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Smith KF, Biessy L, Argyle PA, Trnski T, Halafihi T, Rhodes LL. Molecular Identification of Gambierdiscus and Fukuyoa (Dinophyceae) from Environmental Samples. Mar Drugs 2017; 15:md15080243. [PMID: 28767092 PMCID: PMC5577598 DOI: 10.3390/md15080243] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 07/11/2017] [Accepted: 07/28/2017] [Indexed: 12/03/2022] Open
Abstract
Ciguatera Fish Poisoning (CFP) is increasing across the Pacific and the distribution of the causative dinoflagellates appears to be expanding. Subtle differences in thecal plate morphology are used to distinguish dinoflagellate species, which are difficult to determine using light microscopy. For these reasons we sought to develop a Quantitative PCR assay that would detect all species from both Gambierdiscus and Fukuyoa genera in order to rapidly screen environmental samples for potentially toxic species. Additionally, a specific assay for F. paulensis was developed as this species is of concern in New Zealand coastal waters. Using the assays we analyzed 31 samples from three locations around New Zealand and the Kingdom of Tonga. Fourteen samples in total were positive for Gambierdiscus/Fukuyoa and two samples were also positive using the F. paulensis assay. Samples from the Kermadec Islands were further characterized using high-throughput sequencing metabarcoding. The majority of reads corresponded to Gambierdiscus species with three species identified at all sites (G. australes, G. honu and G. polynesiensis). This is the first confirmed identification of G. polynesiensis, a known ciguatoxin producer, in New Zealand waters. Other known toxin-producing genera were also detected, included Alexandrium, Amphidinium, Azadinium, Dinophysis, Ostreopsis, and Prorocentrum.
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Affiliation(s)
- Kirsty F Smith
- Coastal & Freshwater Group, Cawthron Institute, Private Bag 2, 98 Halifax Street East, Nelson 7042, New Zealand.
| | - Laura Biessy
- Coastal & Freshwater Group, Cawthron Institute, Private Bag 2, 98 Halifax Street East, Nelson 7042, New Zealand.
| | - Phoebe A Argyle
- Coastal & Freshwater Group, Cawthron Institute, Private Bag 2, 98 Halifax Street East, Nelson 7042, New Zealand.
- School of Biological Sciences, University of Canterbury, Private Bag 4800, 20 Kirkwood Avenue, Christchurch 8041, New Zealand.
| | - Tom Trnski
- Auckland War Memorial Museum, Private Bag 92018, Victoria Street West, Auckland 1142, New Zealand.
| | | | - Lesley L Rhodes
- Coastal & Freshwater Group, Cawthron Institute, Private Bag 2, 98 Halifax Street East, Nelson 7042, New Zealand.
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Price DC, Bhattacharya D. Robust Dinoflagellata phylogeny inferred from public transcriptome databases. JOURNAL OF PHYCOLOGY 2017; 53:725-729. [PMID: 28273342 DOI: 10.1111/jpy.12529] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 02/24/2017] [Indexed: 05/13/2023]
Abstract
Dinoflagellates are dominant members of the plankton and play key roles in ocean ecosystems as primary producers, predators, parasites, coral photobionts, and causative agents of algal blooms that produce toxins harmful to humans and commercial fisheries. These unicellular protists exhibit remarkable trophic and morphological diversity and include species with some of the largest reported nuclear genomes. Despite their high ecological and economic importance, comprehensive genome (or transcriptome) based dinoflagellate trees of life are few in number. To address this issue, we used recently generated public sequencing data, including from the Moore Microbial Eukaryote Transcriptome Sequencing Project, to identify dinoflagellate-specific ortholog groups. These orthologs were combined to create a broadly sampled and highly resolved phylogeny of dinoflagellates. Our results emphasize the scope and utility of public sequencing databases in creating broad and robust phylogenies for large and complex taxonomic lineages, while also providing unique insights into the evolution of thecate dinoflagellates.
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Affiliation(s)
- Dana C Price
- Department of Plant Biology, Rutgers University, New Brunswick, New Jersey, 08901, USA
| | - Debashish Bhattacharya
- Department of Ecology, Evolution and Natural Resources, Rutgers University, New Brunswick, New Jersey, 08901, USA
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Jang SH, Jeong HJ, Chon JK, Lee SY. De novo assembly and characterization of the transcriptome of the newly described dinoflagellate Ansanella granifera: Spotlight on flagellum-associated genes. Mar Genomics 2017; 33:47-55. [PMID: 28111206 DOI: 10.1016/j.margen.2017.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/11/2017] [Accepted: 01/11/2017] [Indexed: 11/15/2022]
Abstract
Many dinoflagellates are known to cause red tides and often outgrow non-motile diatoms and motile small flagellates through active vertical migration between well-lit surface and eutrophic deep waters and/or by locating and ingesting prey cells. Their flagella play important roles in these two critical behaviors. However, the structural and functional genes of dinoflagellate flagella are very little known. Thus, a de novo assembly and characterization of the transcriptome of the fast-swimming dinoflagellate Ansanella granifera were conducted and its flagellum genes were compared with those of other dinoflagellates, motile small flagellates, and non-motile protist species. Based on assembled data using Trinity/CLC combined strategy, 83,652 transcripts of A. granifera were identified. The assembled consensus sequences were annotated to the NCBI non-redundant (nr), InterProScan, Gene Ontology (GO), and KEGG pathway analyses. Moreover, 71 structural and 35 functional flagellum-associated genes expressed were identified. The number of expressed flagellar structural and functional genes of A. granifera was not markedly different from those of other dinoflagellates or motile small flagellates, but much greater than those of non-motile species. Furthermore, in both phylogenetic trees based on the outer dynein arm (ODA1, ODA9, and DLC1) and inner dynein arm (IDA4, IDA7, and BOP5) flagellum genes of dinoflagellates, the problem of the long-branch attraction artifacts of Oxyrrhis marina which has been reported in the phylogenetic trees based on ribosomal DNA was removed. Moreover, in both phylogenetic trees based on the ODA and IDA flagellum genes, the species in the order Peridiniales or Gymnodiniales were revealed to belong to a big clade of each order. Therefore, the phylogenetic tree based on the flagellum genes is likely to give a clue to resolve the problem of separation in a big clade of a dinoflagellate order which has also been reported in the phylogenetic trees based on ribosomal DNA.
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Affiliation(s)
- Se Hyeon Jang
- School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Hae Jin Jeong
- School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea; Advanced Institutes of Convergence Technology, Suwon, Gyeonggi-do 16229, Republic of Korea.
| | - Jae Kyung Chon
- Department of Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea
| | - Sung Yeon Lee
- School of Earth and Environmental Sciences, College of Natural Sciences, Seoul National University, Seoul 08826, Republic of Korea
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Verma A, Hoppenrath M, Dorantes-Aranda JJ, Harwood DT, Murray SA. Molecular and phylogenetic characterization of Ostreopsis (Dinophyceae) and the description of a new species, Ostreopsis rhodesae sp. nov., from a subtropical Australian lagoon. HARMFUL ALGAE 2016; 60:116-130. [PMID: 28073555 DOI: 10.1016/j.hal.2016.11.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 11/10/2016] [Accepted: 11/10/2016] [Indexed: 06/06/2023]
Abstract
Cryptic and pseudo-cryptic species are common amongst marine phytoplankton, and may cause misleading inferences of ecological and physiological data of plankton community studies. Deciphering the diversity and distribution of species of the benthic dinoflagellate Ostreopsis is one example, as there are many morphologically indistinct clades that differ greatly genetically and toxicologically from one another. In this study, a new species, Ostreopsis rhodesae from the southern Great Barrier Reef was described. While it initially appeared to be highly similar to several other Ostreopsis species, we found O. rhodesae can be distinguished based on the relative size of the second apical plate (2'), which is twice as long as the APC plate, and separates the third apical (3') from the third precingular (3'') plate. Phylogenetic trees based on the SSU, ITS/5.8S and D1-D2 and D8-D10 regions of the LSU rRNA were well supported, and showed a clear difference to other Ostreopsis clades. Compensatory base changes (CBCs) were identified in helices of the ITS2 between O. rhodesae and O. cf. ovata and O. cf. siamensis, which were also present in the same habitat. Fish gill cell lines were toxic to O. rhodesae, cell extracts but no palytoxin-like analogues were found in them. The findings highlight a case of pseudo-cryptic speciation, found in sympatry with closely related and morphologically similar species, but biologically and functionally distinct.
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Affiliation(s)
- Arjun Verma
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, PO Box 123, Broadway, New South Wales 2007, Australia.
| | - Mona Hoppenrath
- Senckenberg Research Institute, Senckenberg am Meer, German Center for Marine Biodiversity Research (DZMB), Südstrand 44, D-26382 Wilhelmshaven, Germany
| | - Juan José Dorantes-Aranda
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 129, Hobart, Tasmania 7001, Australia
| | - D Tim Harwood
- Cawthron Institute, 98 Halifax Street East, Private Bag 2, Nelson 7010, New Zealand
| | - Shauna A Murray
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, PO Box 123, Broadway, New South Wales 2007, Australia
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Piredda R, Tomasino MP, D'Erchia AM, Manzari C, Pesole G, Montresor M, Kooistra WHCF, Sarno D, Zingone A. Diversity and temporal patterns of planktonic protist assemblages at a Mediterranean Long Term Ecological Research site. FEMS Microbiol Ecol 2016; 93:fiw200. [DOI: 10.1093/femsec/fiw200] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2016] [Indexed: 11/13/2022] Open
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Yoon TH, Kang HE, Kang CK, Lee SH, Ahn DH, Park H, Kim HW. Development of a cost-effective metabarcoding strategy for analysis of the marine phytoplankton community. PeerJ 2016; 4:e2115. [PMID: 27326375 PMCID: PMC4911951 DOI: 10.7717/peerj.2115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 05/17/2016] [Indexed: 01/27/2023] Open
Abstract
We developed a cost-effective metabarcoding strategy to analyze phytoplankton community structure using the Illumina MiSeq system. The amplicons (404-411 bp) obtained by end-pairing of two reads were sufficiently long to distinguish algal species and provided barcode data equivalent to those generated with the Roche 454 system, but at less than 1/20th of the cost. The original universal primer sequences targeting the 23S rDNA region and the PCR strategy were both modified, and this resulted in higher numbers of eukaryotic algal sequences by excluding non-photosynthetic proteobacterial sequences supporting effectiveness of this strategy. The novel strategy was used to analyze the phytoplankton community structure of six water samples from the East/Japan Sea: surface and 50 m depths at coastal and open-sea sites, with collections in May and July 2014. In total, 345 operational taxonomic units (OTUs) were identified, which covered most of the prokaryotic and eukaryotic algal phyla, including Dinophyta, Rhodophyta, Ochrophyta, Chlorophyta, Streptophyta, Cryptophyta, Haptophyta, and Cyanophyta. This highlights the importance of plastid 23S primers, which perform better than the currently used 16S primers for phytoplankton community surveys. The findings also revealed that more efforts should be made to update 23S rDNA sequences as well as those of 16S in the databases. Analysis of algal proportions in the six samples showed that community structure differed depending on location, depth and season. Across the six samples evaluated, the numbers of OTUs in each phylum were similar but their relative proportions varied. This novel strategy would allow laboratories to analyze large numbers of samples at reasonable expense, whereas this has not been possible to date due to cost and time. In addition, we expect that this strategy will generate a large amount of novel data that could potentially change established methods and tools that are currently used in the realms of oceanography and marine ecology.
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Affiliation(s)
- Tae-Ho Yoon
- Interdiciplinary Program of Biomedical Engineering, Pukyong National University, Busan, Republic of Korea
| | - Hye-Eun Kang
- Department of Marine Biology, Pukyong National University, Busan, South Korea
| | - Chang-Keun Kang
- School of Earth Science & Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju, Republic of Korea
| | - Sang Heon Lee
- Department of Oceanography, Pusan National University, Busan, South Korea
| | - Do-Hwan Ahn
- Division of Polar Life Sciences, Korea Polar Research Institute, Incheon, South Korea
| | - Hyun Park
- Korea Polar Research Institute, Korea Ocean Research and Development Institute, Incheon, Republic of Korea
| | - Hyun-Woo Kim
- Interdiciplinary Program of Biomedical Engineering, Pukyong National University, Busan, Republic of Korea
- Department of Marine Biology, Pukyong National University, Busan, South Korea
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