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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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2
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Jinkerson RE, Russo JA, Newkirk CR, Kirk AL, Chi RJ, Martindale MQ, Grossman AR, Hatta M, Xiang T. Cnidarian-Symbiodiniaceae symbiosis establishment is independent of photosynthesis. Curr Biol 2022; 32:2402-2415.e4. [DOI: 10.1016/j.cub.2022.04.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/18/2022] [Accepted: 04/08/2022] [Indexed: 11/29/2022]
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Stephens TG, González-Pech RA, Cheng Y, Mohamed AR, Burt DW, Bhattacharya D, Ragan MA, Chan CX. Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions. BMC Biol 2020; 18:56. [PMID: 32448240 PMCID: PMC7245778 DOI: 10.1186/s12915-020-00782-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 04/20/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Dinoflagellates are taxonomically diverse and ecologically important phytoplankton that are ubiquitously present in marine and freshwater environments. Mostly photosynthetic, dinoflagellates provide the basis of aquatic primary production; most taxa are free-living, while some can form symbiotic and parasitic associations with other organisms. However, knowledge of the molecular mechanisms that underpin the adaptation of these organisms to diverse ecological niches is limited by the scarce availability of genomic data, partly due to their large genome sizes estimated up to 250 Gbp. Currently available dinoflagellate genome data are restricted to Symbiodiniaceae (particularly symbionts of reef-building corals) and parasitic lineages, from taxa that have smaller genome size ranges, while genomic information from more diverse free-living species is still lacking. RESULTS Here, we present two draft diploid genome assemblies of the free-living dinoflagellate Polarella glacialis, isolated from the Arctic and Antarctica. We found that about 68% of the genomes are composed of repetitive sequence, with long terminal repeats likely contributing to intra-species structural divergence and distinct genome sizes (3.0 and 2.7 Gbp). For each genome, guided using full-length transcriptome data, we predicted > 50,000 high-quality protein-coding genes, of which ~40% are in unidirectional gene clusters and ~25% comprise single exons. Multi-genome comparison unveiled genes specific to P. glacialis and a common, putatively bacterial origin of ice-binding domains in cold-adapted dinoflagellates. CONCLUSIONS Our results elucidate how selection acts within the context of a complex genome structure to facilitate local adaptation. Because most dinoflagellate genes are constitutively expressed, Polarella glacialis has enhanced transcriptional responses via unidirectional, tandem duplication of single-exon genes that encode functions critical to survival in cold, low-light polar environments. These genomes provide a foundational reference for future research on dinoflagellate evolution.
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Affiliation(s)
- Timothy G Stephens
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,Present Address: Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Raúl A González-Pech
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.,Present address: Department of Integrative Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Yuanyuan Cheng
- UQ Genomics Initiative, The University of Queensland, Brisbane, QLD, 4072, Australia.,Present Address: Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Amin R Mohamed
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Queensland Bioscience Precinct, Brisbane, QLD, 4067, Australia
| | - David W Burt
- UQ Genomics, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia. .,School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia. .,Australian Centre for Ecogenomics, The University of Queensland, Brisbane, QLD, 4072, Australia.
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Wu Z, Luo H, Yu L, Lee WH, Li L, Mak YL, Lin S, Lam PKS. Characterizing ciguatoxin (CTX)- and Non-CTX-producing strains of Gambierdiscus balechii using comparative transcriptomics. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 717:137184. [PMID: 32084685 DOI: 10.1016/j.scitotenv.2020.137184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/28/2020] [Accepted: 02/06/2020] [Indexed: 06/10/2023]
Abstract
Gambierdiscus spp. can produce the polyketide compound, ciguatoxin (CTX), and are hence responsible for ciguatera fish poisoning (CFP). Studying the molecular mechanism that regulates CTX production is crucial for understanding the environmental trigger of CTX as well as for better informing fishery management. Commonly, polyketide synthases are important for polyketide synthesis; however, no gene has been confirmatively assigned to CTX production. Here, suppression subtractive hybridization (SSH) and transcriptome sequencing (RNA-Seq) were used to compare a CTX-producing strain with a non-CTX-producing strain. Using both methods, a total of 52 polyketide synthase (PKS) genes were identified to be up-regulated in the CTX-producing G. balechii, including transcripts encoding single-domain PKSs as well as transcripts encoding multi-domain PKSs. Using reverse transcription quantitative PCR, the expression of these genes in the CTX-producing strain and in nitrogen-limited cultures of the strain was further documented. These data suggest that PKSs are likely involved in polyketide synthesis and potentially in CTX synthesis in this dinoflagellate species. Our study provides the candidate biomarkers for the detection of CTXs or CFP in waters or any other organisms as well as a valuable genomic resource for the research on Gambierdiscus and other dinoflagellates.
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Affiliation(s)
- Zhen Wu
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China; Department of Chemistry, City University of Hong Kong, Hong Kong, China
| | - Hao Luo
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Liying Yu
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Wai Hin Lee
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China; Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Ling Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yim Ling Mak
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China; Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China; Department of Marine Sciences, University of Connecticut, Groton, CT, USA.
| | - Paul K S Lam
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Hong Kong, China; Department of Chemistry, City University of Hong Kong, Hong Kong, China; Shenzhen Key Laboratory for the Sustainable Use of Marine Biodiversity, Research Centre for the Oceans and Human Health, City University of Hong Kong Shenzhen Research Institute, Shenzhen, China
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Akbar MA, Mohd Yusof NY, Tahir NI, Ahmad A, Usup G, Sahrani FK, Bunawan H. Biosynthesis of Saxitoxin in Marine Dinoflagellates: An Omics Perspective. Mar Drugs 2020; 18:md18020103. [PMID: 32033403 PMCID: PMC7073992 DOI: 10.3390/md18020103] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 01/09/2020] [Accepted: 01/09/2020] [Indexed: 02/07/2023] Open
Abstract
Saxitoxin is an alkaloid neurotoxin originally isolated from the clam Saxidomus giganteus in 1957. This group of neurotoxins is produced by several species of freshwater cyanobacteria and marine dinoflagellates. The saxitoxin biosynthesis pathway was described for the first time in the 1980s and, since then, it was studied in more than seven cyanobacterial genera, comprising 26 genes that form a cluster ranging from 25.7 kb to 35 kb in sequence length. Due to the complexity of the genomic landscape, saxitoxin biosynthesis in dinoflagellates remains unknown. In order to reveal and understand the dynamics of the activity in such impressive unicellular organisms with a complex genome, a strategy that can carefully engage them in a systems view is necessary. Advances in omics technology (the collective tools of biological sciences) facilitated high-throughput studies of the genome, transcriptome, proteome, and metabolome of dinoflagellates. The omics approach was utilized to address saxitoxin-producing dinoflagellates in response to environmental stresses to improve understanding of dinoflagellates gene–environment interactions. Therefore, in this review, the progress in understanding dinoflagellate saxitoxin biosynthesis using an omics approach is emphasized. Further potential applications of metabolomics and genomics to unravel novel insights into saxitoxin biosynthesis in dinoflagellates are also reviewed.
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Affiliation(s)
- Muhamad Afiq Akbar
- School of Bioscience and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia;
| | - Nurul Yuziana Mohd Yusof
- Department of Earth Science and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (N.Y.M.Y.); (F.K.S.)
| | - Noor Idayu Tahir
- Malaysian Palm Oil Board, No 6, Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia;
| | - Asmat Ahmad
- University College Sabah Foundation, Jalan Sanzac, Kota Kinabalu 88100, Sabah, Malaysia; (A.A.); (G.U.)
| | - Gires Usup
- University College Sabah Foundation, Jalan Sanzac, Kota Kinabalu 88100, Sabah, Malaysia; (A.A.); (G.U.)
| | - Fathul Karim Sahrani
- Department of Earth Science and Environment, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia; (N.Y.M.Y.); (F.K.S.)
| | - Hamidun Bunawan
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Bangi 43600, Malaysia
- Correspondence: ; Tel.: +60-389-214-546
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Hennon GMM, Dyhrman ST. Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms. HARMFUL ALGAE 2020; 91:101587. [PMID: 32057337 DOI: 10.1016/j.hal.2019.03.005] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 03/10/2019] [Indexed: 06/10/2023]
Abstract
Climate change is predicted to increase the severity and prevalence of harmful algal blooms (HABs). In the past twenty years, omics techniques such as genomics, transcriptomics, proteomics and metabolomics have transformed that data landscape of many fields including the study of HABs. Advances in technology have facilitated the creation of many publicly available omics datasets that are complementary and shed new light on the mechanisms of HAB formation and toxin production. Genomics have been used to reveal differences in toxicity and nutritional requirements, while transcriptomics and proteomics have been used to explore HAB species responses to environmental stressors, and metabolomics can reveal mechanisms of allelopathy and toxicity. In this review, we explore how omics data may be leveraged to improve predictions of how climate change will impact HAB dynamics. We also highlight important gaps in our knowledge of HAB prediction, which include swimming behaviors, microbial interactions and evolution that can be addressed by future studies with omics tools. Lastly, we discuss approaches to incorporate current omics datasets into predictive numerical models that may enhance HAB prediction in a changing world. With the ever-increasing omics databases, leveraging these data for understanding climate-driven HAB dynamics will be increasingly powerful.
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Affiliation(s)
- Gwenn M M Hennon
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States; College of Fisheries and Ocean Sciences University of Alaska Fairbanks Fairbanks, AK, United States
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, United States; Department of Earth and Environmental Sciences, Columbia University, New York, NY, United States.
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Meng FQ, Song JT, Zhou J, Cai ZH. Transcriptomic Profile and Sexual Reproduction-Relevant Genes of Alexandrium minutum in Response to Nutritional Deficiency. Front Microbiol 2019; 10:2629. [PMID: 31803162 PMCID: PMC6877688 DOI: 10.3389/fmicb.2019.02629] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 10/29/2019] [Indexed: 11/26/2022] Open
Abstract
Alexandrium minutum is a typical marine toxic dinoflagellate responsible for producing paralytic shellfish poisoning (PSP) toxins. Until now, we know little about the genomic information of A. minutum, so a transcriptome study was conducted to clarify the physiological adaptations related to nutritional deficiency. Here, we performed RNA-Seq analysis to assess the gene expression patterns of A. minutum under N and P deficient conditions for 0 (control), 6, and 72 h. Main differences between the control and experimental groups were observed in hydrolase activity and fatty acid, lipid, protein, and P metabolism. Activities of photosystem I (PSI) and PSII were significantly down-regulated, and the endocytosis pathway (clathrin-dependent endocytosis) was significantly enriched under N and P stress compared with the control, indicating that A. minutum shifts its trophy pattern under N and P stress. We also identified several unigenes related to the process of sexual reproduction, including sex determination, sperm-egg recognition, sex differentiation, mating, and fertilization. Approximately 50% of the successfully annotated unigenes were differentially expressed between the short-term stimulated sample (6 h) and control (R). However, the expression level of most unigenes returned to normal levels after 72 h, indicating that N and P stress plays a limited role in the induction of sexual reproduction. Furthermore, the quantitative real-time PCR (qRT-PCR) results of the five representative sex-related unigenes were consistent with sequencing data, which confirmed the authenticity of transcriptomic analysis. Also, qRT-PCR analysis showed that the long and short form transcripts of the saxitoxin biosynthesis gene (sxtA) were down-regulated under the nutrient deficient condition compared with the control, indicating that N and P stress regulates sxtA expression. Overall, transcriptome analysis of A. minutum revealed that N and P deficiency induced responses associated with stress response, photosynthetic efficiency, toxin biosynthesis, and sexual reproduction. Our data indicate that algae change their trophic modes (to facultative mixotrophy) and related physiological reactions under stress conditions; this possibly represents an ecological adaption strategy in the algal life cycle.
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Affiliation(s)
- Fan-Qiang Meng
- School of Life Sciences, Tsinghua University, Beijing, China.,Shenzhen Public Platform of Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jun-Ting Song
- School of Life Sciences, Tsinghua University, Beijing, China.,Shenzhen Public Platform of Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jin Zhou
- Shenzhen Public Platform of Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Zhong-Hua Cai
- Shenzhen Public Platform of Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
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Verma A, Barua A, Ruvindy R, Savela H, Ajani PA, Murray SA. The Genetic Basis of Toxin Biosynthesis in Dinoflagellates. Microorganisms 2019; 7:E222. [PMID: 31362398 PMCID: PMC6722697 DOI: 10.3390/microorganisms7080222] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 07/23/2019] [Accepted: 07/27/2019] [Indexed: 02/07/2023] Open
Abstract
In marine ecosystems, dinoflagellates can become highly abundant and even dominant at times, despite their comparatively slow growth rates. One factor that may play a role in their ecological success is the production of complex secondary metabolite compounds that can have anti-predator, allelopathic, or other toxic effects on marine organisms, and also cause seafood poisoning in humans. Our knowledge about the genes involved in toxin biosynthesis in dinoflagellates is currently limited due to the complex genomic features of these organisms. Most recently, the sequencing of dinoflagellate transcriptomes has provided us with valuable insights into the biosynthesis of polyketide and alkaloid-based toxin molecules in dinoflagellate species. This review synthesizes the recent progress that has been made in understanding the evolution, biosynthetic pathways, and gene regulation in dinoflagellates with the aid of transcriptomic and other molecular genetic tools, and provides a pathway for future studies of dinoflagellates in this exciting omics era.
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Affiliation(s)
- Arjun Verma
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia.
| | - Abanti Barua
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
- Department of Microbiology, Noakhali Science and Technology University, Chittagong 3814, Bangladesh
| | - Rendy Ruvindy
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
| | - Henna Savela
- Finnish Environment Institute, Marine Research Centre, 00790 Helsinki, Finland
| | - Penelope A Ajani
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
| | - Shauna A Murray
- Climate Change Cluster, University of Technology Sydney, Sydney 2007, Australia
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Dinoflagellate nucleus contains an extensive endomembrane network, the nuclear net. Sci Rep 2019; 9:839. [PMID: 30696854 PMCID: PMC6351617 DOI: 10.1038/s41598-018-37065-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 11/28/2018] [Indexed: 12/12/2022] Open
Abstract
Dinoflagellates are some of the most common eukaryotic cells in the ocean, but have very unusual nuclei. Many exhibit a form of closed mitosis (dinomitosis) wherein the nuclear envelope (NE) invaginates to form one or more trans-nuclear tunnels. Rather than contact spindles directly, the chromatids then bind to membrane-based kinetochores on the NE. To better understand these unique mitotic features, we reconstructed the nuclear architecture of Polykrikos kofoidii in 3D using focused ion beam scanning electron microscopy (FIB-SEM) in conjunction with high-pressure freezing, freeze-substitution, TEM, and confocal microscopy. We found that P. kofoidii possessed six nuclear tunnels, which were continuous with a reticulating network of membranes that has thus far gone unnoticed. These membranous extensions interconnect the six tunnels while ramifying throughout the nucleus to form a “nuclear net.” To our knowledge, the nuclear net is the most elaborate endomembrane structure described within a nucleus. Our findings demonstrate the utility of tomographic approaches for detecting 3D membrane networks and show that nuclear complexity has been underestimated in Polykrikos kofoidii and, potentially, in other dinoflagellates.
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Riaz S, Sui Z, Niaz Z, Khan S, Liu Y, Liu H. Distinctive Nuclear Features of Dinoflagellates with A Particular Focus on Histone and Histone-Replacement Proteins. Microorganisms 2018; 6:E128. [PMID: 30558155 PMCID: PMC6313786 DOI: 10.3390/microorganisms6040128] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 11/29/2018] [Accepted: 12/11/2018] [Indexed: 11/30/2022] Open
Abstract
Dinoflagellates are important eukaryotic microorganisms that play critical roles as producers and grazers, and cause harmful algal blooms. The unusual nuclei of dinoflagellates "dinokaryon" have led researchers to investigate their enigmatic nuclear features. Their nuclei are unusual in terms of their permanently condensed nucleosome-less chromatin, immense genome, low protein to DNA ratio, guanine-cytosine rich methylated DNA, and unique mitosis process. Furthermore, dinoflagellates are the only known group of eukaryotes that apparently lack histone proteins. Over the course of evolution, dinoflagellates have recruited other proteins, e.g., histone-like proteins (HLPs), from bacteria and dinoflagellates/viral nucleoproteins (DVNPs) from viruses as histone substitutes. Expression diversity of these nucleoproteins has greatly influenced the chromatin structure and gene expression regulation in dinoflagellates. Histone replacement proteins (HLPs and DVNPs) are hypothesized to perform a few similar roles as histone proteins do in other eukaryotes, i.e., gene expression regulation and repairing DNA. However, their role in bulk packaging of DNA is not significant as low amounts of proteins are associated with the gigantic genome. This review intends to summarize the discoveries encompassing unique nuclear features of dinoflagellates, particularly focusing on histone and histone replacement proteins. In addition, a comprehensive view of the evolution of dinoflagellate nuclei is presented.
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Affiliation(s)
- Sadaf Riaz
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
- Department of Microbiology, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan.
| | - Zhenghong Sui
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
| | - Zeeshan Niaz
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
- Department of Microbiology, Hazara University, Mansehra 21120, Pakistan.
| | - Sohrab Khan
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
- Department of Microbiology, Hazara University, Mansehra 21120, Pakistan.
| | - Yuan Liu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
| | - Haoxin Liu
- Key Laboratory of Marine Genetics and Breeding (Ocean University of China), Ministry of Education, Qingdao, 266003, China.
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Berthelier J, Casse N, Daccord N, Jamilloux V, Saint-Jean B, Carrier G. A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea. BMC Genomics 2018. [PMID: 29783941 DOI: 10.17882/52231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND Transposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. In a previous study, we compared the genetic polymorphisms between strains of the haptophyte microalga Tisochrysis lutea and suggested the involvement of active autonomous TEs in their genome evolution. RESULTS To identify potentially autonomous TEs, we designed a pipeline named PiRATE (Pipeline to Retrieve and Annotate Transposable Elements, download: https://doi.org/10.17882/51795 ), and conducted an accurate TE annotation on a new genome assembly of T. lutea. PiRATE is composed of detection, classification and annotation steps. Its detection step combines multiple, existing analysis packages representing all major approaches for TE detection and its classification step was optimized for microalgal genomes. The efficiency of the detection and classification steps was evaluated with data on the model species Arabidopsis thaliana. PiRATE detected 81% of the TE families of A. thaliana and correctly classified 75% of them. We applied PiRATE to T. lutea genomic data and established that its genome contains 15.89% Class I and 4.95% Class II TEs. In these, 3.79 and 17.05% correspond to potentially autonomous and non-autonomous TEs, respectively. Annotation data was combined with transcriptomic and proteomic data to identify potentially active autonomous TEs. We identified 17 expressed TE families and, among these, a TIR/Mariner and a TIR/hAT family were able to synthesize their transposase. Both these TE families were among the three highest expressed genes in a previous transcriptomic study and are composed of highly similar copies throughout the genome of T. lutea. This sum of evidence reveals that both these TE families could be capable of transposing or triggering the transposition of potential related MITE elements. CONCLUSION This manuscript provides an example of a de novo transposable element annotation of a non-model organism characterized by a fragmented genome assembly and belonging to a poorly studied phylum at genomic level. Integration of multi-omics data enabled the discovery of potential mobile TEs and opens the way for new discoveries on the role of these repeated elements in genomic evolution of microalgae.
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Affiliation(s)
- Jérémy Berthelier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France.
- Mer Molécules Santé, EA 2160 IUML - FR 3473 CNRS, Le Mans University, Le Mans, France.
| | - Nathalie Casse
- Mer Molécules Santé, EA 2160 IUML - FR 3473 CNRS, Le Mans University, Le Mans, France
| | - Nicolas Daccord
- Institut de Recherche en Horticulture et Semences, INRA of Angers, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d'Angers, Angers, France
- Université Bretagne Loire, Angers, France
| | | | - Bruno Saint-Jean
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
| | - Grégory Carrier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
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Berthelier J, Casse N, Daccord N, Jamilloux V, Saint-Jean B, Carrier G. A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea. BMC Genomics 2018; 19:378. [PMID: 29783941 PMCID: PMC5963040 DOI: 10.1186/s12864-018-4763-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/07/2018] [Indexed: 01/01/2023] Open
Abstract
Background Transposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. In a previous study, we compared the genetic polymorphisms between strains of the haptophyte microalga Tisochrysis lutea and suggested the involvement of active autonomous TEs in their genome evolution. Results To identify potentially autonomous TEs, we designed a pipeline named PiRATE (Pipeline to Retrieve and Annotate Transposable Elements, download: 10.17882/51795), and conducted an accurate TE annotation on a new genome assembly of T. lutea. PiRATE is composed of detection, classification and annotation steps. Its detection step combines multiple, existing analysis packages representing all major approaches for TE detection and its classification step was optimized for microalgal genomes. The efficiency of the detection and classification steps was evaluated with data on the model species Arabidopsis thaliana. PiRATE detected 81% of the TE families of A. thaliana and correctly classified 75% of them. We applied PiRATE to T. lutea genomic data and established that its genome contains 15.89% Class I and 4.95% Class II TEs. In these, 3.79 and 17.05% correspond to potentially autonomous and non-autonomous TEs, respectively. Annotation data was combined with transcriptomic and proteomic data to identify potentially active autonomous TEs. We identified 17 expressed TE families and, among these, a TIR/Mariner and a TIR/hAT family were able to synthesize their transposase. Both these TE families were among the three highest expressed genes in a previous transcriptomic study and are composed of highly similar copies throughout the genome of T. lutea. This sum of evidence reveals that both these TE families could be capable of transposing or triggering the transposition of potential related MITE elements. Conclusion This manuscript provides an example of a de novo transposable element annotation of a non-model organism characterized by a fragmented genome assembly and belonging to a poorly studied phylum at genomic level. Integration of multi-omics data enabled the discovery of potential mobile TEs and opens the way for new discoveries on the role of these repeated elements in genomic evolution of microalgae. Electronic supplementary material The online version of this article (10.1186/s12864-018-4763-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jérémy Berthelier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France. .,Mer Molécules Santé, EA 2160 IUML - FR 3473 CNRS, Le Mans University, Le Mans, France.
| | - Nathalie Casse
- Mer Molécules Santé, EA 2160 IUML - FR 3473 CNRS, Le Mans University, Le Mans, France
| | - Nicolas Daccord
- Institut de Recherche en Horticulture et Semences, INRA of Angers, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université d'Angers, Angers, France.,Université Bretagne Loire, Angers, France
| | | | - Bruno Saint-Jean
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
| | - Grégory Carrier
- IFREMER, Physiology and Biotechnology of Algae Laboratory, rue de l'Ile d'Yeu, 44311, Nantes, France
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Abstract
Viruses are integral to ecological and evolutionary processes, but we have a poor understanding of what drives variation in key traits across diverse viruses. For lytic viruses, burst size, latent period, and genome size are primary characteristics controlling host-virus dynamics. Here we synthesize data on these traits for 75 strains of phytoplankton viruses, which play an important role in global biogeochemistry. We find that primary traits of the host (genome size, growth rate) explain 40%-50% of variation in burst size and latent period. Specifically, burst size and latent period both exhibit saturating relationships versus the host∶virus genome size ratio, with both traits increasing at low genome size ratios while showing no relationship at high size ratios. In addition, latent period declines as host growth rate increases. We analyze a model of latent period evolution to explore mechanisms that could cause these patterns. The model predicts that burst size may often be set by the host genomic resources available for viral construction, while latent period evolves to permit this maximal burst size, modulated by host metabolic rate. These results suggest that general mechanisms may underlie the evolution of diverse viruses. Future extensions of this work could help explain viral regulation of host populations, viral influence on community structure and diversity, and viral roles in biogeochemical cycles.
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Assunção J, Guedes AC, Malcata FX. Biotechnological and Pharmacological Applications of Biotoxins and Other Bioactive Molecules from Dinoflagellates. Mar Drugs 2017; 15:E393. [PMID: 29261163 PMCID: PMC5742853 DOI: 10.3390/md15120393] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/12/2017] [Accepted: 12/15/2017] [Indexed: 12/26/2022] Open
Abstract
The long-lasting interest in bioactive molecules (namely toxins) produced by (microalga) dinoflagellates has risen in recent years. Exhibiting wide diversity and complexity, said compounds are well-recognized for their biological features, with great potential for use as pharmaceutical therapies and biological research probes. Unfortunately, provision of those compounds is still far from sufficient, especially in view of an increasing demand for preclinical testing. Despite the difficulties to establish dinoflagellate cultures and obtain reasonable productivities of such compounds, intensive research has permitted a number of advances in the field. This paper accordingly reviews the characteristics of some of the most important biotoxins (and other bioactive substances) produced by dinoflagellates. It also presents and discusses (to some length) the main advances pertaining to dinoflagellate production, from bench to large scale-with an emphasis on material published since the latest review available on the subject. Such advances encompass improvements in nutrient formulation and light supply as major operational conditions; they have permitted adaptation of classical designs, and aided the development of novel configurations for dinoflagellate growth-even though shearing-related issues remain a major challenge.
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Affiliation(s)
- Joana Assunção
- LEPABE-Laboratory of Process Engineering, Environment, Biotechnology and Energy, Rua Dr. Roberto Frias, s/n, P-4200-465 Porto, Portugal.
| | - A Catarina Guedes
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, s/n, P-4450-208 Matosinhos, Portugal.
| | - F Xavier Malcata
- LEPABE-Laboratory of Process Engineering, Environment, Biotechnology and Energy, Rua Dr. Roberto Frias, s/n, P-4200-465 Porto, Portugal.
- Department of Chemical Engineering, University of Porto, Rua Dr. Roberto Frias, s/n, P-4200-465 Porto, Portugal.
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15
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Brodie J, Ball SG, Bouget FY, Chan CX, De Clerck O, Cock JM, Gachon C, Grossman AR, Mock T, Raven JA, Saha M, Smith AG, Vardi A, Yoon HS, Bhattacharya D. Biotic interactions as drivers of algal origin and evolution. THE NEW PHYTOLOGIST 2017; 216:670-681. [PMID: 28857164 DOI: 10.1111/nph.14760] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/10/2017] [Indexed: 05/07/2023]
Abstract
Contents 670 I. 671 II. 671 III. 676 IV. 678 678 References 678 SUMMARY: Biotic interactions underlie life's diversity and are the lynchpin to understanding its complexity and resilience within an ecological niche. Algal biologists have embraced this paradigm, and studies building on the explosive growth in omics and cell biology methods have facilitated the in-depth analysis of nonmodel organisms and communities from a variety of ecosystems. In turn, these advances have enabled a major revision of our understanding of the origin and evolution of photosynthesis in eukaryotes, bacterial-algal interactions, control of massive algal blooms in the ocean, and the maintenance and degradation of coral reefs. Here, we review some of the most exciting developments in the field of algal biotic interactions and identify challenges for scientists in the coming years. We foresee the development of an algal knowledgebase that integrates ecosystem-wide omics data and the development of molecular tools/resources to perform functional analyses of individuals in isolation and in populations. These assets will allow us to move beyond mechanistic studies of a single species towards understanding the interactions amongst algae and other organisms in both the laboratory and the field.
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Affiliation(s)
- Juliet Brodie
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Steven G Ball
- UMR 8576 - UGSF - Unité de Glycobiologie Structurale et Fonctionnelle, Université de Lille CNRS, F 59000, Lille, France
| | - François-Yves Bouget
- Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, University Pierre et Marie Curie, University of Paris VI, CNRS, F-66650, Banyuls-sur-Mer, France
| | - Cheong Xin Chan
- Institute for Molecular Bioscience and School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Olivier De Clerck
- Phycology Research Group, Ghent University, Krijgslaan 281, S8, 9000, Gent, Belgium
| | - J Mark Cock
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, F-29688, France
| | | | - Arthur R Grossman
- Department of Plant Biology, The Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee, DD2 5DA, UK
| | - Mahasweta Saha
- Helmholtz Center for Ocean Research, Kiel, 24105, Germany
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 440-746, South Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, 08901, USA
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16
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Shi X, Ma M, Lin S. Cell Cycle-Dependent Expression Dynamics of G1/S Specific Cyclin, Cellulose Synthase and Cellulase in the Dinoflagellate Prorocentrum donghaiense. Front Microbiol 2017; 8:1118. [PMID: 28676796 PMCID: PMC5476699 DOI: 10.3389/fmicb.2017.01118] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 06/01/2017] [Indexed: 01/02/2023] Open
Abstract
Dinoflagellates undergo a typical eukaryotic cell cycle consisting of G1, S, G2, and M phases and some of the typical cell cycle related genes have been computationally identified. However, very few of these genes have been experimentally linked to the cell cycle phases. Besides, although thecate dinoflagellates are known to possess theca composed of cellulose, information on cellulose synthesis and degradation associated with the cell cycle is also limited. In this study, we isolated G1/S cyclin, cellulose synthase and cellulase encoding genes in dinoflagellate Prorocentrum donghaiense. Further, using reverse transcription quantitative PCR (RT-qPCR), we characterized the expression profiles of the three genes throughout the cell cycle. All three showed clear expression dynamics throughout the cell cycle, with fold changes of 26, 2.4 and 9.3 for G1/S cyclin, cellulose synthase and cellulase gene, respectively. The transcript abundance of G1/S cyclin increased in late G1 phase and dropped in early S phase, indicating that this protein is involved in the G1/S transition. Throughout the cell cycle, the average transcript level of cellulose synthase was 4.5-fold higher than that of cellulase. Cellulose synthase and cellulase gene expressions showed peak transcript abundances at middle G1 phase and G2M phase, respectively, indicating the respective roles of these enzymes in the growth of newly divided cells and in cytokinesis. Our results suggest that G1/S cyclin, cellulase, and cellulose synthase genes associated with G1/S transition, G2M, and G1 phases of the cell cycle and are candidates of biomarkers for assessing growth status of P. donghaiense.
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Affiliation(s)
- Xinguo Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
| | - Minglei Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen UniversityXiamen, China.,Department of Marine Sciences, University of Connecticut, GrotonCT, United States
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17
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Animal–Symbiodinium Symbioses: Foundations of Coral Reef Ecosystems. ADVANCES IN ENVIRONMENTAL MICROBIOLOGY 2016. [DOI: 10.1007/978-3-319-28068-4_10] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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18
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Beedessee G, Hisata K, Roy MC, Satoh N, Shoguchi E. Multifunctional polyketide synthase genes identified by genomic survey of the symbiotic dinoflagellate, Symbiodinium minutum. BMC Genomics 2015; 16:941. [PMID: 26573520 PMCID: PMC4647583 DOI: 10.1186/s12864-015-2195-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 11/05/2015] [Indexed: 11/17/2022] Open
Abstract
Background Dinoflagellates are unicellular marine and freshwater eukaryotes. They possess large nuclear genomes (1.5–245 gigabases) and produce structurally unique and biologically active polyketide secondary metabolites. Although polyketide biosynthesis is well studied in terrestrial and freshwater organisms, only recently have dinoflagellate polyketides been investigated. Transcriptomic analyses have characterized dinoflagellate polyketide synthase genes having single domains. The Genus Symbiodinium, with a comparatively small genome, is a group of major coral symbionts, and the S. minutum nuclear genome has been decoded. Results The present survey investigated the assembled S. minutum genome and identified 25 candidate polyketide synthase (PKS) genes that encode proteins with mono- and multifunctional domains. Predicted proteins retain functionally important amino acids in the catalytic ketosynthase (KS) domain. Molecular phylogenetic analyses of KS domains form a clade in which S. minutum domains cluster within the protist Type I PKS clade with those of other dinoflagellates and other eukaryotes. Single-domain PKS genes are likely expanded in dinoflagellate lineage. Two PKS genes of bacterial origin are found in the S. minutum genome. Interestingly, the largest enzyme is likely expressed as a hybrid non-ribosomal peptide synthetase-polyketide synthase (NRPS-PKS) assembly of 10,601 amino acids, containing NRPS and PKS modules and a thioesterase (TE) domain. We also found intron-rich genes with the minimal set of catalytic domains needed to produce polyketides. Ketosynthase (KS), acyltransferase (AT), and acyl carrier protein (ACP) along with other optional domains are present. Mapping of transcripts to the genome with the dinoflagellate-specific spliced leader sequence, supports expression of multifunctional PKS genes. Metabolite profiling of cultured S. minutum confirmed production of zooxanthellamide D, a polyhydroxy amide polyketide and other unknown polyketide secondary metabolites. Conclusion This genomic survey demonstrates that S. minutum contains genes with the minimal set of catalytic domains needed to produce polyketides and provides evidence of the modular nature of Type I PKS, unlike monofunctional Type I PKS from other dinoflagellates. In addition, our study suggests that diversification of dinoflagellate PKS genes comprises dinoflagellate-specific PKS genes with single domains, multifunctional PKS genes with KS domains orthologous to those of other protists, and PKS genes of bacterial origin. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2195-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Michael C Roy
- Imaging and Instrumental Analysis Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
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19
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Kimura K, Okuda S, Nakayama K, Shikata T, Takahashi F, Yamaguchi H, Skamoto S, Yamaguchi M, Tomaru Y. RNA Sequencing Revealed Numerous Polyketide Synthase Genes in the Harmful Dinoflagellate Karenia mikimotoi. PLoS One 2015; 10:e0142731. [PMID: 26561394 PMCID: PMC4641656 DOI: 10.1371/journal.pone.0142731] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 10/26/2015] [Indexed: 12/03/2022] Open
Abstract
The dinoflagellate Karenia mikimotoi forms blooms in the coastal waters of temperate regions and occasionally causes massive fish and invertebrate mortality. This study aimed to elucidate the toxic effect of K. mikimotoi on marine organisms by using the genomics approach; RNA-sequence libraries were constructed, and data were analyzed to identify toxin-related genes. Next-generation sequencing produced 153,406 transcript contigs from the axenic culture of K. mikimotoi. BLASTX analysis against all assembled contigs revealed that 208 contigs were polyketide synthase (PKS) sequences. Thus, K. mikimotoi was thought to have several genes encoding PKS metabolites and to likely produce toxin-like polyketide molecules. Of all the sequences, approximately 30 encoded eight PKS genes, which were remarkably similar to those of Karenia brevis. Our phylogenetic analyses showed that these genes belonged to a new group of PKS type-I genes. Phylogenetic and active domain analyses showed that the amino acid sequence of four among eight Karenia PKS genes was not similar to any of the reported PKS genes. These PKS genes might possibly be associated with the synthesis of polyketide toxins produced by Karenia species. Further, a homology search revealed 10 contigs that were similar to a toxin gene responsible for the synthesis of saxitoxin (sxtA) in the toxic dinoflagellate Alexandrium fundyense. These contigs encoded A1-A3 domains of sxtA genes. Thus, this study identified some transcripts in K. mikimotoi that might be associated with several putative toxin-related genes. The findings of this study might help understand the mechanism of toxicity of K. mikimotoi and other dinoflagellates.
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Affiliation(s)
- Kei Kimura
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, Japan
- Research Fellow of the Japan Society for the Promotion of Science, Kojimachi Business Center Building, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, Japan
| | - Shujiro Okuda
- Niigata University Graduate School of Medical and Dental Sciences, 1–757 Asahimachi-dori, Chuo-ku, Niigata, Japan
| | - Kei Nakayama
- Center for Marine Environmental Studies (CMES), Ehime University, 2–5 Bunkyo-cho, Matsuyama, Ehime, Japan
| | - Tomoyuki Shikata
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, Japan
| | - Fumio Takahashi
- Department of Biotechnology, College of Life Sciences, Rhitsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, Japan
| | - Haruo Yamaguchi
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture, Kochi University, 200, Monobe, Nankoku, Kochi, Japan
| | - Setsuko Skamoto
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, Japan
| | - Mineo Yamaguchi
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, Japan
| | - Yuji Tomaru
- National Research Institute of Fisheries and Environment of Inland Sea, Fisheries Research Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, Japan
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20
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Beligni MV, Bagnato C, Prados MB, Bondino H, Laxalt AM, Munnik T, Ten Have A. The diversity of algal phospholipase D homologs revealed by biocomputational analysis. JOURNAL OF PHYCOLOGY 2015; 51:943-962. [PMID: 26986890 DOI: 10.1111/jpy.12334] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 07/09/2015] [Indexed: 06/05/2023]
Abstract
Phospholipase D (PLD) participates in the formation of phosphatidic acid, a precursor in glycerolipid biosynthesis and a second messenger. PLDs are part of a superfamily of proteins that hydrolyze phosphodiesters and share a catalytic motif, HxKxxxxD, and hence a mechanism of action. Although HKD-PLDs have been thoroughly characterized in plants, animals and bacteria, very little is known about these enzymes in algae. To fill this gap in knowledge, we performed a biocomputational analysis by means of HMMER iterative profiling, using most eukaryotic algae genomes available. Phylogenetic analysis revealed that algae exhibit very few eukaryotic-type PLDs but possess, instead, many bacteria-like PLDs. Among algae eukaryotic-type PLDs, we identified C2-PLDs and PXPH-like PLDs. In addition, the dinoflagellate Alexandrium tamarense features several proteins phylogenetically related to oomycete PLDs. Our phylogenetic analysis also showed that algae bacteria-like PLDs (proteins with putative PLD activity) fall into five clades, three of which are novel lineages in eukaryotes, composed almost entirely of algae. Specifically, Clade II is almost exclusive to diatoms, whereas Clade I and IV are mainly represented by proteins from prasinophytes. The other two clades are composed of mitochondrial PLDs (Clade V or Mito-PLDs), previously found in mammals, and a subfamily of potentially secreted proteins (Clade III or SP-PLDs), which includes a homolog formerly characterized in rice. In addition, our phylogenetic analysis shows that algae have non-PLD members within the bacteria-like HKD superfamily with putative cardiolipin synthase and phosphatidylserine/phosphatidylglycerophosphate synthase activities. Altogether, our results show that eukaryotic algae possess a moderate number of PLDs that belong to very diverse phylogenetic groups.
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Affiliation(s)
- María Verónica Beligni
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, Mar del Plata, 7600, Argentina
| | - Carolina Bagnato
- Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Río Negro, Mitre 630. S. C. de Bariloche 8400, Río Negro, Argentina
| | - María Belén Prados
- Instituto de Energía y Desarrollo Sustentable - Comisión Nacional de Energía Atómica, Centro Atómico Bariloche, Av. Bustillo 9500, S. C. de Bariloche 8400, Río Negro, Argentina
| | - Hernán Bondino
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, Mar del Plata, 7600, Argentina
| | - Ana María Laxalt
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, Mar del Plata, 7600, Argentina
| | - Teun Munnik
- Department of Plant Physiology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, NL-1098 XH, the Netherlands
| | - Arjen Ten Have
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, CC 1245, Mar del Plata, 7600, Argentina
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21
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Mendez GS, Delwiche CF, Apt KE, Lippmeier JC. Dinoflagellate Gene Structure and Intron Splice Sites in a Genomic Tandem Array. J Eukaryot Microbiol 2015; 62:679-87. [PMID: 25963315 PMCID: PMC5032977 DOI: 10.1111/jeu.12230] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 04/06/2015] [Accepted: 04/22/2015] [Indexed: 11/24/2022]
Abstract
Dinoflagellates are one of the last major lineages of eukaryotes for which little is known about genome structure and organization. We report here the sequence and gene structure of a clone isolated from a cosmid library which, to our knowledge, represents the largest contiguously sequenced, dinoflagellate genomic, tandem gene array. These data, combined with information from a large transcriptomic library, allowed a high level of confidence of every base pair call. This degree of confidence is not possible with PCR‐based contigs. The sequence contains an intron‐rich set of five highly expressed gene repeats arranged in tandem. One of the tandem repeat gene members contains an intron 26,372 bp long. This study characterizes a splice site consensus sequence for dinoflagellate introns. Two to nine base pairs around the 3′ splice site are repeated by an identical two to nine base pairs around the 5′ splice site. The 5′ and 3′ splice sites are in the same locations within each repeat so that the repeat is found only once in the mature mRNA. This identically repeated intron boundary sequence might be useful in gene modeling and annotation of genomes.
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Affiliation(s)
- Gregory S Mendez
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, Maryland, 20742-5815
| | - Charles F Delwiche
- Department of Cell Biology and Molecular Genetics, University of Maryland College Park, College Park, Maryland, 20742-5815.,Maryland Agricultural Experiment Station, College Park, Maryland, 20742
| | - Kirk E Apt
- DSM Nutritional Products, 6480 Dobbin Rd, Columbia, Maryland, 21045
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22
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Stüken A, Riobó P, Franco J, Jakobsen KS, Guillou L, Figueroa RI. Paralytic shellfish toxin content is related to genomic sxtA4 copy number in Alexandrium minutum strains. Front Microbiol 2015; 6:404. [PMID: 25983733 PMCID: PMC4416454 DOI: 10.3389/fmicb.2015.00404] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 04/17/2015] [Indexed: 11/27/2022] Open
Abstract
Dinoflagellates are microscopic aquatic eukaryotes with huge genomes and an unusual cell regulation. For example, most genes are present in numerous copies and all copies seem to be obligatorily transcribed. The consequence of the gene copy number (CPN) for final protein synthesis is, however, not clear. One such gene is sxtA, the starting gene of paralytic shellfish toxin (PST) synthesis. PSTs are small neurotoxic compounds that can accumulate in the food chain and cause serious poisoning incidences when ingested. They are produced by dinoflagellates of the genera Alexandrium, Gymnodium, and Pyrodinium. Here we investigated if the genomic CPN of sxtA4 is related to PST content in Alexandrium minutum cells. SxtA4 is the 4th domain of the sxtA gene and its presence is essential for PST synthesis in dinoflagellates. We used PST and genome size measurements as well as quantitative PCR to analyze sxtA4 CPN and toxin content in 15 A. minutum strains. Our results show a strong positive correlation between the sxtA4 CPN and the total amount of PST produced in actively growing A. minutum cells. This correlation was independent of the toxin profile produced, as long as the strain contained the genomic domains sxtA1 and sxtA4.
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Affiliation(s)
- Anke Stüken
- Department of Biosciences, University of Oslo Oslo, Norway
| | - Pilar Riobó
- U.A. Microalgas Nocivas (Consejo Superior de Investigaciones Científicas - Instituto Español de Oceanografía), Instituto de Investigaciones Marinas Vigo, Spain
| | - José Franco
- U.A. Microalgas Nocivas (Consejo Superior de Investigaciones Científicas - Instituto Español de Oceanografía), Instituto de Investigaciones Marinas Vigo, Spain
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo Oslo, Norway
| | - Laure Guillou
- Laboratoire Adaptation et Diversité en Milieu Marin, CNRS, UMR 7144 Roscoff, France ; Sorbonne Universités - Université Pierre et Marie Curie, UMR 7144 Roscoff, France
| | - Rosa I Figueroa
- Aquatic Ecology, Lund University Lund, Sweden ; U.A. Microalgas Nocivas (Consejo Superior de Investigaciones Científicas - Instituto Español de Oceanografía), Instituto Español de Oceanografía Vigo, Spain
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Meyer JM, Rödelsperger C, Eichholz K, Tillmann U, Cembella A, McGaughran A, John U. Transcriptomic characterisation and genomic glimps into the toxigenic dinoflagellate Azadinium spinosum, with emphasis on polykeitde synthase genes. BMC Genomics 2015; 16:27. [PMID: 25612855 PMCID: PMC4316588 DOI: 10.1186/s12864-014-1205-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 12/24/2014] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Unicellular dinoflagellates are an important group of primary producers within the marine plankton community. Many of these species are capable of forming harmful algae blooms (HABs) and of producing potent phycotoxins, thereby causing deleterious impacts on their environment and posing a threat to human health. The recently discovered toxigenic dinoflagellate Azadinium spinosum is known to produce azaspiracid toxins. These toxins are most likely produced by polyketide synthases (PKS). Recently, PKS I-like transcripts have been identified in a number of dinoflagellate species. Despite the global distribution of A. spinosum, little is known about molecular features. In this study, we investigate the genomic and transcriptomic features of A. spinosum with a focus on polyketide synthesis and PKS evolution. RESULTS We identify orphan and homologous genes by comparing the transcriptome data of A. spinosum with a diverse set of 18 other dinoflagellates, five further species out of the Rhizaria Alveolate Stramelopile (RAS)-group, and one representative from the Plantae. The number of orphan genes in the analysed dinoflagellate species averaged 27%. In contrast, within the A. spinosum transcriptome, we discovered 12,661 orphan transcripts (18%). The dinoflagellates toxins known as azaspiracids (AZAs) are structurally polyethers; we therefore analyse the transcriptome of A. spinosum with respect to polyketide synthases (PKSs), the primary biosynthetic enzymes in polyketide synthesis. We find all the genes thought to be potentially essential for polyketide toxin synthesis to be expressed in A. spinosum, whose PKS transcripts fall into the dinoflagellate sub-clade in PKS evolution. CONCLUSIONS Overall, we demonstrate that the number of orphan genes in the A. spinosum genome is relatively small compared to other dinoflagellate species. In addition, all PKS domains needed to produce the azaspiracid carbon backbone are present in A. spinosum. Our study underscores the extraordinary evolution of such gene clusters and, in particular, supports the proposed structural and functional paradigm for PKS Type I genes in dinoflagellates.
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Affiliation(s)
- Jan M Meyer
- Ecological Chemistry, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany. .,Evolutionary biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
| | - Christian Rödelsperger
- Evolutionary biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
| | - Karsten Eichholz
- Ecological Chemistry, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany. .,Adenoviridae: Receptors, Trafficking and Vectorology, Institut de Génétique Moléculaire de Montpellier, Montpellier, France.
| | - Urban Tillmann
- Ecological Chemistry, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
| | - Allan Cembella
- Ecological Chemistry, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
| | - Angela McGaughran
- Evolutionary biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
| | - Uwe John
- Ecological Chemistry, Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.
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Transcriptome de novo assembly sequencing and analysis of the toxic dinoflagellate Alexandrium catenella using the Illumina platform. Gene 2014; 537:285-93. [PMID: 24440238 DOI: 10.1016/j.gene.2013.12.041] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Revised: 11/27/2013] [Accepted: 12/17/2013] [Indexed: 11/21/2022]
Abstract
In this article, high-throughput de novo transcriptomic sequencing was performed in Alexandrium catenella, which provided the first view of the gene repertoire in this dinoflagellate based on next-generation sequencing (NGS) technologies. A total of 118,304 unigenes were identified with an average length of 673bp (base pair). Of these unigenes, 77,936 (65.9%) were annotated with known proteins based on sequence similarities, among which 24,149 and 22,956 unigenes were assigned to gene ontology categories (GO) and clusters of orthologous groups (COGs), respectively. Furthermore, 16,467 unigenes were mapped onto 322 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). We also detected 1143 simple sequence repeats (SSRs), in which the tri-nucleotide repeat motif (69.3%) was the most abundant. The genetic facts and significance derived from the transcriptome dataset were suggested and discussed. All four core nucleosomal histones and linker histones were detected, in addition to the unigenes involved in histone modifications.190 unigenes were identified as being involved in the endocytosis pathway, and clathrin-dependent endocytosis was suggested to play a role in the heterotrophy of A. catenella. A conserved 22-nt spliced leader (SL) was identified in 21 unigenes which suggested the existence of trans-splicing processing of mRNA in A. catenella.
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25
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Matantseva OV, Skarlato SO. Mixotrophy in microorganisms: Ecological and cytophysiological aspects. J EVOL BIOCHEM PHYS+ 2013. [DOI: 10.1134/s0022093013040014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Mackiewicz P, Bodył A, Moszczyński K. The case of horizontal gene transfer from bacteria to the peculiar dinoflagellate plastid genome. Mob Genet Elements 2013; 3:e25845. [PMID: 24195014 PMCID: PMC3812789 DOI: 10.4161/mge.25845] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 07/14/2013] [Accepted: 07/22/2013] [Indexed: 12/19/2022] Open
Abstract
Organelle genomes lose their genes by transfer to host nuclear genomes, but only occasionally are enriched by foreign genes from other sources. In contrast to mitochondria, plastid genomes are especially resistant to such horizontal gene transfer (HGT), and thus every gene acquired in this way is notable. An exceptional case of HGT was recently recognized in the peculiar peridinin plastid genome of dinoflagellates, which is organized in plasmid-like minicircles. Genomic and phylogenetic analyses of Ceratium horridum and Pyrocystis lunula minicircles revealed four genes and one unannotated open reading frame that probably were gained from bacteria belonging to the Bacteroidetes. Such bacteria seem to be a good source of genes because close endosymbiotic associations between them and dinoflagellates have been observed. The HGT-acquired genes are involved in plastid functions characteristic of other photosynthetic eukaryotes, and their arrangement resembles bacterial operons. These studies indicate that the peridinin plastid genome, usually regarded as having resulted from reduction and fragmentation of a typical plastid genome derived from red algae, may have a chimeric origin that includes bacterial contributions. Potential contamination of the Ceratium and Pyrocystis plastid genomes by bacterial sequences and the controversial localization of their minicircles in the nucleus are also discussed.
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Affiliation(s)
- Paweł Mackiewicz
- Department of Genomics; Faculty of Biotechnology; University of Wrocław; Wrocław, Poland
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27
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Teng CY, Dang Y, Danne JC, Waller RF, Green BR. Mitochondrial Genes of Dinoflagellates Are Transcribed by a Nuclear-Encoded Single-Subunit RNA Polymerase. PLoS One 2013; 8:e65387. [PMID: 23840326 PMCID: PMC3686807 DOI: 10.1371/journal.pone.0065387] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 04/27/2013] [Indexed: 11/18/2022] Open
Abstract
Dinoflagellates are a large group of algae that contribute significantly to marine productivity and are essential photosynthetic symbionts of corals. Although these algae have fully-functioning mitochondria and chloroplasts, both their organelle genomes have been highly reduced and the genes fragmented and rearranged, with many aberrant transcripts. However, nothing is known about their RNA polymerases. We cloned and sequenced the gene for the nuclear-encoded mitochondrial polymerase (RpoTm) of the dinoflagellate Heterocapsa triquetra and showed that the protein presequence targeted a GFP construct into yeast mitochondria. The gene belongs to a small gene family, which includes a variety of 3′-truncated copies that may have originated by retroposition. The catalytic C-terminal domain of the protein shares nine conserved sequence blocks with other single-subunit polymerases and is predicted to have the same fold as the human enzyme. However, the N-terminal (promoter binding/transcription initiation) domain is not well-conserved. In conjunction with the degenerate nature of the mitochondrial genome, this suggests a requirement for novel accessory factors to ensure the accurate production of functional mRNAs.
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Affiliation(s)
- Chang Ying Teng
- Botany Department, University of British Columbia, Vancouver, B.C., Canada
- Life Sciences Department, Ludong University, Yantai, Shandong, China
| | - Yunkun Dang
- Botany Department, University of British Columbia, Vancouver, B.C., Canada
| | - Jillian C. Danne
- School of Botany, University of Melbourne, Melbourne, Victoria, Australia
| | - Ross F. Waller
- School of Botany, University of Melbourne, Melbourne, Victoria, Australia
| | - Beverley R. Green
- Botany Department, University of British Columbia, Vancouver, B.C., Canada
- * E-mail:
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28
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Eichholz K, Beszteri B, John U. Putative monofunctional type I polyketide synthase units: a dinoflagellate-specific feature? PLoS One 2012; 7:e48624. [PMID: 23139807 PMCID: PMC3489724 DOI: 10.1371/journal.pone.0048624] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 10/02/2012] [Indexed: 11/19/2022] Open
Abstract
Marine dinoflagellates (alveolata) are microalgae of which some cause harmful algal blooms and produce a broad variety of most likely polyketide synthesis derived phycotoxins. Recently, novel polyketide synthesase (PKS) transcripts have been described from the Florida red tide dinoflagellate Karenia brevis (gymnodiniales) which are evolutionarily related to Type I PKS but were apparently expressed as monofunctional proteins, a feature typical of Type II PKS. Here, we investigated expression units of PKS I-like sequences in Alexandrium ostenfeldii (gonyaulacales) and Heterocapsa triquetra (peridiniales) at the transcript and protein level. The five full length transcripts we obtained were all characterized by polyadenylation, a 3′ UTR and the dinoflagellate specific spliced leader sequence at the 5′end. Each of the five transcripts encoded a single ketoacylsynthase (KS) domain showing high similarity to K. brevis KS sequences. The monofunctional structure was also confirmed using dinoflagellate specific KS antibodies in Western Blots. In a maximum likelihood phylogenetic analysis of KS domains from diverse PKSs, dinoflagellate KSs formed a clade placed well within the protist Type I PKS clade between apicomplexa, haptophytes and chlorophytes. These findings indicate that the atypical PKS I structure, i.e., expression as putative monofunctional units, might be a dinoflagellate specific feature. In addition, the sequenced transcripts harbored a previously unknown, apparently dinoflagellate specific conserved N-terminal domain. We discuss the implications of this novel region with regard to the putative monofunctional organization of Type I PKS in dinoflagellates.
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Affiliation(s)
- Karsten Eichholz
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Bánk Beszteri
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Uwe John
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
- * E-mail:
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29
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Wada K, Kimura K, Hasegawa A, Fukuyama K, Nagasaki K. Establishment of a bacterial expression system and immunoassay platform for the major capsid protein of HcRNAV, a dinoflagellate-infecting RNA virus. Microbes Environ 2012; 27:483-9. [PMID: 23047150 PMCID: PMC4103558 DOI: 10.1264/jsme2.me12046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
HcRNAV is a small icosahedral virus that infects the shellfish-killing marine dinoflagellate Heterocapsa circularisquama, which harbors a dicistronic linear single-stranded RNA (ssRNA) genome ca. 4.4 kb in length. Its major capsid protein (MCP) gene sequence is not expressed by various strains of Escherichia coli, possibly because of a codon usage problem. To solve this problem, a chemically modified (i.e., de novo synthesized) gene was designed and cloned into the pCold-GST expression vector, and transformed into E. coli strain C41 (DE3), in which codon usage was universally optimized to efficiently express the polypeptide having the viral MCP amino acid sequence. The bacterially expressed protein, which was purified after a procedure involving denaturation and refolding, successfully formed virus-like particles that significantly resembled native HcRNAV particles. The purified, denatured protein was used as an antigen to immunize rabbits, and the resulting antiserum was shown to be strongly reactive to not only the bacterially expressed recombinant protein, but also to native HcRNAV MCP by Western blotting and dot immunoassays, respectively. These results indicate that an antiserum recognizing native HcRNAV MCP was successfully obtained using bacterially expressed HcRNAV MCP as the antigen.
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Affiliation(s)
- Kei Wada
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560–0043, Japan
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30
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Coelho SM, Simon N, Ahmed S, Cock JM, Partensky F. Ecological and evolutionary genomics of marine photosynthetic organisms. Mol Ecol 2012; 22:867-907. [PMID: 22989289 DOI: 10.1111/mec.12000] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/10/2012] [Accepted: 07/15/2012] [Indexed: 01/05/2023]
Abstract
Environmental (ecological) genomics aims to understand the genetic basis of relationships between organisms and their abiotic and biotic environments. It is a rapidly progressing field of research largely due to recent advances in the speed and volume of genomic data being produced by next generation sequencing (NGS) technologies. Building on information generated by NGS-based approaches, functional genomic methodologies are being applied to identify and characterize genes and gene systems of both environmental and evolutionary relevance. Marine photosynthetic organisms (MPOs) were poorly represented amongst the early genomic models, but this situation is changing rapidly. Here we provide an overview of the recent advances in the application of ecological genomic approaches to both prokaryotic and eukaryotic MPOs. We describe how these approaches are being used to explore the biology and ecology of marine cyanobacteria and algae, particularly with regard to their functions in a broad range of marine ecosystems. Specifically, we review the ecological and evolutionary insights gained from whole genome and transcriptome sequencing projects applied to MPOs and illustrate how their genomes are yielding information on the specific features of these organisms.
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Affiliation(s)
- Susana M Coelho
- UPMC-Université Paris 06, Station Biologique de Roscoff, Roscoff, France.
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31
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Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic. Proc Natl Acad Sci U S A 2012; 109:15793-8. [PMID: 23019363 DOI: 10.1073/pnas.1206683109] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dinoflagellates are an important component of the marine biota, but a large genome with high-copy number (up to 5,000) tandem gene arrays has made genomic sequencing problematic. More importantly, little is known about the expression and conservation of these unusual gene arrays. We assembled de novo a gene catalog of 74,655 contigs for the dinoflagellate Lingulodinium polyedrum from RNA-Seq (Illumina) reads. The catalog contains 93% of a Lingulodinium EST dataset deposited in GenBank and 94% of the enzymes in 16 primary metabolic KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, indicating it is a good representation of the transcriptome. Analysis of the catalog shows a marked underrepresentation of DNA-binding proteins and DNA-binding domains compared with other algae. Despite this, we found no evidence to support the proposal of polycistronic transcription, including a marked underrepresentation of sequences corresponding to the intergenic spacers of two tandem array genes. We also have used RNA-Seq to assess the degree of sequence conservation in tandem array genes and found their transcripts to be highly conserved. Interestingly, some of the sequences in the catalog have only bacterial homologs and are potential candidates for horizontal gene transfer. These presumably were transferred as single-copy genes, and because they are now all GC-rich, any derived from AT-rich contexts must have experienced extensive mutation. Our study not only has provided the most complete dinoflagellate gene catalog known to date, it has also exploited RNA-Seq to address fundamental issues in basic transcription mechanisms and sequence conservation in these algae.
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32
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Gallardo-Rodríguez J, Sánchez-Mirón A, García-Camacho F, López-Rosales L, Chisti Y, Molina-Grima E. Bioactives from microalgal dinoflagellates. Biotechnol Adv 2012; 30:1673-84. [PMID: 22884890 DOI: 10.1016/j.biotechadv.2012.07.005] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 07/27/2012] [Accepted: 07/29/2012] [Indexed: 01/12/2023]
Abstract
Dinoflagellate microalgae are an important source of marine biotoxins. Bioactives from dinoflagellates are attracting increasing attention because of their impact on the safety of seafood and potential uses in biomedical, toxicological and pharmacological research. Here we review the potential applications of dinoflagellate toxins and the methods for producing them. Only sparing quantities of dinoflagellate toxins are generally available and this hinders bioactivity characterization and evaluation in possible applications. Approaches to production of increased quantities of dinoflagellate bioactives are discussed. Although many dinoflagellates are fragile and grow slowly, controlled culture in bioreactors appears to be generally suitable for producing many of the metabolites of interest.
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33
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Jaeckisch N, Yang I, Wohlrab S, Glöckner G, Kroymann J, Vogel H, Cembella A, John U. Comparative genomic and transcriptomic characterization of the toxigenic marine dinoflagellate Alexandrium ostenfeldii. PLoS One 2011; 6:e28012. [PMID: 22164224 PMCID: PMC3229502 DOI: 10.1371/journal.pone.0028012] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Accepted: 10/29/2011] [Indexed: 01/09/2023] Open
Abstract
Many dinoflagellate species are notorious for the toxins they produce and ecological and human health consequences associated with harmful algal blooms (HABs). Dinoflagellates are particularly refractory to genomic analysis due to the enormous genome size, lack of knowledge about their DNA composition and structure, and peculiarities of gene regulation, such as spliced leader (SL) trans-splicing and mRNA transposition mechanisms. Alexandrium ostenfeldii is known to produce macrocyclic imine toxins, described as spirolides. We characterized the genome of A. ostenfeldii using a combination of transcriptomic data and random genomic clones for comparison with other dinoflagellates, particularly Alexandrium species. Examination of SL sequences revealed similar features as in other dinoflagellates, including Alexandrium species. SL sequences in decay indicate frequent retro-transposition of mRNA species. This probably contributes to overall genome complexity by generating additional gene copies. Sequencing of several thousand fosmid and bacterial artificial chromosome (BAC) ends yielded a wealth of simple repeats and tandemly repeated longer sequence stretches which we estimated to comprise more than half of the whole genome. Surprisingly, the repeats comprise a very limited set of 79–97 bp sequences; in part the genome is thus a relatively uniform sequence space interrupted by coding sequences. Our genomic sequence survey (GSS) represents the largest genomic data set of a dinoflagellate to date. Alexandrium ostenfeldii is a typical dinoflagellate with respect to its transcriptome and mRNA transposition but demonstrates Alexandrium-like stop codon usage. The large portion of repetitive sequences and the organization within the genome is in agreement with several other studies on dinoflagellates using different approaches. It remains to be determined whether this unusual composition is directly correlated to the exceptionally genome organization of dinoflagellates with a low amount of histones and histone-like proteins.
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Affiliation(s)
- Nina Jaeckisch
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
- * E-mail: (NJ); (UJ)
| | - Ines Yang
- Medizinische Hochschule Hannover, Institut für Medizinische Mikrobiologie und Krankenhaushygiene, Hannover, Germany
| | - Sylke Wohlrab
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Gernot Glöckner
- Berlin Center for Genomics in Biodiversity Research, Berlin, Germany
- Institute for Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Juergen Kroymann
- Université Paris-Sud/CNRS, Laboratoire d'Ecologie, Systématique et Evolution, Orsay, France
| | - Heiko Vogel
- Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Allan Cembella
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
| | - Uwe John
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany
- * E-mail: (NJ); (UJ)
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34
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Moszczynski K, Mackiewicz P, Bodyl A. Evidence for horizontal gene transfer from bacteroidetes bacteria to dinoflagellate minicircles. Mol Biol Evol 2011; 29:887-92. [PMID: 22075114 DOI: 10.1093/molbev/msr276] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Dinoflagellate protists harbor a characteristic peridinin-containing plastid that evolved from a red or haptophyte alga. In contrast to typical plastids that have ∼100-200 kb circular genomes, the dinoflagellate plastid genome is composed of minicircles that each encode 0-5 genes. It is commonly assumed that dinoflagellate minicircles are derived from a standard plastid genome through drastic reduction and fragmentation. However, we demonstrate that the ycf16 and ycf24 genes (encoded on the Ceratium AF490364 minicircle), as well as rpl28 and rpl33 (encoded on the Pyrocystis AF490367 minicircle), are related to sequences from Algoriphagus and/or Cytophaga bacteria belonging to the Bacteroidetes clade. Moreover, we identified a new open reading frame on the Pyrocystis minicircle encoding a SRP54 N domain, which is typical of FtsY proteins. Because neither of these minicircles share sequence similarity with any other dinoflagellate minicircles, and their genes resemble bacterial operons, we propose that these Ceratium and Pyrocystis minicircles resulted from a horizontal gene transfer (HGT) from a Bacteroidetes donor. Our findings are the first indication of HGT to dinoflagellate minicircles, highlighting yet another peculiar aspect of this plastid genome.
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Affiliation(s)
- Krzysztof Moszczynski
- Faculty of Humanities and Social Sciences, Warsaw School of Social Sciences and Humanities (SWPS), Campus in Wrocław, Wrocław, Poland
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35
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Affiliation(s)
| | - Jeremiah D. Hackett
- Ecology and Evolutionary Biology Department, University of Arizona, Tucson, Arizona 85721;
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36
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Lin S. Genomic understanding of dinoflagellates. Res Microbiol 2011; 162:551-69. [PMID: 21514379 DOI: 10.1016/j.resmic.2011.04.006] [Citation(s) in RCA: 185] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 03/02/2011] [Indexed: 10/18/2022]
Abstract
The phylum of dinoflagellates is characterized by many unusual and interesting genomic and physiological features, the imprint of which, in its immense genome, remains elusive. Much novel understanding has been achieved in the last decade on various aspects of dinoflagellate biology, but most remarkably about the structure, expression pattern and epigenetic modification of protein-coding genes in the nuclear and organellar genomes. Major findings include: 1) the great diversity of dinoflagellates, especially at the base of the dinoflagellate tree of life; 2) mini-circularization of the genomes of typical dinoflagellate plastids (with three membranes, chlorophylls a, c1 and c2, and carotenoid peridinin), the scrambled mitochondrial genome and the extensive mRNA editing occurring in both systems; 3) ubiquitous spliced leader trans-splicing of nuclear-encoded mRNA and demonstrated potential as a novel tool for studying dinoflagellate transcriptomes in mixed cultures and natural assemblages; 4) existence and expression of histones and other nucleosomal proteins; 5) a ribosomal protein set expected of typical eukaryotes; 6) genetic potential of non-photosynthetic solar energy utilization via proton-pump rhodopsin; 7) gene candidates in the toxin synthesis pathways; and 8) evidence of a highly redundant, high gene number and highly recombined genome. Despite this progress, much more work awaits genome-wide transcriptome and whole genome sequencing in order to unfold the molecular mechanisms underlying the numerous mysterious attributes of dinoflagellates.
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Affiliation(s)
- Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA.
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Analysis of Codon Usage Patterns in Toxic Dinoflagellate Alexandrium tamarense through Expressed Sequence Tag Data. Comp Funct Genomics 2010; 2010:138538. [PMID: 21052492 PMCID: PMC2967832 DOI: 10.1155/2010/138538] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2010] [Accepted: 10/01/2010] [Indexed: 11/29/2022] Open
Abstract
We have analyzed synonymous codon usage in the genome of A. tamarense CCMP 1598 for protein-coding sequences from 10865 expressed sequence tags (ESTs). We reconstructed a total of 4284 unigenes, including 74 ribosomal protein and 40 plastid-related genes, from ESTs using FrameDP, an open reading frame (ORF) prediction program. Correspondence analysis of A. tamarense genes based on codon usage showed that the GC content at the third base of synonymous codons (GC3s) was strongly correlated with the first axis (r = 0.93 with P < .001). On the other hand, the second axis discriminated between presumed highly and low expressed genes, with expression levels being confirmed by the analysis of EST frequencies (r = −0.89 with P < .001). Our results suggest that mutational bias is the major factor in shaping codon usage in A. tamarense genome, but other factors, namely, translational selection, hydropathy, and aromaticity, also appear to influence the selection of codon usage in this species.
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Clayton C, Michaeli S. 3' processing in protists. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:247-55. [PMID: 21957009 DOI: 10.1002/wrna.49] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Molecular biologists have traditionally focused on the very small corner of eukaryotic evolution that includes yeast and animals; even plants have been neglected. In this article, we describe the scant information that is available concerning RNA processing in the other four major eukaryotic groups, especially pathogenic protists. We focus mainly on polyadenylation and nuclear processing of stable RNAs. These processes have--where examined--been shown to be conserved, but there are many novel details. We also briefly mention other processing reactions such as splicing.
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Affiliation(s)
- Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, Heidelberg, Germany.
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Yang I, John U, Beszteri S, Glöckner G, Krock B, Goesmann A, Cembella AD. Comparative gene expression in toxic versus non-toxic strains of the marine dinoflagellate Alexandrium minutum. BMC Genomics 2010; 11:248. [PMID: 20403159 PMCID: PMC2874808 DOI: 10.1186/1471-2164-11-248] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 04/19/2010] [Indexed: 12/05/2022] Open
Abstract
Background The dinoflagellate Alexandrium minutum typically produces paralytic shellfish poisoning (PSP) toxins, which are known only from cyanobacteria and dinoflagellates. While a PSP toxin gene cluster has recently been characterized in cyanobacteria, the genetic background of PSP toxin production in dinoflagellates remains elusive. Results We constructed and analysed an expressed sequence tag (EST) library of A. minutum, which contained 15,703 read sequences yielding a total of 4,320 unique expressed clusters. Of these clusters, 72% combined the forward-and reverse reads of at least one bacterial clone. This sequence resource was then used to construct an oligonucleotide microarray. We analysed the expression of all clusters in three different strains. While the cyanobacterial PSP toxin genes were not found among the A. minutum sequences, 192 genes were differentially expressed between toxic and non-toxic strains. Conclusions Based on this study and on the lack of identified PSP synthesis genes in the two existent Alexandrium tamarense EST libraries, we propose that the PSP toxin genes in dinoflagellates might be more different from their cyanobacterial counterparts than would be expected in the case of a recent gene transfer. As a starting point to identify possible PSP toxin-associated genes in dinoflagellates without relying on a priori sequence information, the sequences only present in mRNA pools of the toxic strain can be seen as putative candidates involved in toxin synthesis and regulation, or acclimation to intracellular PSP toxins.
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Affiliation(s)
- Ines Yang
- Alfred-Wegener-Institut für Polar-und Meeresforschung, Bremerhaven, Germany
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Hou Y, Lin S. Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes. PLoS One 2009; 4:e6978. [PMID: 19750009 PMCID: PMC2737104 DOI: 10.1371/journal.pone.0006978] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Accepted: 08/14/2009] [Indexed: 11/18/2022] Open
Abstract
The ability to predict gene content is highly desirable for characterization of not-yet sequenced genomes like those of dinoflagellates. Using data from completely sequenced and annotated genomes from phylogenetically diverse lineages, we investigated the relationship between gene content and genome size using regression analyses. Distinct relationships between log(10)-transformed protein-coding gene number (Y') versus log(10)-transformed genome size (X', genome size in kbp) were found for eukaryotes and non-eukaryotes. Eukaryotes best fit a logarithmic model, Y' = ln(-46.200+22.678X', whereas non-eukaryotes a linear model, Y' = 0.045+0.977X', both with high significance (p<0.001, R(2)>0.91). Total gene number shows similar trends in both groups to their respective protein coding regressions. The distinct correlations reflect lower and decreasing gene-coding percentages as genome size increases in eukaryotes (82%-1%) compared to higher and relatively stable percentages in prokaryotes and viruses (97%-47%). The eukaryotic regression models project that the smallest dinoflagellate genome (3x10(6) kbp) contains 38,188 protein-coding (40,086 total) genes and the largest (245x10(6) kbp) 87,688 protein-coding (92,013 total) genes, corresponding to 1.8% and 0.05% gene-coding percentages. These estimates do not likely represent extraordinarily high functional diversity of the encoded proteome but rather highly redundant genomes as evidenced by high gene copy numbers documented for various dinoflagellate species.
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Affiliation(s)
- Yubo Hou
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, Connecticut, United States of America
- * E-mail:
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Cascades of convergent evolution: the corresponding evolutionary histories of euglenozoans and dinoflagellates. Proc Natl Acad Sci U S A 2009; 106 Suppl 1:9963-70. [PMID: 19528647 DOI: 10.1073/pnas.0901004106] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The majority of eukaryotic diversity is hidden in protists, yet our current knowledge of processes and structures in the eukaryotic cell is almost exclusively derived from multicellular organisms. The increasing sensitivity of molecular methods and growing interest in microeukaryotes has only recently demonstrated that many features so far considered to be universal for eukaryotes actually exist in strikingly different versions. In other words, during their long evolutionary histories, protists have solved general biological problems in many more ways than previously appreciated. Interestingly, some groups have broken more rules than others, and the Euglenozoa and the Alveolata stand out in this respect. A review of the numerous odd features in these 2 groups allows us to draw attention to the high level of convergent evolution in protists, which perhaps reflects the limits that certain features can be altered. Moreover, the appearance of one deviation in an ancestor can constrain the set of possible downstream deviations in its descendents, so features that might be independent functionally, can still be evolutionarily linked. What functional advantage may be conferred by the excessive complexity of euglenozoan and alveolate gene expression, organellar genome structure, and RNA editing and processing has been thoroughly debated, but we suggest these are more likely the products of constructive neutral evolution, and as such do not necessarily confer any selective advantage at all.
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