Y, Luo H, Li H, Li T, Li L. Active meiosis during dinoflagellate blooms: A 'sex for proliferation' hypothesis. HARMFUL ALGAE 2022; 118:102307. [PMID: 36195414 DOI: 10.1016/j.hal.2022.102307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 06/16/2023]
Abstract
In dinoflagellates, sexual reproduction is best known to be induced by adverse environmental conditions and culminate in encystment for survival ('sex for encystment'). Although increasing laboratory observations indicate that sex can lead to production of vegetative cells bypassing encystment, the occurrence of this alternative pathway in natural populations and its ecological roles remain poorly understood. Here we report evidence that sex in dinoflagellates can potentially be an instrument for bloom proliferation or extension. By bloom metatranscriptome profiling, we documented elevated expression of meiosis genes in two evolutionarily distinct species (Prorocentrum shikokuense and Karenia mikimotoi) during bloom, a timing unexpected of the 'sex for encystment' scenario. To link these genes to meiosis, we induced encystment and cyst germination in the cyst-forming species Scrippsiella acuminata, and found that five of these genes were upregulated during cyst germination, when meiosis occurs. Integrating data from all three species revealed that SPO11, MND1, and DMC1 were likely common between cyst-forming and non-encysting sex in dinoflagellates. Furthermore, flow cytometric analyses revealed consecutive rounds of DNA halving during blooms of P. shikokuense and K. mikimotoi, evidencing meiosis. These data provided novel evidence that sexual reproduction in dinoflagellates might serve to promote cell proliferation, and along with the consequent enhancement of genetic diversity facilitating resistance against pathogens and environmental stress, to boost or extend a bloom ('sex for proliferation'). The putative meiosis-specific genes and insights reported here will prove to be helpful for rigorously testing the hypothesis and addressing whether the two modes of sex are genetically predisposed (i.e. species-specific) or environmentally induced (switchable within species), and if the latter what triggers the switch.
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Affiliation(s)
- Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xiaomei Wu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Meizhen Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yaqun Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Hao Luo
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Hongfei Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Tangcheng Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian 361102, China
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25
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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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26
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Williams E, Bachvaroff T, Place A. A Comparison of Dinoflagellate Thiolation Domain Binding Proteins Using In Vitro and Molecular Methods. Mar Drugs 2022; 20:md20090581. [PMID: 36135770 PMCID: PMC9500876 DOI: 10.3390/md20090581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/17/2022] Open
Abstract
Dinoflagellates play important roles in ecosystems as primary producers and consumers making natural products that can benefit or harm environmental and human health but are also potential therapeutics with unique chemistries. Annotations of dinoflagellate genes have been hampered by large genomes with many gene copies that reduce the reliability of transcriptomics, quantitative PCR, and targeted knockouts. This study aimed to functionally characterize dinoflagellate proteins by testing their interactions through in vitro assays. Specifically, nine Amphidinium carterae thiolation domains that scaffold natural product synthesis were substituted into an indigoidine synthesizing gene from the bacterium Streptomyces lavendulae and exposed to three A. carterae phosphopantetheinyl transferases that activate synthesis. Unsurprisingly, several of the dinoflagellate versions inhibited the ability to synthesize indigoidine despite being successfully phosphopantetheinated. However, all the transferases were able to phosphopantetheinate all the thiolation domains nearly equally, defying the canon that transferases participate in segregated processes via binding specificity. Moreover, two of the transferases were expressed during growth in alternating patterns while the final transferase was only observed as a breakdown product common to all three. The broad substrate recognition and compensatory expression shown here help explain why phosphopantetheinyl transferases are lost throughout dinoflagellate evolution without a loss in a biochemical process.
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27
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Gornik SG, Flores V, Reinhardt F, Erber L, Salas-Leiva DE, Douvropoulou O, Lassadi I, Einarsson E, Mörl M, Git A, Stadler PF, Pain A, Waller RF. Mitochondrial Genomes in Perkinsus Decode Conserved Frameshifts in All Genes. Mol Biol Evol 2022; 39:6701636. [PMID: 36108082 PMCID: PMC9550989 DOI: 10.1093/molbev/msac191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial genomes of apicomplexans, dinoflagellates, and chrompodellids that collectively make up the Myzozoa, encode only three proteins (Cytochrome b [COB], Cytochrome c oxidase subunit 1 [COX1], Cytochrome c oxidase subunit 3 [COX3]), contain fragmented ribosomal RNAs, and display extensive recombination, RNA trans-splicing, and RNA-editing. The early-diverging Perkinsozoa is the final major myzozoan lineage whose mitochondrial genomes remained poorly characterized. Previous reports of Perkinsus genes indicated independent acquisition of non-canonical features, namely the occurrence of multiple frameshifts. To determine both ancestral myzozoan and novel perkinsozoan mitochondrial genome features, we sequenced and assembled mitochondrial genomes of four Perkinsus species. These data show a simple ancestral genome with the common reduced coding capacity but disposition for rearrangement. We identified 75 frameshifts across the four species that occur as distinct types and that are highly conserved in gene location. A decoding mechanism apparently employs unused codons at the frameshift sites that advance translation either +1 or +2 frames to the next used codon. The locations of frameshifts are seemingly positioned to regulate protein folding of the nascent protein as it emerges from the ribosome. The cox3 gene is distinct in containing only one frameshift and showing strong selection against residues that are otherwise frequently encoded at the frameshift positions in cox1 and cob. All genes lack cysteine codons implying a reduction to 19 amino acids in these genomes. Furthermore, mitochondrion-encoded rRNA fragment complements are incomplete in Perkinsus spp. but some are found in the nuclear DNA suggesting import into the organelle. Perkinsus demonstrates further remarkable trajectories of organelle genome evolution including pervasive integration of frameshift translation into genome expression.
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Affiliation(s)
| | - Victor Flores
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Franziska Reinhardt
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Lieselotte Erber
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Dayana E Salas-Leiva
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Olga Douvropoulou
- Pathogen Genomics Group, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Elin Einarsson
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Mario Mörl
- Institute for Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Anna Git
- Department of Biochemistry, University of Cambridge, Hopkins Building, Downing Site, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany,Discrete Biomathematics, Max Planck Institute for Mathematics in the Sciences, 04103 Leipzig, Germany,Theoretical Biochemistry Group, Institute for Theoretical Chemistry, University of Vienna, Währinger Str. 17, Alsergrund, Vienna 1090, Austria,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Arnab Pain
- Pathogen Genomics Group, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia,International Institute for Zoonosis Control, Hokkaido University, 001-0020 North 20, West 10 Kita-ku, Sapporo 001-0020, Japan
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28
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Alacid E, Irwin NAT, Smilansky V, Milner DS, Kilias ES, Leonard G, Richards TA. A diversified and segregated mRNA spliced-leader system in the parasitic Perkinsozoa. Open Biol 2022; 12:220126. [PMID: 36000319 PMCID: PMC9399869 DOI: 10.1098/rsob.220126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Spliced-leader trans-splicing (SLTS) has been described in distantly related eukaryotes and acts to mark mRNAs with a short 5′ exon, giving different mRNAs identical 5′ sequence-signatures. The function of these systems is obscure. Perkinsozoa encompasses a diversity of parasitic protists that infect bivalves, toxic-tide dinoflagellates, fish and frog tadpoles. Here, we report considerable sequence variation in the SLTS-system across the Perkinsozoa and find that multiple variant SLTS-systems are encoded in parallel in the ecologically important Perkinsozoa parasite Parvilucifera sinerae. These results demonstrate that the transcriptome of P. sinerae is segregated based on the addition of different spliced-leader (SL) exons. This segregation marks different gene categories, suggesting that SL-segregation relates to functional differentiation of the transcriptome. By contrast, both sets of gene categories are present in the single SL-transcript type sampled from Maranthos, implying that the SL-segregation of the Parvilucifera transcriptome is a recent evolutionary innovation. Furthermore, we show that the SLTS-system marks a subsection of the transcriptome with increased mRNA abundance and includes genes that encode the spliceosome system necessary for SLTS-function. Collectively, these data provide a picture of how the SLTS-systems can vary within a major evolutionary group and identify how additional transcriptional-complexity can be achieved through SL-segregation.
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Affiliation(s)
- Elisabet Alacid
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK
| | - Nicholas A T Irwin
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK.,Merton College, University of Oxford, Oxford, Oxfordshire OX1 4JD, UK
| | - Vanessa Smilansky
- Living Systems Institute, University of Exeter, Exeter, Devon EX4 4QD, UK
| | - David S Milner
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK
| | - Estelle S Kilias
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK
| | - Guy Leonard
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK
| | - Thomas A Richards
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SZ, UK
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29
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Rozenberg A, Kaczmarczyk I, Matzov D, Vierock J, Nagata T, Sugiura M, Katayama K, Kawasaki Y, Konno M, Nagasaka Y, Aoyama M, Das I, Pahima E, Church J, Adam S, Borin VA, Chazan A, Augustin S, Wietek J, Dine J, Peleg Y, Kawanabe A, Fujiwara Y, Yizhar O, Sheves M, Schapiro I, Furutani Y, Kandori H, Inoue K, Hegemann P, Béjà O, Shalev-Benami M. Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels. Nat Struct Mol Biol 2022; 29:592-603. [PMID: 35710843 DOI: 10.1038/s41594-022-00783-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 04/27/2022] [Indexed: 11/09/2022]
Abstract
Many organisms sense light using rhodopsins, photoreceptive proteins containing a retinal chromophore. Here we report the discovery, structure and biophysical characterization of bestrhodopsins, a microbial rhodopsin subfamily from marine unicellular algae, in which one rhodopsin domain of eight transmembrane helices or, more often, two such domains in tandem, are C-terminally fused to a bestrophin channel. Cryo-EM analysis of a rhodopsin-rhodopsin-bestrophin fusion revealed that it forms a pentameric megacomplex (~700 kDa) with five rhodopsin pseudodimers surrounding the channel in the center. Bestrhodopsins are metastable and undergo photoconversion between red- and green-absorbing or green- and UVA-absorbing forms in the different variants. The retinal chromophore, in a unique binding pocket, photoisomerizes from all-trans to 11-cis form. Heterologously expressed bestrhodopsin behaves as a light-modulated anion channel.
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Affiliation(s)
- Andrey Rozenberg
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Igor Kaczmarczyk
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Donna Matzov
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Johannes Vierock
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Masahiro Sugiura
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan
| | - Kota Katayama
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan.,Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Japan
| | - Yuma Kawasaki
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Yujiro Nagasaka
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Mako Aoyama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan
| | - Ishita Das
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Efrat Pahima
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Jonathan Church
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Suliman Adam
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Veniamin A Borin
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ariel Chazan
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel
| | - Sandra Augustin
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jonas Wietek
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Julien Dine
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot, Israel
| | - Akira Kawanabe
- Laboratory of Molecular Physiology & Biophysics, Faculty of Medicine, Kagawa University, Miki-cho, Japan
| | - Yuichiro Fujiwara
- Laboratory of Molecular Physiology & Biophysics, Faculty of Medicine, Kagawa University, Miki-cho, Japan
| | - Ofer Yizhar
- Department of Neurobiology, Weizmann Institute of Science, Rehovot, Israel
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Peter Hegemann
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Oded Béjà
- Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.
| | - Moran Shalev-Benami
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel.
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30
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Description of an Enigmatic Alveolate, Platyproteum noduliferae n. sp., and Reconstruction of its Flagellar Apparatus. Protist 2022; 173:125878. [DOI: 10.1016/j.protis.2022.125878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 03/02/2022] [Accepted: 03/27/2022] [Indexed: 11/23/2022]
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31
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Sanders WB. The photoaerogens: algae and plants reunited conceptually. AMERICAN JOURNAL OF BOTANY 2022; 109:363-365. [PMID: 35257370 DOI: 10.1002/ajb2.1828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/16/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Affiliation(s)
- William B Sanders
- Department of Biological Sciences, Florida Gulf Coast University, Ft. Myers, FL 33965-6565, USA
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32
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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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33
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Shoguchi E. Gene clusters for biosynthesis of mycosporine-like amino acids in dinoflagellate nuclear genomes: Possible recent horizontal gene transfer between species of Symbiodiniaceae (Dinophyceae). JOURNAL OF PHYCOLOGY 2022; 58:1-11. [PMID: 34699617 PMCID: PMC9298759 DOI: 10.1111/jpy.13219] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 10/01/2021] [Accepted: 10/12/2021] [Indexed: 05/12/2023]
Abstract
Global warming increases the temperature of the ocean surface, which can disrupt dinoflagellate-coral symbioses and result in coral bleaching. Photosynthetic dinoflagellates of the family Symbiodiniaceae include bleaching-tolerant and bleaching-sensitive coral symbionts. Therefore, understanding the molecular mechanisms for changing symbiont diversity is potentially useful to assist recovery of coral holobionts (corals and their associated microbes, including multiple species of Symbiodiniaceae), although sexual reproduction has not been observed in the Symbiodiniaceae. Recent molecular phylogenetic analyses estimate that the Symbiodiniaceae appeared 160 million years ago and diversified into 15 groups, five genera of which now have available draft genomes (i.e., Symbiodinium, Durusdinium, Breviolum, Fugacium, and Cladocopium). Comparative genomic analyses have suggested that crown groups have fewer gene families than early-diverging groups, although many genes that were probably acquired via gene duplications and horizontal gene transfers (HGTs) have been found in each decoded genome. Because UV stress is likely a contributor to coral bleaching, and because the highly conserved gene cluster for mycosporine-like amino acid (MAA) biosynthesis has been found in thermal-tolerant symbiont genomes, I reviewed genomic features of the Symbiodiniaceae, focusing on possible acquisition of a biosynthetic gene cluster for MAAs, which absorb UV radiation. On the basis of highly conserved noncoding sequences, I hypothesized that HGTs have occurred among members of the Symbiodiniaceae and have contributed to the diversification of Symbiodiniaceae-host relationships. Finally, I proposed that bleaching tolerance may be strengthened by multiple MAAs from both symbiotic dinoflagellates and corals.
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Affiliation(s)
- Eiichi Shoguchi
- Marine Genomics UnitOkinawa Institute of Science and Technology Graduate UniversityOnnaOkinawa904‐0495Japan
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34
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Suzuki S, Matsuzaki R, Yamaguchi H, Kawachi M. What happened before losses of photosynthesis in cryptophyte algae? Mol Biol Evol 2022; 39:6513384. [PMID: 35079797 PMCID: PMC8829904 DOI: 10.1093/molbev/msac001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
In many lineages of algae and land plants, photosynthesis was lost multiple times independently. Comparative analyses of photosynthetic and secondary nonphotosynthetic relatives have revealed the essential functions of plastids, beyond photosynthesis. However, evolutionary triggers and processes that drive the loss of photosynthesis remain unknown. Cryptophytes are microalgae with complex plastids derived from a red alga. They include several secondary nonphotosynthetic species with closely related photosynthetic taxa. In this study, we found that a cryptophyte, Cryptomonas borealis, is in a stage just prior to the loss of photosynthesis. Cryptomonas borealis was mixotrophic, possessed photosynthetic activity, and grew independent of light. The plastid genome of C. borealis had distinct features, including increases of group II introns with mobility, frequent genome rearrangements, incomplete loss of inverted repeats, and abundant small/medium/large-sized structural variants. These features provide insight into the evolutionary process leading to the loss of photosynthesis.
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Affiliation(s)
- Shigekatsu Suzuki
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, 305-8506, Japan
| | - Ryo Matsuzaki
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, 305-8506, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8577, Japan
| | - Haruyo Yamaguchi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, 305-8506, Japan
| | - Masanobu Kawachi
- Biodiversity Division, National Institute for Environmental Studies, Tsukuba, Ibaraki, 305-8506, Japan
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35
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Coelho JC, Calhoun ED, Calhoun GN, Poole AZ. Patchy Distribution of GTPases of Immunity Associated Proteins (GIMAP) within Cnidarians and Dinoflagellates Suggests a Complex Evolutionary History. Genome Biol Evol 2022; 14:6500283. [PMID: 35015849 PMCID: PMC8857920 DOI: 10.1093/gbe/evac002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2022] [Indexed: 11/24/2022] Open
Abstract
GTPases of Immunity-Associated Proteins (GIMAP) are a group of small GTP-binding proteins found in a variety of organisms, including vertebrates, invertebrates, and plants. These proteins are characterized by the highly conserved AIG1 domain, and in vertebrates, have been implicated in regulation of the immune system as well as apoptosis and autophagy, though their exact mechanism of action remains unclear. Recent work on cnidarian GIMAPs suggests a conserved role in immunity, apoptosis, and autophagy—three processes involved in coral bleaching, or the breakdown of cnidarian-dinoflagellate symbiosis. Therefore, to further understand the evolution of GIMAPs in this group of organisms, the purpose of this study was to characterize GIMAP or GIMAP-like sequences utilizing publicly available genomic and transcriptomic data in species across the cnidarian phylogeny. The results revealed a patchy distribution of GIMAPs in cnidarians, with three distinct types referred to as L-GIMAP, S-GIMAP, and GIMAP-like. Additionally, GIMAPs were present in most dinoflagellate species and formed seven well-supported clades. Overall, these results elucidate the distribution of GIMAPs within two distantly related eukaryotic groups and represent the first in-depth investigation on the evolution of these proteins within both protists and basal metazoans.
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Affiliation(s)
- Jenny C Coelho
- Department of Biology, Berry College, 2277 Martha Berry Highway NW, Mt. Berry GA, 30149, USA.,Department of Biology, University of North Carolina at Chapel Hill, 120 South Rd, Chapel Hill, NC 27599, USA
| | - Ethan D Calhoun
- Department of Biology, Berry College, 2277 Martha Berry Highway NW, Mt. Berry GA, 30149, USA
| | - Grant N Calhoun
- Department of Biology, Berry College, 2277 Martha Berry Highway NW, Mt. Berry GA, 30149, USA
| | - Angela Z Poole
- Department of Biology, Berry College, 2277 Martha Berry Highway NW, Mt. Berry GA, 30149, USA
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36
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Sprecher BN, Zhang H, Park G, Lin S. Isolation from a fish kill and transcriptomic characterization of Gyrodinium jinhaense off Long Island Sound. HARMFUL ALGAE 2021; 110:102136. [PMID: 34887013 DOI: 10.1016/j.hal.2021.102136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/01/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
First found in Korean coastal water, the dinoflagellate Gyrodinium jinhaense is a recently established species with unclear global distribution and unexplored genomic characteristics. From a laboratory fish mortality event off Long Island Sound, USA, we isolated a dinoflagellate, and by microscopic and molecular (18S rRNA gene; >99% identical) analyses found that it resembles G. jinhaense, hence named G. jinhaense strain AP17. Towards developing a genetic database for this dinoflagellate, a transcriptome of this species was sequenced using RNA-seq, producing 6 Gbp of data that was assembled into over 70,000 unigenes. The assembled transcriptome GC content was approximately 56% and the total Benchmarking Universal Single-Copy Orthologs for Eukaryota and Alveolata databases were approximately 50% and 57%, respectfully. Genes involved in grazing, energy generation, genome architecture, and protein synthesis, processing, and degradation were highly represented in the transcriptome. Moreover, fragments of polyketide synthase and saxitoxin genes were found but saxitoxins were not detected in high performance liquid chromatography measurements. With the first reported transcriptome for the Gyrodinium genus, this study will serve as a baseline for future Gyrodinium genomics and toxicological studies.
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Affiliation(s)
- Brittany N Sprecher
- University of Connecticut Avery Point, 1084 Shennecossett Rd, Groton, CT 06340, United States; Current Address - University of Konstanz, Universitätsstraße 10, 78462 Konstanz, Germany.
| | - Huan Zhang
- University of Connecticut Avery Point, 1084 Shennecossett Rd, Groton, CT 06340, United States
| | - Gihong Park
- University of Connecticut Avery Point, 1084 Shennecossett Rd, Groton, CT 06340, United States
| | - Senjie Lin
- University of Connecticut Avery Point, 1084 Shennecossett Rd, Groton, CT 06340, United States.
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37
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Lin S, Song B, Morse D. Spatial organization of dinoflagellate genomes: Novel insights and remaining critical questions. JOURNAL OF PHYCOLOGY 2021; 57:1674-1678. [PMID: 34389979 DOI: 10.1111/jpy.13206] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
As is true for many other aspects, genome architecture, evolution, and function in dinoflagellates are enigmatic and, in the meantime, continuous inspiration for scientific quests. Recent third-generation sequencing and Hi-C linkage analyses brought new insights into the spatial organization of symbiodiniacean genomes, revealing the topologically associated domains, discrete gene clusters and their cis and trans orientations, and relationships with transcription. Where do these new findings bring us in dinoflagellate genomics? Here, we aim to place these new results in the backdrop of the long history of research on this topic and in the context of what critical questions remain to be pursued in the future. The new data suggest, pending verification of other complete chromosome assemblies, a potential evolutionary trend in chromosome number decrease and length increase within the Symbiodiniaceae. While questions remain about the mechanics of the three-dimensional chromosome structure and cell cycle-related DNA replication, the mechanisms of gene transcription and genome size evolution, these latest findings set new starting points for further inquiries.
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Affiliation(s)
- Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, 06340, USA
| | - Bo Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China
| | - David Morse
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Quebec, H1X 2B2, Canada
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38
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Berná L, Rego N, Francia ME. The Elusive Mitochondrial Genomes of Apicomplexa: Where Are We Now? Front Microbiol 2021; 12:751775. [PMID: 34721355 PMCID: PMC8554336 DOI: 10.3389/fmicb.2021.751775] [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: 08/02/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Mitochondria are vital organelles of eukaryotic cells, participating in key metabolic pathways such as cellular respiration, thermogenesis, maintenance of cellular redox potential, calcium homeostasis, cell signaling, and cell death. The phylum Apicomplexa is entirely composed of obligate intracellular parasites, causing a plethora of severe diseases in humans, wild and domestic animals. These pathogens include the causative agents of malaria, cryptosporidiosis, neosporosis, East Coast fever and toxoplasmosis, among others. The mitochondria in Apicomplexa has been put forward as a promising source of undiscovered drug targets, and it has been validated as the target of atovaquone, a drug currently used in the clinic to counter malaria. Apicomplexans present a single tubular mitochondria that varies widely both in structure and in genomic content across the phylum. The organelle is characterized by massive gene migrations to the nucleus, sequence rearrangements and drastic functional reductions in some species. Recent third generation sequencing studies have reignited an interest for elucidating the extensive diversity displayed by the mitochondrial genomes of apicomplexans and their intriguing genomic features. The underlying mechanisms of gene transcription and translation are also ill-understood. In this review, we present the state of the art on mitochondrial genome structure, composition and organization in the apicomplexan phylum revisiting topological and biochemical information gathered through classical techniques. We contextualize this in light of the genomic insight gained by second and, more recently, third generation sequencing technologies. We discuss the mitochondrial genomic and mechanistic features found in evolutionarily related alveolates, and discuss the common and distinct origins of the apicomplexan mitochondria peculiarities.
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Affiliation(s)
- Luisa Berná
- Laboratory of Apicomplexan Biology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Molecular Biology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Sección Biomatemática-Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Rego
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - María E Francia
- Laboratory of Apicomplexan Biology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Departamento de Parasitología y Micología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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39
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Burki F, Sandin MM, Jamy M. Diversity and ecology of protists revealed by metabarcoding. Curr Biol 2021; 31:R1267-R1280. [PMID: 34637739 DOI: 10.1016/j.cub.2021.07.066] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protists are the dominant eukaryotes in the biosphere where they play key functional roles. While protists have been studied for over a century, it is the high-throughput sequencing of molecular markers from environmental samples - the approach of metabarcoding - that has revealed just how diverse, and abundant, these small organisms are. Metabarcoding is now routine to survey environmental diversity, so data have rapidly accumulated from a multitude of environments and at different sampling scales. This mass of data has provided unprecedented opportunities to study the taxonomic and functional diversity of protists, and how this diversity is organised in space and time. Here, we use metabarcoding as a common thread to discuss the state of knowledge in protist diversity research, from technical considerations of the approach to important insights gained on diversity patterns and the processes that might have structured this diversity. In addition to these insights, we conclude that metabarcoding is on the verge of an exciting added dimension thanks to the maturation of high-throughput long-read sequencing, so that a robust eco-evolutionary framework of protist diversity is within reach.
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Affiliation(s)
- Fabien Burki
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden; Science For Life Laboratory, Uppsala University, 75236 Uppsala, Sweden.
| | - Miguel M Sandin
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden
| | - Mahwash Jamy
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden
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40
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Cooney EC, Okamoto N, Cho A, Hehenberger E, Richards TA, Santoro AE, Worden AZ, Leander BS, Keeling PJ. Single-Cell Transcriptomics of Abedinium Reveals a New Early-Branching Dinoflagellate Lineage. Genome Biol Evol 2021; 12:2417-2428. [PMID: 33045041 DOI: 10.1093/gbe/evaa196] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2020] [Indexed: 12/12/2022] Open
Abstract
Dinoflagellates possess many cellular characteristics with unresolved evolutionary histories. These include nuclei with greatly expanded genomes and chromatin packaged using histone-like proteins and dinoflagellate-viral nucleoproteins instead of histones, highly reduced mitochondrial genomes with extensive RNA editing, a mix of photosynthetic and cryptic secondary plastids, and tertiary plastids. Resolving the evolutionary origin of these traits requires understanding their ancestral states and early intermediates. Several early-branching dinoflagellate lineages are good candidates for such reconstruction, however these cells tend to be delicate and environmentally sparse, complicating such analyses. Here, we employ transcriptome sequencing from manually isolated and microscopically documented cells to resolve the placement of two cells of one such genus, Abedinium, collected by remotely operated vehicle in deep waters off the coast of Monterey Bay, CA. One cell corresponds to the only described species, Abedinium dasypus, whereas the second cell is distinct and formally described as Abedinium folium, sp. nov. Abedinium has classically been assigned to the early-branching dinoflagellate subgroup Noctilucales, which is weakly supported by phylogenetic analyses of small subunit ribosomal RNA, the single characterized gene from any member of the order. However, an analysis based on 221 proteins from the transcriptome places Abedinium as a distinct lineage, separate from and basal to Noctilucales and the rest of the core dinoflagellates. The transcriptome also contains evidence of a cryptic plastid functioning in the biosynthesis of isoprenoids, iron-sulfur clusters, and heme, a mitochondrial genome with all three expected protein-coding genes (cob, cox1, and cox3), and the presence of some but not all dinoflagellate-specific chromatin packaging proteins.
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Affiliation(s)
- Elizabeth C Cooney
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Noriko Okamoto
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anna Cho
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elisabeth Hehenberger
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Ocean Ecosystems Biology Unit, GEOMAR-Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
| | | | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara
| | - Alexandra Z Worden
- Ocean Ecosystems Biology Unit, GEOMAR-Helmholtz Centre for Ocean Research Kiel, Kiel, Germany
- Kiel University, Germany
| | - Brian S Leander
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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41
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Einarsson E, Lassadi I, Zielinski J, Guan Q, Wyler T, Pain A, Gornik SG, Waller RF. Development of the Myzozoan Aquatic Parasite Perkinsus marinus as A Versatile Experimental Genetic Model Organism. Protist 2021; 172:125830. [PMID: 34555729 DOI: 10.1016/j.protis.2021.125830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 11/17/2022]
Abstract
The phylum Perkinsozoa is an aquatic parasite lineage that has devastating effects on commercial and natural mollusc populations, and also comprises parasites of algae, fish and amphibians. They are related to dinoflagellates and apicomplexans and thus offer excellent genetic models for both parasitological and evolutionary studies. Genetic transformation was previously achieved for Perkinsus spp. but with few tools for transgene expression and limited selection efficacy. We sought to expand the power of experimental genetic tools for Perkinsus using P. marinus as a model. We constructed a modular plasmid assembly system for expression of multiple genes simultaneously. We developed efficient selection systems for three drugs, puromycin, bleomycin and blasticidin, that are effective in as little as three weeks. We developed eleven new promoters of variable expression strength. Furthermore, we identified that genomic integration of transgenes is predominantly via non-homologous recombination but with transgene fragmentation including deletion of some elements. To counter these dynamic processes, we show that bi-cistronic transcripts using the viral 2A peptides can couple selection to the maintenance of the expression of a transgene of interest. Collectively, these new tools and insights provide great new capacity to genetically modify and study Perkinsus as an aquatic parasite and evolutionary model.
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Affiliation(s)
- Elin Einarsson
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jana Zielinski
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Qingtian Guan
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Tobias Wyler
- Department of Biochemistry, University of Cambridge, Cambridge, UK; Eidgenössische Technische Hochschule (ETH), Zürich, Switzerland
| | - Arnab Pain
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Sebastian G Gornik
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
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42
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Tsarkova AS. Luciferins Under Construction: A Review of Known Biosynthetic Pathways. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.667829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bioluminescence, or the ability of a living organism to generate visible light, occurs as a result of biochemical reaction where enzyme, known as a luciferase, catalyzes the oxidation of a small-molecule substrate, known as luciferin. This advantageous trait has independently evolved dozens of times, with current estimates ranging from the most conservative 40, based on the biochemical diversity found across bioluminescence systems (Haddock et al., 2010) to 100, taking into account the physiological mechanisms involved in the behavioral control of light production across a wide range of taxa (Davis et al., 2016; Verdes and Gruber, 2017; Bessho-Uehara et al., 2020a; Lau and Oakley, 2021). Chemical structures of ten biochemically unrelated luciferins and several luciferase gene families have been described; however, a full biochemical pathway leading to light emission has been elucidated only for two: bacterial and fungal bioluminescence systems. Although the recent years have been marked by extraordinary discoveries and promising breakthroughs in understanding the molecular basis of multiple bioluminescence systems, the mechanisms of luciferin biosynthesis for many organisms remain almost entirely unknown. This article seeks to provide a succinct overview of currently known luciferins’ biosynthetic pathways.
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43
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Chan KKY, Kong HK, Tse SPK, Chan Z, Lo PY, Kwok KWH, Lo SCL. Finding Species-Specific Extracellular Surface-Facing Proteomes in Toxic Dinoflagellates. Toxins (Basel) 2021; 13:624. [PMID: 34564629 PMCID: PMC8473415 DOI: 10.3390/toxins13090624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/31/2021] [Accepted: 09/01/2021] [Indexed: 11/27/2022] Open
Abstract
As a sequel to our previous report of the existence of species-specific protein/peptide expression profiles (PEPs) acquired by mass spectrometry in some dinoflagellates, we established, with the help of a plasma-membrane-impermeable labeling agent, a surface amphiesmal protein extraction method (SAPE) to label and capture species-specific surface proteins (SSSPs) as well as saxitoxins-producing-species-specific surface proteins (Stx-SSPs) that face the extracellular space (i.e., SSSPsEf and Stx-SSPsEf). Five selected toxic dinoflagellates, Alexandrium minutum, A. lusitanicum, A. tamarense, Gymnodinium catenatum, and Karenia mikimotoi, were used in this study. Transcriptomic databases of these five species were also constructed. With the aid of liquid chromatography linked-tandem mass spectrometry (LC-MS/MS) and the transcriptomic databases of these species, extracellularly facing membrane proteomes of the five different species were identified. Within these proteomes, 16 extracellular-facing and functionally significant transport proteins were found. Furthermore, 10 SSSPs and 6 Stx-SSPs were identified as amphiesmal proteins but not facing outward to the extracellular environment. We also found SSSPsEf and Stx-SSPsEf in the proteomes. The potential functional correlation of these proteins towards the production of saxitoxins in dinoflagellates and the degree of species specificity were discussed accordingly.
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Affiliation(s)
- Kenrick Kai-yuen Chan
- Department of Applied Biology and Chemical Technology, Faculty of Applied Science and Textiles, The Hong Kong Polytechnic University, Hung Hom, Hong Kong; (K.K.-y.C.); (H.-k.K.); (S.P.-k.T.); (Z.C.); (P.-y.L.); (K.W.H.K.)
| | - Hang-kin Kong
- Department of Applied Biology and Chemical Technology, Faculty of Applied Science and Textiles, The Hong Kong Polytechnic University, Hung Hom, Hong Kong; (K.K.-y.C.); (H.-k.K.); (S.P.-k.T.); (Z.C.); (P.-y.L.); (K.W.H.K.)
- Research Institute for Future Food, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Sirius Pui-kam Tse
- Department of Applied Biology and Chemical Technology, Faculty of Applied Science and Textiles, The Hong Kong Polytechnic University, Hung Hom, Hong Kong; (K.K.-y.C.); (H.-k.K.); (S.P.-k.T.); (Z.C.); (P.-y.L.); (K.W.H.K.)
| | - Zoe Chan
- Department of Applied Biology and Chemical Technology, Faculty of Applied Science and Textiles, The Hong Kong Polytechnic University, Hung Hom, Hong Kong; (K.K.-y.C.); (H.-k.K.); (S.P.-k.T.); (Z.C.); (P.-y.L.); (K.W.H.K.)
| | - Pak-yeung Lo
- Department of Applied Biology and Chemical Technology, Faculty of Applied Science and Textiles, The Hong Kong Polytechnic University, Hung Hom, Hong Kong; (K.K.-y.C.); (H.-k.K.); (S.P.-k.T.); (Z.C.); (P.-y.L.); (K.W.H.K.)
| | - Kevin W. H. Kwok
- Department of Applied Biology and Chemical Technology, Faculty of Applied Science and Textiles, The Hong Kong Polytechnic University, Hung Hom, Hong Kong; (K.K.-y.C.); (H.-k.K.); (S.P.-k.T.); (Z.C.); (P.-y.L.); (K.W.H.K.)
- Research Institute for Future Food, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
| | - Samuel Chun-lap Lo
- Department of Applied Biology and Chemical Technology, Faculty of Applied Science and Textiles, The Hong Kong Polytechnic University, Hung Hom, Hong Kong; (K.K.-y.C.); (H.-k.K.); (S.P.-k.T.); (Z.C.); (P.-y.L.); (K.W.H.K.)
- Research Institute for Future Food, The Hong Kong Polytechnic University, Hung Hom, Hong Kong
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44
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Kořený L, Oborník M, Horáková E, Waller RF, Lukeš J. The convoluted history of haem biosynthesis. Biol Rev Camb Philos Soc 2021; 97:141-162. [PMID: 34472688 DOI: 10.1111/brv.12794] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 08/12/2021] [Accepted: 08/19/2021] [Indexed: 01/14/2023]
Abstract
The capacity of haem to transfer electrons, bind diatomic gases, and catalyse various biochemical reactions makes it one of the essential biomolecules on Earth and one that was likely used by the earliest forms of cellular life. Since the description of haem biosynthesis, our understanding of this multi-step pathway has been almost exclusively derived from a handful of model organisms from narrow taxonomic contexts. Recent advances in genome sequencing and functional studies of diverse and previously neglected groups have led to discoveries of alternative routes of haem biosynthesis that deviate from the 'classical' pathway. In this review, we take an evolutionarily broad approach to illuminate the remarkable diversity and adaptability of haem synthesis, from prokaryotes to eukaryotes, showing the range of strategies that organisms employ to obtain and utilise haem. In particular, the complex evolutionary histories of eukaryotes that involve multiple endosymbioses and horizontal gene transfers are reflected in the mosaic origin of numerous metabolic pathways with haem biosynthesis being a striking case. We show how different evolutionary trajectories and distinct life strategies resulted in pronounced tensions and differences in the spatial organisation of the haem biosynthesis pathway, in some cases leading to a complete loss of a haem-synthesis capacity and, rarely, even loss of a requirement for haem altogether.
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Affiliation(s)
- Luděk Kořený
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, U.K
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice (Budweis), 370 05, Czech Republic.,Faculty of Sciences, University of South Bohemia, Branišovská, České Budějovice (Budweis), 31, Czech Republic
| | - Eva Horáková
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice (Budweis), 370 05, Czech Republic
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Hopkins Building, Tennis Court Road, Cambridge, CB2 1QW, U.K
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branišovská 31, České Budějovice (Budweis), 370 05, Czech Republic.,Faculty of Sciences, University of South Bohemia, Branišovská, České Budějovice (Budweis), 31, Czech Republic
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45
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Kinjo Y, Lo N, Martín PV, Tokuda G, Pigolotti S, Bourguignon T. Enhanced Mutation Rate, Relaxed Selection, and the "Domino Effect" are associated with Gene Loss in Blattabacterium, A Cockroach Endosymbiont. Mol Biol Evol 2021; 38:3820-3831. [PMID: 34426845 PMCID: PMC8382890 DOI: 10.1093/molbev/msab159] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Intracellular endosymbionts have reduced genomes that progressively lose genes at a timescale of tens of million years. We previously reported that gene loss rate is linked to mutation rate in Blattabacterium, however, the mechanisms causing gene loss are not yet fully understood. Here, we carried out comparative genomic analyses on the complete genome sequences of a representative set of 67 Blattabacterium strains, with sizes ranging between 511 and 645 kb. We found that 200 of the 566 analyzed protein-coding genes were lost in at least one lineage of Blattabacterium, with the most extreme case being one gene that was lost independently in 24 lineages. We found evidence for three mechanisms influencing gene loss in Blattabacterium. First, gene loss rates were found to increase exponentially with the accumulation of substitutions. Second, genes involved in vitamin and amino acid metabolism experienced relaxed selection in Cryptocercus and Mastotermes, possibly triggered by their vertically inherited gut symbionts. Third, we found evidence of epistatic interactions among genes leading to a "domino effect" of gene loss within pathways. Our results highlight the complexity of the process of genome erosion in an endosymbiont.
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Affiliation(s)
- Yukihiro Kinjo
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Paula Villa Martín
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
| | - Gaku Tokuda
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Simone Pigolotti
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
| | - Thomas Bourguignon
- Okinawa Institute of Science & Technology Graduate University, Tancha, Onna-son, Okinawa, Japan
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46
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Gornik SG, Bergheim BG, Morel B, Stamatakis A, Foulkes NS, Guse A. Photoreceptor Diversification Accompanies the Evolution of Anthozoa. Mol Biol Evol 2021; 38:1744-1760. [PMID: 33226083 PMCID: PMC8097283 DOI: 10.1093/molbev/msaa304] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Anthozoan corals are an ecologically important group of cnidarians, which power the productivity of reef ecosystems. They are sessile, inhabit shallow, tropical oceans and are highly dependent on sun- and moonlight to regulate sexual reproduction, phototaxis, and photosymbiosis. However, their exposure to high levels of sunlight also imposes an increased risk of UV-induced DNA damage. How have these challenging photic environments influenced photoreceptor evolution and function in these animals? To address this question, we initially screened the cnidarian photoreceptor repertoire for Anthozoa-specific signatures by a broad-scale evolutionary analysis. We compared transcriptomic data of more than 36 cnidarian species and revealed a more diverse photoreceptor repertoire in the anthozoan subphylum than in the subphylum Medusozoa. We classified the three principle opsin classes into distinct subtypes and showed that Anthozoa retained all three classes, which diversified into at least six subtypes. In contrast, in Medusozoa, only one class with a single subtype persists. Similarly, in Anthozoa, we documented three photolyase classes and two cryptochrome (CRY) classes, whereas CRYs are entirely absent in Medusozoa. Interestingly, we also identified one anthozoan CRY class, which exhibited unique tandem duplications of the core functional domains. We next explored the functionality of anthozoan photoreceptors in the model species Exaiptasia diaphana (Aiptasia), which recapitulates key photo-behaviors of corals. We show that the diverse opsin genes are differentially expressed in important life stages common to reef-building corals and Aiptasia and that CRY expression is light regulated. We thereby provide important clues linking coral evolution with photoreceptor diversification.
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Affiliation(s)
- Sebastian G Gornik
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | | | - Benoit Morel
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Nicholas S Foulkes
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany.,Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Annika Guse
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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47
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Williams EP, Bachvaroff TR, Place AR. A Global Approach to Estimating the Abundance and Duplication of Polyketide Synthase Domains in Dinoflagellates. Evol Bioinform Online 2021; 17:11769343211031871. [PMID: 34345159 PMCID: PMC8283056 DOI: 10.1177/11769343211031871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 06/23/2021] [Indexed: 11/17/2022] Open
Abstract
Many dinoflagellate species make toxins in a myriad of different molecular configurations but the underlying chemistry in all cases is presumably via modular synthases, primarily polyketide synthases. In many organisms modular synthases occur as discrete synthetic genes or domains within a gene that act in coordination thus forming a module that produces a particular fragment of a natural product. The modules usually occur in tandem as gene clusters with a syntenic arrangement that is often predictive of the resultant structure. Dinoflagellate genomes however are notoriously complex with individual genes present in many tandem repeats and very few synthetic modules occurring as gene clusters, unlike what has been seen in bacteria and fungi. However, modular synthesis in all organisms requires a free thiol group that acts as a carrier for sequential synthesis called a thiolation domain. We scanned 47 dinoflagellate transcriptomes for 23 modular synthase domain models and compared their abundance among 10 orders of dinoflagellates as well as their co-occurrence with thiolation domains. The total count of domain types was quite large with over thirty-thousand identified, 29 000 of which were in the core dinoflagellates. Although there were no specific trends in domain abundance associated with types of toxins, there were readily observable lineage specific differences. The Gymnodiniales, makers of long polyketide toxins such as brevetoxin and karlotoxin had a high relative abundance of thiolation domains as well as multiple thiolation domains within a single transcript. Orders such as the Gonyaulacales, makers of small polyketides such as spirolides, had fewer thiolation domains but a relative increase in the number of acyl transferases. Unique to the core dinoflagellates, however, were thiolation domains occurring alongside tetratricopeptide repeats that facilitate protein-protein interactions, especially hexa and hepta-repeats, that may explain the scaffolding required for synthetic complexes capable of making large toxins. Clustering analysis for each type of domain was also used to discern possible origins of duplication for the multitude of single domain transcripts. Single domain transcripts frequently clustered with synonymous domains from multi-domain transcripts such as the BurA and ZmaK like genes as well as the multi-ketosynthase genes, sometimes with a large degree of apparent gene duplication, while fatty acid synthesis genes formed distinct clusters. Surprisingly the acyl-transferases and ketoreductases involved in fatty acid synthesis (FabD and FabG, respectively) were found in very large clusters indicating an unprecedented degree of gene duplication for these genes. These results demonstrate a complex evolutionary history of core dinoflagellate modular synthases with domain specific duplications throughout the lineage as well as clues to how large protein complexes can be assembled to synthesize the largest natural products known.
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Affiliation(s)
- Ernest P Williams
- Institute of Marine and Environmental Technologies, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Tsvetan R Bachvaroff
- Institute of Marine and Environmental Technologies, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Allen R Place
- Institute of Marine and Environmental Technologies, University of Maryland Center for Environmental Science, Baltimore, MD, USA
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48
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Abstract
The origin of plastids (chloroplasts) by endosymbiosis stands as one of the most important events in the history of eukaryotic life. The genetic, biochemical, and cell biological integration of a cyanobacterial endosymbiont into a heterotrophic host eukaryote approximately a billion years ago paved the way for the evolution of diverse algal groups in a wide range of aquatic and, eventually, terrestrial environments. Plastids have on multiple occasions also moved horizontally from eukaryote to eukaryote by secondary and tertiary endosymbiotic events. The overall picture of extant photosynthetic diversity can best be described as “patchy”: Plastid-bearing lineages are spread far and wide across the eukaryotic tree of life, nested within heterotrophic groups. The algae do not constitute a monophyletic entity, and understanding how, and how often, plastids have moved from branch to branch on the eukaryotic tree remains one of the most fundamental unsolved problems in the field of cell evolution. In this review, we provide an overview of recent advances in our understanding of the origin and spread of plastids from the perspective of comparative genomics. Recent years have seen significant improvements in genomic sampling from photosynthetic and nonphotosynthetic lineages, both of which have added important pieces to the puzzle of plastid evolution. Comparative genomics has also allowed us to better understand how endosymbionts become organelles.
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Affiliation(s)
- Shannon J Sibbald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John M Archibald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
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49
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Bucchini F, Del Cortona A, Kreft Ł, Botzki A, Van Bel M, Vandepoele K. TRAPID 2.0: a web application for taxonomic and functional analysis of de novo transcriptomes. Nucleic Acids Res 2021; 49:e101. [PMID: 34197621 PMCID: PMC8464036 DOI: 10.1093/nar/gkab565] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 06/07/2021] [Accepted: 06/16/2021] [Indexed: 12/24/2022] Open
Abstract
Advances in high-throughput sequencing have resulted in a massive increase of RNA-Seq transcriptome data. However, the promise of rapid gene expression profiling in a specific tissue, condition, unicellular organism or microbial community comes with new computational challenges. Owing to the limited availability of well-resolved reference genomes, de novo assembled (meta)transcriptomes have emerged as popular tools for investigating the gene repertoire of previously uncharacterized organisms. Yet, despite their potential, these datasets often contain fragmented or contaminant sequences, and their analysis remains difficult. To alleviate some of these challenges, we developed TRAPID 2.0, a web application for the fast and efficient processing of assembled transcriptome data. The initial processing phase performs a global characterization of the input data, providing each transcript with several layers of annotation, comprising structural, functional, and taxonomic information. The exploratory phase enables downstream analyses from the web application. Available analyses include the assessment of gene space completeness, the functional analysis and comparison of transcript subsets, and the study of transcripts in an evolutionary context. A comparison with similar tools highlights TRAPID’s unique features. Finally, analyses performed within TRAPID 2.0 are complemented by interactive data visualizations, facilitating the extraction of new biological insights, as demonstrated with diatom community metatranscriptomes.
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Affiliation(s)
- François Bucchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Andrea Del Cortona
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Łukasz Kreft
- VIB Bioinformatics Core, VIB, 9052 Ghent, Belgium
| | | | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.,Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium.,Bioinformatics Institute Ghent, Ghent University, 9052 Ghent, Belgium
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50
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Vandergrift SL, Elkins LC, Alves-de-Souza C, Leblond JD. First examination of sterols in the marine dinoflagellate genus Vulcanodinium. J Eukaryot Microbiol 2021; 68:e12863. [PMID: 34142408 DOI: 10.1111/jeu.12863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vulcanodinium is an ecologically relevant dinoflagellate genus due to its production of neurotoxins known as pinnatoxins. We present here the first examination of the sterols of a Vulcanodinium rugosum isolate. Sterols are ringed lipids that assist in maintaining rigidity of cellular membranes, and the Dinophyceae are well-studied for their ability to produce a diverse array of sterols, many of which have chemotaxonomic utility. We have determined that V. rugosum produces a set of major sterols, namely cholesterol, dinosterol, 4α,24-dimethyl-5α-cholest-22E-en-3β-ol, and 4α,24-dimethyl-5α-cholestan-3β-ol, common to the Dinophyceae. However, this displayed marked differences from those studied members of the genera Scrippsiella and Peridinium, the closest phylogenetic relatives. Included in these differences is production by V. rugosum of a much lower percentage of dinostanol, a saturated form of dinosterol.
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Affiliation(s)
- Stephanie L Vandergrift
- Ecology and Evolution Group, Middle Tennessee State University, Murfreesboro, TN, USA.,Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Lindsey C Elkins
- Ecology and Evolution Group, Middle Tennessee State University, Murfreesboro, TN, USA.,Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Catharina Alves-de-Souza
- Algal Resources Collection, MARBIONC, CREST Research Park, University of North Carolina Wilmington, Wilmington, NC, USA
| | - Jeffrey D Leblond
- Ecology and Evolution Group, Middle Tennessee State University, Murfreesboro, TN, USA.,Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
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