1
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Orr RJS, Littner E, Larigauderie G, Lonsdale CL, Dybwad M. Complete reference genome assemblies and annotations of three Escherichia coli MRE162 clones. Microbiol Resour Announc 2023; 12:e0049023. [PMID: 37811945 PMCID: PMC10652920 DOI: 10.1128/mra.00490-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/31/2023] [Indexed: 10/10/2023] Open
Abstract
Escherichia coli MRE162 was originally isolated from a toilet pan in 1949 and since been utilized in numerous studies. Here, we sequence, assemble, and annotate clones held at three laboratories providing reference-level assemblies. We show the uniqueness of MRE162 to strains in open databases and make the UK clone publically available.
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Affiliation(s)
- Russell J. S. Orr
- Total Defence, Norwegian Defence Research Establishment (FFI), Kjeller, Norway
| | - Eloi Littner
- Division Biologie, DGA Maîtrise NRBC, Vert-le-Petit, France
| | | | | | - Marius Dybwad
- Total Defence, Norwegian Defence Research Establishment (FFI), Kjeller, Norway
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2
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Orr RJS, Brynildsrud OB, Abdelli M, Ramisse V, Dybwad M. Reference genome assembly and annotation of two Bacillus cereus sensu lato strains from Etosha National Park, Namibia. Microbiol Resour Announc 2023; 12:e0054423. [PMID: 37855617 PMCID: PMC10652954 DOI: 10.1128/mra.00544-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 09/21/2023] [Indexed: 10/20/2023] Open
Abstract
Bacillus cereus sensu lato (s.l.) poses health and security issues. Here, we report the reference genome assembly of two Bacillus cereus s.l. strains, isolated from Etosha National Park, Namibia (FFI_BCgr36 and FFI_BCgr46). These unique genomes open for better understanding of environmental diversity and improvements in detection of threatening species.
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Affiliation(s)
- Russell J. S. Orr
- Total Defence Division, Norwegian Defence Research Establishment FFI, Kjeller, Norway
| | - Ola B. Brynildsrud
- Total Defence Division, Norwegian Defence Research Establishment FFI, Kjeller, Norway
| | - Mehdi Abdelli
- Division Biologie, DGA Maîtrise NRBC, Vert-le-Petit, France
| | | | - Marius Dybwad
- Total Defence Division, Norwegian Defence Research Establishment FFI, Kjeller, Norway
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3
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Orr RJS, Di Martino E, Ramsfjell MH, Gordon DP, Berning B, Chowdhury I, Craig S, Cumming RL, Figuerola B, Florence W, Harmelin JG, Hirose M, Huang D, Jain SS, Jenkins HL, Kotenko ON, Kuklinski P, Lee HE, Madurell T, McCann L, Mello HL, Obst M, Ostrovsky AN, Paulay G, Porter JS, Shunatova NN, Smith AM, Souto-Derungs J, Vieira LM, Voje KL, Waeschenbach A, Zágoršek K, Warnock RCM, Liow LH. Paleozoic origins of cheilostome bryozoans and their parental care inferred by a new genome-skimmed phylogeny. Sci Adv 2022; 8:eabm7452. [PMID: 35353568 PMCID: PMC8967238 DOI: 10.1126/sciadv.abm7452] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Phylogenetic relationships and the timing of evolutionary events are essential for understanding evolution on longer time scales. Cheilostome bryozoans are a group of ubiquitous, species-rich, marine colonial organisms with an excellent fossil record but lack phylogenetic relationships inferred from molecular data. We present genome-skimmed data for 395 cheilostomes and combine these with 315 published sequences to infer relationships and the timing of key events among c. 500 cheilostome species. We find that named cheilostome genera and species are phylogenetically coherent, rendering fossil or contemporary specimens readily delimited using only skeletal morphology. Our phylogeny shows that parental care in the form of brooding evolved several times independently but was never lost in cheilostomes. Our fossil calibration, robust to varied assumptions, indicates that the cheilostome lineage and parental care therein could have Paleozoic origins, much older than the first known fossil record of cheilostomes in the Late Jurassic.
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Affiliation(s)
| | | | | | - Dennis P. Gordon
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Björn Berning
- Geoscience Collections, Oberösterreichische Landes-Kultur GmbH, Linz, Austria
| | - Ismael Chowdhury
- Department of Biological Sciences, Humboldt State University, Arcata, CA, USA
| | - Sean Craig
- Department of Biological Sciences, Humboldt State University, Arcata, CA, USA
| | | | | | - Wayne Florence
- Department of Research and Exhibitions, Iziko Museums of South Africa, Cape Town, South Africa
| | - Jean-Georges Harmelin
- Station marine d’Endoume, OSU Pytheas, MIO, GIS Posidonie, Université Aix-Marseille, Marseille, France
| | - Masato Hirose
- School of Marine Biosciences, Kitasato University, Kanagawa, Japan
| | - Danwei Huang
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Sudhanshi S. Jain
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Helen L. Jenkins
- Marine Biological Association of the UK, Plymouth, UK
- Natural History Museum, London, UK
| | - Olga N. Kotenko
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Piotr Kuklinski
- Institute of Oceanology, Polish Academy of Sciences, Sopot, Poland
| | - Hannah E. Lee
- Department of Biological Sciences, Humboldt State University, Arcata, CA, USA
| | | | - Linda McCann
- Smithsonian Environmental Research Center, TIburon, CA, USA
| | | | - Matthias Obst
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Andrew N. Ostrovsky
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
- Department of Palaeontology, Faculty of Earth Sciences, Geography and Astronomy, University of Vienna, Vienna, Austria
| | - Gustav Paulay
- Florida Museum of Natural History, Gainesville, FL, USA
| | - Joanne S. Porter
- International Centre for Island Technology, Heriot-Watt University, Stromness, UK
| | - Natalia N. Shunatova
- Department of Invertebrate Zoology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Javier Souto-Derungs
- Department of Palaeontology, Faculty of Earth Sciences, Geography and Astronomy, University of Vienna, Vienna, Austria
| | - Leandro M. Vieira
- Natural History Museum, London, UK
- Department of Zoology, Universidade Federal de Pernambuco, Recife, Brazil
| | - Kjetil L. Voje
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Kamil Zágoršek
- Department of Geography, Technical University of Liberec, Liberec, Czech Republic
| | - Rachel C. M. Warnock
- GeoZentrum Nordbayern, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Lee Hsiang Liow
- Natural History Museum, University of Oslo, Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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4
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Orr RJS, Di Martino E, Gordon DP, Ramsfjell MH, Mello HL, Smith AM, Liow LH. A broadly resolved molecular phylogeny of New Zealand cheilostome bryozoans as a framework for hypotheses of morphological evolution. Mol Phylogenet Evol 2021; 161:107172. [PMID: 33813020 DOI: 10.1016/j.ympev.2021.107172] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/04/2021] [Accepted: 03/29/2021] [Indexed: 10/21/2022]
Abstract
Larger molecular phylogenies based on ever more genes are becoming commonplace with the advent of cheaper and more streamlined sequencing and bioinformatics pipelines. However, many groups of inconspicuous but no less evolutionarily or ecologically important marine invertebrates are still neglected in the quest for understanding species- and higher-level phylogenetic relationships. Here, we alleviate this issue by presenting the molecular sequences of 165 cheilostome bryozoan species from New Zealand waters. New Zealand is our geographic region of choice as its cheilostome fauna is taxonomically, functionally and ecologically diverse, and better characterized than many other such faunas in the world. Using this most taxonomically broadly-sampled and statistically-supported cheilostome phylogeny comprising 214 species, when including previously published sequences, and 17 genes (2 nuclear and 15 mitochondrial) we tested several existing systematic hypotheses based solely on morphological observations. We find that lower taxonomic level hypotheses (species and genera) are robust while our inferred trees did not reflect current higher-level systematics (family and above), illustrating a general need for the rethinking of current hypotheses. To illustrate the utility of our new phylogeny, we reconstruct the evolutionary history of frontal shields (i.e., a calcified body-wall layer in ascus-bearing cheilostomes) and ask if its presence has any bearing on the diversification rates of cheilostomes.
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Affiliation(s)
- R J S Orr
- Natural History Museum, University of Oslo, Oslo, Norway.
| | - E Di Martino
- Natural History Museum, University of Oslo, Oslo, Norway
| | - D P Gordon
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - M H Ramsfjell
- Natural History Museum, University of Oslo, Oslo, Norway
| | - H L Mello
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - A M Smith
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - L H Liow
- Natural History Museum, University of Oslo, Oslo, Norway; Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.
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5
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Orr RJS, Sannum MM, Boessenkool S, Di Martino E, Gordon DP, Mello HL, Obst M, Ramsfjell MH, Smith AM, Liow LH. A molecular phylogeny of historical and contemporary specimens of an under-studied micro-invertebrate group. Ecol Evol 2021; 11:309-320. [PMID: 33437431 PMCID: PMC7790615 DOI: 10.1002/ece3.7042] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/08/2020] [Accepted: 10/28/2020] [Indexed: 11/06/2022] Open
Abstract
Resolution of relationships at lower taxonomic levels is crucial for answering many evolutionary questions, and as such, sufficiently varied species representation is vital. This latter goal is not always achievable with relatively fresh samples. To alleviate the difficulties in procuring rarer taxa, we have seen increasing utilization of historical specimens in building molecular phylogenies using high throughput sequencing. This effort, however, has mainly focused on large-bodied or well-studied groups, with small-bodied and under-studied taxa under-prioritized. Here, we utilize both historical and contemporary specimens, to increase the resolution of phylogenetic relationships among a group of under-studied and small-bodied metazoans, namely, cheilostome bryozoans. In this study, we pioneer the sequencing of air-dried cheilostomes, utilizing a recently developed library preparation method for low DNA input. We evaluate a de novo mitogenome assembly and two iterative methods, using the sequenced target specimen as a reference for mapping, for our sequences. In doing so, we present mitochondrial and ribosomal RNA sequences of 43 cheilostomes representing 37 species, including 14 from historical samples ranging from 50 to 149 years old. The inferred phylogenetic relationships of these samples, analyzed together with publicly available sequence data, are shown in a statistically well-supported 65 taxa and 17 genes cheilostome tree, which is also the most broadly sampled and largest to date. The robust phylogenetic placement of historical samples whose contemporary conspecifics and/or congenerics have been sequenced verifies the appropriateness of our workflow and gives confidence in the phylogenetic placement of those historical samples for which there are no close relatives sequenced. The success of our workflow is highlighted by the circularization of a total of 27 mitogenomes, seven from historical cheilostome samples. Our study highlights the potential of utilizing DNA from micro-invertebrate specimens stored in natural history collections for resolving phylogenetic relationships among species.
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Affiliation(s)
| | | | - Sanne Boessenkool
- Department of BiosciencesCentre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
| | | | - Dennis P. Gordon
- National Institute of Water and Atmospheric ResearchWellingtonNew Zealand
| | - Hannah L. Mello
- Department of Marine ScienceUniversity of OtagoDunedinNew Zealand
| | - Matthias Obst
- Department of Marine SciencesUniversity of GothenburgGothenburgSweden
| | | | - Abigail M. Smith
- Department of Marine ScienceUniversity of OtagoDunedinNew Zealand
| | - Lee Hsiang Liow
- Natural History MuseumUniversity of OsloOsloNorway
- Department of BiosciencesCentre for Ecological and Evolutionary SynthesisUniversity of OsloOsloNorway
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Nilsson P, Solbakken MH, Schmid BV, Orr RJS, Lv R, Cui Y, Song Y, Zhang Y, Baalsrud HT, Tørresen OK, Stenseth NC, Yang R, Jakobsen KS, Easterday WR, Jentoft S. The Genome of the Great Gerbil Reveals Species-Specific Duplication of an MHCII Gene. Genome Biol Evol 2020; 12:3832-3849. [PMID: 31971556 PMCID: PMC7046166 DOI: 10.1093/gbe/evaa008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2020] [Indexed: 12/13/2022] Open
Abstract
The great gerbil (Rhombomys opimus) is a social rodent living in permanent, complex burrow systems distributed throughout Central Asia, where it serves as the main host of several important vector-borne infectious pathogens including the well-known plague bacterium (Yersinia pestis). Here, we present a continuous annotated genome assembly of the great gerbil, covering over 96% of the estimated 2.47-Gb genome. Taking advantage of the recent genome assemblies of the sand rat (Psammomys obesus) and the Mongolian gerbil (Meriones unguiculatus), comparative immunogenomic analyses reveal shared gene losses within TLR gene families (i.e., TLR8, TLR10, and the entire TLR11-subfamily) for Gerbillinae, accompanied with signs of diversifying selection of TLR7 and TLR9. Most notably, we find a great gerbil-specific duplication of the MHCII DRB locus. In silico analyses suggest that the duplicated gene provides high peptide binding affinity for Yersiniae epitopes as well as Leishmania and Leptospira epitopes, putatively leading to increased capability to withstand infections by these pathogens. Our study demonstrates the power of whole-genome sequencing combined with comparative genomic analyses to gain deeper insight into the immunogenomic landscape of the great gerbil and its close relatives.
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Affiliation(s)
- Pernille Nilsson
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Monica H Solbakken
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Boris V Schmid
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | | | - Ruichen Lv
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujun Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yujiang Zhang
- Xinjiang Center for Disease Control and Prevention, Urumqi, China
| | - Helle T Baalsrud
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Ole K Tørresen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
- Ministry of Education Key Laboratory for Earth System Modeling, Department of Earth System Science, Tsinghua University, Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - William Ryan Easterday
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
| | - Sissel Jentoft
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway
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Orr RJS, Haugen MN, Berning B, Bock P, Cumming RL, Florence WK, Hirose M, Di Martino E, Ramsfjell MH, Sannum MM, Smith AM, Vieira LM, Waeschenbach A, Liow LH. A genome-skimmed phylogeny of a widespread bryozoan family, Adeonidae. BMC Evol Biol 2019; 19:235. [PMID: 31881939 PMCID: PMC6935126 DOI: 10.1186/s12862-019-1563-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/15/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the phylogenetic relationships among species is one of the main goals of systematic biology. Simultaneously, credible phylogenetic hypotheses are often the first requirement for unveiling the evolutionary history of traits and for modelling macroevolutionary processes. However, many non-model taxa have not yet been sequenced to an extent such that statistically well-supported molecular phylogenies can be constructed for these purposes. Here, we use a genome-skimming approach to extract sequence information for 15 mitochondrial and 2 ribosomal operon genes from the cheilostome bryozoan family, Adeonidae, Busk, 1884, whose current systematics is based purely on morphological traits. The members of the Adeonidae are, like all cheilostome bryozoans, benthic, colonial, marine organisms. Adeonids are also geographically widely-distributed, often locally common, and are sometimes important habitat-builders. RESULTS We successfully genome-skimmed 35 adeonid colonies representing 6 genera (Adeona, Adeonellopsis, Bracebridgia, Adeonella, Laminopora and Cucullipora). We also contributed 16 new, circularised mitochondrial genomes to the eight previously published for cheilostome bryozoans. Using the aforementioned mitochondrial and ribosomal genes, we inferred the relationships among these 35 samples. Contrary to some previous suggestions, the Adeonidae is a robustly supported monophyletic clade. However, the genera Adeonella and Laminopora are in need of revision: Adeonella is polyphyletic and Laminopora paraphyletically forms a clade with some Adeonella species. Additionally, we assign a sequence clustering identity using cox1 barcoding region of 99% at the species and 83% at the genus level. CONCLUSIONS We provide sequence data, obtained via genome-skimming, that greatly increases the resolution of the phylogenetic relationships within the adeonids. We present a highly-supported topology based on 17 genes and substantially increase availability of circularised cheilostome mitochondrial genomes, and highlight how we can extend our pipeline to other bryozoans.
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Affiliation(s)
| | - Marianne N Haugen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Björn Berning
- Geoscience Collections, Upper Austrian State Museum, Linz, Austria
| | - Philip Bock
- Museum Victoria, Melbourne, Victoria, Australia
| | | | - Wayne K Florence
- Department of Research and Exhibitions, Iziko Museums of South Africa, Cape Town, South Africa
| | - Masato Hirose
- School of Marine Biosciences, Kitasato University, Kanagawa, Japan
| | | | | | - Maja M Sannum
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Abigail M Smith
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - Leandro M Vieira
- Department of Zoology, Universidade Federal de Pernambuco, Recife, Brazil
| | | | - Lee Hsiang Liow
- Natural History Museum, University of Oslo, Oslo, Norway.
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway.
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Orr RJS, Waeschenbach A, Enevoldsen ELG, Boeve JP, Haugen MN, Voje KL, Porter J, Zágoršek K, Smith AM, Gordon DP, Liow LH. Bryozoan genera Fenestrulina and Microporella no longer confamilial; multi-gene phylogeny supports separation. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly055] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
| | | | - Emily L G Enevoldsen
- Centre for Ecological & Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Jeroen P Boeve
- Centre for Ecological & Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Marianne N Haugen
- Centre for Ecological & Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Kjetil L Voje
- Centre for Ecological & Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Joanne Porter
- Centre for Marine Biodiversity and Biotechnology, School of Life Sciences, Heriot Watt University, Edinburgh, UK
| | - Kamil Zágoršek
- Department of Geography, Technical University of Liberec, Czech Republic
| | - Abigail M Smith
- Department of Marine Science, University of Otago, Dunedin, New Zealand
| | - Dennis P Gordon
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
| | - Lee Hsiang Liow
- Natural History Museum, University of Oslo, Oslo, Norway
- Centre for Ecological & Evolutionary Synthesis, Department of Biosciences, University of Oslo, Oslo, Norway
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Orr RJS, Zhao S, Klaveness D, Yabuki A, Ikeda K, Watanabe MM, Shalchian-Tabrizi K. Correction to: Enigmatic Diphyllatea eukaryotes: culturing and targeted PacBio RS amplicon sequencing reveals a higher order taxonomic diversity and global distribution. BMC Evol Biol 2018; 18:118. [PMID: 30075698 PMCID: PMC6074036 DOI: 10.1186/s12862-018-1233-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 07/26/2018] [Indexed: 11/19/2022] Open
Affiliation(s)
- Russell J S Orr
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Kristine Bonnevies hus, Blindernveien 31, 0371, Oslo, Norway. .,Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Kristine Bonnevies hus, Blindernveien 31, 0371, Oslo, Norway.
| | - Sen Zhao
- Department of Molecular Oncology, Institute of Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway.,Medical Faculty, Center for Cancer Biomedicine, University of Oslo University Hospital, Oslo, Norway
| | - Dag Klaveness
- Section for Aquatic Biology and Toxicology (AQUA), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa, 237-0061, Japan
| | - Keiji Ikeda
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Makoto M Watanabe
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan
| | - Kamran Shalchian-Tabrizi
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Kristine Bonnevies hus, Blindernveien 31, 0371, Oslo, Norway. .,Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Kristine Bonnevies hus, Blindernveien 31, 0371, Oslo, Norway.
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10
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Orr RJS, Zhao S, Klaveness D, Yabuki A, Ikeda K, Makoto WM, Shalchian-Tabrizi K. Enigmatic Diphyllatea eukaryotes: culturing and targeted PacBio RS amplicon sequencing reveals a higher order taxonomic diversity and global distribution. BMC Evol Biol 2018; 18:115. [PMID: 30021531 PMCID: PMC6052632 DOI: 10.1186/s12862-018-1224-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/29/2018] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The class Diphyllatea belongs to a group of enigmatic unicellular eukaryotes that play a key role in reconstructing the morphological innovation and diversification of early eukaryotic evolution. Despite its evolutionary significance, very little is known about the phylogeny and species diversity of Diphyllatea. Only three species have described morphology, being taxonomically divided by flagella number, two or four, and cell size. Currently, one 18S rRNA Diphyllatea sequence is available, with environmental sequencing surveys reporting only a single partial sequence from a Diphyllatea-like organism. Accordingly, geographical distribution of Diphyllatea based on molecular data is limited, despite morphological data suggesting the class has a global distribution. We here present a first attempt to understand species distribution, diversity and higher order structure of Diphyllatea. RESULTS We cultured 11 new strains, characterised these morphologically and amplified their rRNA for a combined 18S-28S rRNA phylogeny. We sampled environmental DNA from multiple sites and designed new Diphyllatea-specific PCR primers for long-read PacBio RSII technology. Near full-length 18S rRNA sequences from environmental DNA, in addition to supplementary Diphyllatea sequence data mined from public databases, resolved the phylogeny into three deeply branching and distinct clades (Diphy I - III). Of these, the Diphy III clade is entirely novel, and in congruence with Diphy II, composed of species morphologically consistent with the earlier described Collodictyon triciliatum. The phylogenetic split between the Diphy I and Diphy II + III clades corresponds with a morphological division of Diphyllatea into bi- and quadriflagellate cell forms. CONCLUSIONS This altered flagella composition must have occurred early in the diversification of Diphyllatea and may represent one of the earliest known morphological transitions among eukaryotes. Further, the substantial increase in molecular data presented here confirms Diphyllatea has a global distribution, seemingly restricted to freshwater habitats. Altogether, the results reveal the advantage of combining a group-specific PCR approach and long-read high-throughput amplicon sequencing in surveying enigmatic eukaryote lineages. Lastly, our study shows the capacity of PacBio RS when targeting a protist class for increasing phylogenetic resolution.
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Affiliation(s)
- Russell J. S. Orr
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Kristine Bonnevies hus, Blindernveien 31, 0371 Oslo, Norway
- Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Kristine Bonnevies hus, Blindernveien 31, 0371 Oslo, Norway
| | - Sen Zhao
- Department of Molecular Oncology, Institute of Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
- Medical Faculty, Center for Cancer Biomedicine, University of Oslo University Hospital, Oslo, Norway
| | - Dag Klaveness
- Section for Aquatic Biology and Toxicology (AQUA), Department of Biosciences, University of Oslo, Oslo, Norway
| | - Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061 Japan
| | - Keiji Ikeda
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572 Japan
| | - Watanabe M. Makoto
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572 Japan
| | - Kamran Shalchian-Tabrizi
- Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Kristine Bonnevies hus, Blindernveien 31, 0371 Oslo, Norway
- Centre for Integrative Microbial Evolution (CIME), Section for Genetics and Evolutionary Biology (EVOGENE), Department of Biosciences, University of Oslo, Kristine Bonnevies hus, Blindernveien 31, 0371 Oslo, Norway
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11
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Krabberød AK, Orr RJS, Bråte J, Kristensen T, Bjørklund KR, Shalchian-Tabrizi K. Single Cell Transcriptomics, Mega-Phylogeny, and the Genetic Basis of Morphological Innovations in Rhizaria. Mol Biol Evol 2017; 34:1557-1573. [PMID: 28333264 PMCID: PMC5455982 DOI: 10.1093/molbev/msx075] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The innovation of the eukaryote cytoskeleton enabled phagocytosis, intracellular transport, and cytokinesis, and is largely responsible for the diversity of morphologies among eukaryotes. Still, the relationship between phenotypic innovations in the cytoskeleton and their underlying genotype is poorly understood. To explore the genetic mechanism of morphological evolution of the eukaryotic cytoskeleton, we provide the first single cell transcriptomes from uncultured, free-living unicellular eukaryotes: the polycystine radiolarian Lithomelissa setosa (Nassellaria) and Sticholonche zanclea (Taxopodida). A phylogenomic approach using 255 genes finds Radiolaria and Foraminifera as separate monophyletic groups (together as Retaria), while Cercozoa is shown to be paraphyletic where Endomyxa is sister to Retaria. Analysis of the genetic components of the cytoskeleton and mapping of the evolution of these on the revised phylogeny of Rhizaria reveal lineage-specific gene duplications and neofunctionalization of α and β tubulin in Retaria, actin in Retaria and Endomyxa, and Arp2/3 complex genes in Chlorarachniophyta. We show how genetic innovations have shaped cytoskeletal structures in Rhizaria, and how single cell transcriptomics can be applied for resolving deep phylogenies and studying gene evolution in uncultured protist species.
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Affiliation(s)
- Anders K Krabberød
- Department of Biosciences, Centre for Integrative Microbial Evolution (CIME) and Centre for Epigenetics Development and Evolution (CEDE), University of Oslo, Oslo, Norway
| | - Russell J S Orr
- Department of Biosciences, Centre for Integrative Microbial Evolution (CIME) and Centre for Epigenetics Development and Evolution (CEDE), University of Oslo, Oslo, Norway
| | - Jon Bråte
- Department of Biosciences, Centre for Integrative Microbial Evolution (CIME) and Centre for Epigenetics Development and Evolution (CEDE), University of Oslo, Oslo, Norway
| | - Tom Kristensen
- Department of Biosciences, Centre for Integrative Microbial Evolution (CIME) and Centre for Epigenetics Development and Evolution (CEDE), University of Oslo, Oslo, Norway
| | - Kjell R Bjørklund
- Department of Research and Collections, Natural History Museum, University of Oslo, Oslo, Norway
| | - Kamran Shalchian-Tabrizi
- Department of Biosciences, Centre for Integrative Microbial Evolution (CIME) and Centre for Epigenetics Development and Evolution (CEDE), University of Oslo, Oslo, Norway
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12
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Stø IM, Orr RJS, Fooyontphanich K, Jin X, Knutsen JMB, Fischer U, Tranbarger TJ, Nordal I, Aalen RB. Conservation of the abscission signaling peptide IDA during Angiosperm evolution: withstanding genome duplications and gain and loss of the receptors HAE/HSL2. Front Plant Sci 2015; 6:931. [PMID: 26579174 PMCID: PMC4627355 DOI: 10.3389/fpls.2015.00931] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/15/2015] [Indexed: 11/13/2022]
Abstract
The peptide INFLORESCENCE DEFICIENT IN ABSCISSION (IDA), which signals through the leucine-rich repeat receptor-like kinases HAESA (HAE) and HAESA-LIKE2 (HSL2), controls different cell separation events in Arabidopsis thaliana. We hypothesize the involvement of this signaling module in abscission processes in other plant species even though they may shed other organs than A. thaliana. As the first step toward testing this hypothesis from an evolutionarily perspective we have identified genes encoding putative orthologs of IDA and its receptors by BLAST searches of publically available protein, nucleotide and genome databases for angiosperms. Genes encoding IDA or IDA-LIKE (IDL) peptides and HSL proteins were found in all investigated species, which were selected as to represent each angiosperm order with available genomic sequences. The 12 amino acids representing the bioactive peptide in A. thaliana have virtually been unchanged throughout the evolution of the angiosperms; however, the number of IDL and HSL genes varies between different orders and species. The phylogenetic analyses suggest that IDA, HSL2, and the related HSL1 gene, were present in the species that gave rise to the angiosperms. HAE has arisen from HSL1 after a genome duplication that took place after the monocot-eudicots split. HSL1 has also independently been duplicated in the monocots, while HSL2 has been lost in gingers (Zingiberales) and grasses (Poales). IDA has been duplicated in eudicots to give rise to functionally divergent IDL peptides. We postulate that the high number of IDL homologs present in the core eudicots is a result of multiple whole genome duplications (WGD). We substantiate the involvement of IDA and HAE/HSL2 homologs in abscission by providing gene expression data of different organ separation events from various species.
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Affiliation(s)
- Ida M Stø
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo Oslo, Norway
| | - Russell J S Orr
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo Oslo, Norway
| | - Kim Fooyontphanich
- UMR Diversité et Adaptation et Développement des Plantes, Institut de Recherche pour le Développement Montpellier, France
| | - Xu Jin
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences Umeå, Sweden
| | - Jonfinn M B Knutsen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo Oslo, Norway
| | - Urs Fischer
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences Umeå, Sweden
| | - Timothy J Tranbarger
- UMR Diversité et Adaptation et Développement des Plantes, Institut de Recherche pour le Développement Montpellier, France
| | - Inger Nordal
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo Oslo, Norway
| | - Reidunn B Aalen
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo Oslo, Norway
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13
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Murray SA, Diwan R, Orr RJS, Kohli GS, John U. Gene duplication, loss and selection in the evolution of saxitoxin biosynthesis in alveolates. Mol Phylogenet Evol 2015; 92:165-80. [PMID: 26140862 DOI: 10.1016/j.ympev.2015.06.017] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 06/01/2015] [Accepted: 06/25/2015] [Indexed: 11/29/2022]
Abstract
A group of marine dinoflagellates (Alveolata, Eukaryota), consisting of ∼10 species of the genus Alexandrium, Gymnodinium catenatum and Pyrodinium bahamense, produce the toxin saxitoxin and its analogues (STX), which can accumulate in shellfish, leading to ecosystem and human health impacts. The genes, sxt, putatively involved in STX biosynthesis, have recently been identified, however, the evolution of these genes within dinoflagellates is not clear. There are two reasons for this: uncertainty over the phylogeny of dinoflagellates; and that the sxt genes of many species of Alexandrium and other dinoflagellate genera are not known. Here, we determined the phylogeny of STX-producing and other dinoflagellates based on a concatenated eight-gene alignment. We determined the presence, diversity and phylogeny of sxtA, domains A1 and A4 and sxtG in 52 strains of Alexandrium, and a further 43 species of dinoflagellates and thirteen other alveolates. We confirmed the presence and high sequence conservation of sxtA, domain A4, in 40 strains (35 Alexandrium, 1 Pyrodinium, 4 Gymnodinium) of 8 species of STX-producing dinoflagellates, and absence from non-producing species. We found three paralogs of sxtA, domain A1, and a widespread distribution of sxtA1 in non-STX producing dinoflagellates, indicating duplication events in the evolution of this gene. One paralog, clade 2, of sxtA1 may be particularly related to STX biosynthesis. Similarly, sxtG appears to be generally restricted to STX-producing species, while three amidinotransferase gene paralogs were found in dinoflagellates. We investigated the role of positive (diversifying) selection following duplication in sxtA1 and sxtG, and found negative selection in clades of sxtG and sxtA1, clade 2, suggesting they were functionally constrained. Significant episodic diversifying selection was found in some strains in clade 3 of sxtA1, a clade that may not be involved in STX biosynthesis, indicating pressure for diversification of function.
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Affiliation(s)
- Shauna A Murray
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia; Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, NSW, Australia.
| | - Rutuja Diwan
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia; Sydney Institute of Marine Science, Chowder Bay Rd, Mosman, NSW, Australia
| | - Russell J S Orr
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Norway
| | - Gurjeet S Kohli
- Plant Functional Biology and Climate Change Cluster, University of Technology Sydney, NSW 2007, Australia
| | - Uwe John
- Section Ecological Chemistry, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
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14
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Murray SA, Hoppenrath M, Orr RJS, Bolch C, John U, Diwan R, Yauwenas R, Harwood T, de Salas M, Neilan B, Hallegraeff G. Alexandrium diversaporum sp. nov., a new non-saxitoxin producing species: Phylogeny, morphology and sxtA genes. Harmful Algae 2014; 31:54-65. [PMID: 28040111 DOI: 10.1016/j.hal.2013.09.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/16/2013] [Accepted: 09/16/2013] [Indexed: 06/06/2023]
Abstract
Species of the PST producing planktonic marine dinoflagellate genus Alexandrium have been intensively scrutinised, and it is therefore surprising that new taxa can still be found. Here we report a new species, Alexandrium diversaporum nov. sp., isolated from spherical cysts found at two sites in Tasmania, Australia. This species differs in its morphology from all previously reported Alexandrium species, possessing a unique combination of morphological features: the presence of 2 size classes of thecal pores on the cell surface, a medium cell size, the size and shape of the 6″, 1', 2⁗ and Sp plates, the lack of a ventral pore, a lack of anterior and posterior connecting pores, and a lack of chain formation. We determined the relationship of the two strains to other species of Alexandrium based on an alignment of concatenated SSU-ITS1, 5.8S, ITS2 and partial LSU ribosomal RNA sequences, and found A. diversaporum to be a sister group to Alexandrium leei with high support. A. leei shares several morphological features, including the relative size and shapes of the 6″, 1', 2⁗ and Sp plates and the fact that some strains of A. leei have two size classes of thecal pores. We examined A. diversaporum strains for saxitoxin production and found them to be non-toxic. The species lacked sequences for the domain A4 of sxtA, as has been previously found for non-saxitoxin producing species of Alexandrium.
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Affiliation(s)
- Shauna A Murray
- Sydney Institute of Marine Science, Chowder Bay Road, Mosman, NSW, Australia; School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Mona Hoppenrath
- Senckenberg Research Institute, Senckenberg am Meer, German Center for Marine Biodiversity Research (DZMB), Südstrand 44, D-26382 Wilhelmshaven, Germany
| | - Russell J S Orr
- Microbial Evolution Research Group, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Christopher Bolch
- National Centre for Marine Conservation and Resource Sustainability, Australian Maritime College, University of Tasmania, Locked Bag 1370, Launceston, Tasmania 7250, Australia
| | - Uwe John
- Section Ecological Chemistry, Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Germany
| | - Rutuja Diwan
- Sydney Institute of Marine Science, Chowder Bay Road, Mosman, NSW, Australia
| | - Rouna Yauwenas
- Sydney Institute of Marine Science, Chowder Bay Road, Mosman, NSW, Australia
| | - Tim Harwood
- Cawthron Institute, Private Bag 2, Nelson 7042, New Zealand
| | - Miguel de Salas
- Tasmanian Herbarium, University of Tasmania, Private Bag 4, Hobart, Tasmania 7001, Australia
| | - Brett Neilan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Gustaaf Hallegraeff
- Institute for Marine and Antarctic Studies, University of Tasmania, Private Bag 55, Hobart, Tasmania 7001, Australia
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15
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Orr RJS, Stüken A, Murray SA, Jakobsen KS. Evolution and distribution of saxitoxin biosynthesis in dinoflagellates. Mar Drugs 2013; 11:2814-28. [PMID: 23966031 PMCID: PMC3766867 DOI: 10.3390/md11082814] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 07/04/2013] [Accepted: 07/08/2013] [Indexed: 11/16/2022] Open
Abstract
Numerous species of marine dinoflagellates synthesize the potent environmental neurotoxic alkaloid, saxitoxin, the agent of the human illness, paralytic shellfish poisoning. In addition, certain freshwater species of cyanobacteria also synthesize the same toxic compound, with the biosynthetic pathway and genes responsible being recently reported. Three theories have been postulated to explain the origin of saxitoxin in dinoflagellates: The production of saxitoxin by co-cultured bacteria rather than the dinoflagellates themselves, convergent evolution within both dinoflagellates and bacteria and horizontal gene transfer between dinoflagellates and bacteria. The discovery of cyanobacterial saxitoxin homologs in dinoflagellates has enabled us for the first time to evaluate these theories. Here, we review the distribution of saxitoxin within the dinoflagellates and our knowledge of its genetic basis to determine the likely evolutionary origins of this potent neurotoxin.
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Affiliation(s)
- Russell J. S. Orr
- Microbial Evolution Research Group (MERG), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway; E-Mails: (R.J.S.O.); (A.S.)
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway
| | - Anke Stüken
- Microbial Evolution Research Group (MERG), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway; E-Mails: (R.J.S.O.); (A.S.)
| | - Shauna A. Murray
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology, Sydney, PO Box 123 Broadway, NSW 2007, Australia; E-Mail:
- Sydney Institute of Marine Science, Mosman, NSW 2088, Australia
| | - Kjetill S. Jakobsen
- Microbial Evolution Research Group (MERG), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway; E-Mails: (R.J.S.O.); (A.S.)
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, Oslo 0316, Norway
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +47-22854602; Fax: +47-22854001
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16
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Abstract
The dinoflagellates are a diverse lineage of microbial eukaryotes. Dinoflagellate monophyly and their position within the group Alveolata are well established. However, phylogenetic relationships between dinoflagellate orders remain unresolved. To date, only a limited number of dinoflagellate studies have used a broad taxon sample with more than two concatenated markers. This lack of resolution makes it difficult to determine the evolution of major phenotypic characters such as morphological features or toxin production e.g. saxitoxin. Here we present an improved dinoflagellate phylogeny, based on eight genes, with the broadest taxon sampling to date. Fifty-five sequences for eight phylogenetic markers from nuclear and mitochondrial regions were amplified from 13 species, four orders, and concatenated phylogenetic inferences were conducted with orthologous sequences. Phylogenetic resolution is increased with addition of support for the deepest branches, though can be improved yet further. We show for the first time that the characteristic dinoflagellate thecal plates, cellulosic material that is present within the sub-cuticular alveoli, appears to have had a single origin. In addition, the monophyly of most dinoflagellate orders is confirmed: the Dinophysiales, the Gonyaulacales, the Prorocentrales, the Suessiales, and the Syndiniales. Our improved phylogeny, along with results of PCR to detect the sxtA gene in various lineages, allows us to suggest that this gene was probably acquired separately in Gymnodinium and the common ancestor of Alexandrium and Pyrodinium and subsequently lost in some descendent species of Alexandrium.
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Affiliation(s)
- Russell J. S. Orr
- Microbial Evolution Research Group (MERG), Department of Biology, University of Oslo, Oslo, Norway
| | - Shauna A. Murray
- Ecology and Evolution Research Centre and School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Sydney Institute of Marine Sciences, Mosman, New South Wales, Australia
| | - Anke Stüken
- Microbial Evolution Research Group (MERG), Department of Biology, University of Oslo, Oslo, Norway
| | | | - Kjetill S. Jakobsen
- Microbial Evolution Research Group (MERG), Department of Biology, University of Oslo, Oslo, Norway
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Oslo, Norway
- * E-mail:
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17
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Stüken A, Orr RJS, Kellmann R, Murray SA, Neilan BA, Jakobsen KS. Discovery of nuclear-encoded genes for the neurotoxin saxitoxin in dinoflagellates. PLoS One 2011; 6:e20096. [PMID: 21625593 PMCID: PMC3097229 DOI: 10.1371/journal.pone.0020096] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 04/12/2011] [Indexed: 11/26/2022] Open
Abstract
Saxitoxin is a potent neurotoxin that occurs in aquatic environments worldwide.
Ingestion of vector species can lead to paralytic shellfish poisoning, a severe
human illness that may lead to paralysis and death. In freshwaters, the toxin is
produced by prokaryotic cyanobacteria; in marine waters, it is associated with
eukaryotic dinoflagellates. However, several studies suggest that saxitoxin is
not produced by dinoflagellates themselves, but by co-cultured bacteria. Here,
we show that genes required for saxitoxin synthesis are encoded in the nuclear
genomes of dinoflagellates. We sequenced >1.2×106 mRNA
transcripts from the two saxitoxin-producing dinoflagellate strains
Alexandrium fundyense CCMP1719 and A.
minutum CCMP113 using high-throughput sequencing technology. In
addition, we used in silico transcriptome analyses, RACE, qPCR
and conventional PCR coupled with Sanger sequencing. These approaches
successfully identified genes required for saxitoxin-synthesis in the two
transcriptomes. We focused on sxtA, the unique starting gene of
saxitoxin synthesis, and show that the dinoflagellate transcripts of
sxtA have the same domain structure as the cyanobacterial
sxtA genes. But, in contrast to the bacterial homologs, the
dinoflagellate transcripts are monocistronic, have a higher GC content, occur in
multiple copies, contain typical dinoflagellate spliced-leader sequences and
eukaryotic polyA-tails. Further, we investigated 28 saxitoxin-producing and
non-producing dinoflagellate strains from six different genera for the presence
of genomic sxtA homologs. Our results show very good agreement
between the presence of sxtA and saxitoxin-synthesis, except in
three strains of A. tamarense, for which we amplified
sxtA, but did not detect the toxin. Our work opens for
possibilities to develop molecular tools to detect saxitoxin-producing
dinoflagellates in the environment.
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Affiliation(s)
- Anke Stüken
- Microbial Evolution Research Group (MERG), Department of Biology,
University of Oslo, Oslo, Norway
| | - Russell J. S. Orr
- Microbial Evolution Research Group (MERG), Department of Biology,
University of Oslo, Oslo, Norway
| | - Ralf Kellmann
- Department of Molecular Biology, University of Bergen, Bergen,
Norway
| | - Shauna A. Murray
- School of Biotechnology and Biomolecular Sciences and Australian Centre
for Astrobiology, University of New South Wales, Sydney, Australia
- Sydney Institute of Marine Sciences, Mosman, New South Wales,
Australia
| | - Brett A. Neilan
- School of Biotechnology and Biomolecular Sciences and Australian Centre
for Astrobiology, University of New South Wales, Sydney, Australia
- Sydney Institute of Marine Sciences, Mosman, New South Wales,
Australia
| | - Kjetill S. Jakobsen
- Microbial Evolution Research Group (MERG), Department of Biology,
University of Oslo, Oslo, Norway
- Department of Biology, Centre for Ecological and Evolutionary Synthesis
(CEES), University of Oslo, Oslo, Norway
- * E-mail:
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Kellmann R, Stüken A, Orr RJS, Svendsen HM, Jakobsen KS. Biosynthesis and molecular genetics of polyketides in marine dinoflagellates. Mar Drugs 2010; 8:1011-48. [PMID: 20479965 PMCID: PMC2866473 DOI: 10.3390/md8041011] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2010] [Revised: 03/17/2010] [Accepted: 03/26/2010] [Indexed: 11/20/2022] Open
Abstract
Marine dinoflagellates are the single most important group of algae that produce toxins, which have a global impact on human activities. The toxins are chemically diverse, and include macrolides, cyclic polyethers, spirolides and purine alkaloids. Whereas there is a multitude of studies describing the pharmacology of these toxins, there is limited or no knowledge regarding the biochemistry and molecular genetics involved in their biosynthesis. Recently, however, exciting advances have been made. Expressed sequence tag sequencing studies have revealed important insights into the transcriptomes of dinoflagellates, whereas other studies have implicated polyketide synthase genes in the biosynthesis of cyclic polyether toxins, and the molecular genetic basis for the biosynthesis of paralytic shellfish toxins has been elucidated in cyanobacteria. This review summarises the recent progress that has been made regarding the unusual genomes of dinoflagellates, the biosynthesis and molecular genetics of dinoflagellate toxins. In addition, the evolution of these metabolic pathways will be discussed, and an outlook for future research and possible applications is provided.
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Affiliation(s)
- Ralf Kellmann
- University of Bergen, Department of Molecular Biology, 5020 Bergen, Norway; E-Mail:
- *Author to whom correspondence should be addressed; E-Mail:
; Tel.: +47-5558-4556; Fax: +47-5558-9683
| | - Anke Stüken
- University of Oslo, Department of Biology, Centre for Ecological and Evolutionary Synthesis (CEES), 0316 Oslo, Norway; E-Mails:
(A.S.);
(K.S.J.)
- University of Oslo, Department of Biology, Microbial Evolution Research Group (MERG), 0316 Oslo, Norway; E-Mail:
| | - Russell J. S. Orr
- University of Oslo, Department of Biology, Microbial Evolution Research Group (MERG), 0316 Oslo, Norway; E-Mail:
| | - Helene M. Svendsen
- University of Bergen, Department of Molecular Biology, 5020 Bergen, Norway; E-Mail:
| | - Kjetill S. Jakobsen
- University of Oslo, Department of Biology, Centre for Ecological and Evolutionary Synthesis (CEES), 0316 Oslo, Norway; E-Mails:
(A.S.);
(K.S.J.)
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Minge MA, Silberman JD, Orr RJS, Cavalier-Smith T, Shalchian-Tabrizi K, Burki F, Skjaeveland A, Jakobsen KS. Evolutionary position of breviate amoebae and the primary eukaryote divergence. Proc Biol Sci 2009; 276:597-604. [PMID: 19004754 DOI: 10.1098/rspb.2008.1358] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Integration of ultrastructural and molecular sequence data has revealed six supergroups of eukaryote organisms (excavates, Rhizaria, chromalveolates, Plantae, Amoebozoa and opisthokonts), and the root of the eukaryote evolutionary tree is suggested to lie between unikonts (Amoebozoa, opisthokonts) and bikonts (the other supergroups). However, some smaller lineages remain of uncertain affinity. One of these unassigned taxa is the anaerobic, free-living, amoeboid flagellate Breviata anathema, which is of key significance as it is unclear whether it is a unikont (i.e. possibly the deepest branching amoebozoan) or a bikont. To establish its evolutionary position, we sequenced thousands of Breviata genes and calculated trees using 78 protein sequences. Our trees and specific substitutions in the 18S RNA sequence indicate that Breviata is related to other Amoebozoa, thereby significantly increasing the cellular diversity of this phylum and establishing Breviata as a deep-branching unikont. We discuss the implications of these results for the ancestral state of Amoebozoa and eukaryotes generally, demonstrating that phylogenomics of phylogenetically 'nomadic' species can elucidate key questions in eukaryote evolution. Furthermore, mitochondrial genes among the Breviata ESTs demonstrate that Breviata probably contains a modified anaerobic mitochondrion. With these findings, remnants of mitochondria have been detected in all putatively deep-branching amitochondriate organisms.
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Affiliation(s)
- Marianne A Minge
- Department of Biology, Centre for Ecological and Evolutionary Synthesis, University of Oslo, 0316 Oslo, Norway
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20
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Riisberg I, Orr RJS, Kluge R, Shalchian-Tabrizi K, Bowers HA, Patil V, Edvardsen B, Jakobsen KS. Seven gene phylogeny of heterokonts. Protist 2009; 160:191-204. [PMID: 19213601 DOI: 10.1016/j.protis.2008.11.004] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2008] [Accepted: 11/15/2008] [Indexed: 11/26/2022]
Abstract
Nucleotide ssu and lsu rDNA sequences of all major lineages of autotrophic (Ochrophyta) and heterotrophic (Bigyra and Pseudofungi) heterokonts were combined with amino acid sequences from four protein-coding genes (actin, beta-tubulin, cox1 and hsp90) in a multigene approach for resolving the relationship between heterokont lineages. Applying these multigene data in Bayesian and maximum likelihood analyses improved the heterokont tree compared to previous rDNA analyses by placing all plastid-lacking heterotrophic heterokonts sister to Ochrophyta with robust support, and divided the heterotrophic heterokonts into the previously recognized phyla, Bigyra and Pseudofungi. Our trees identified the heterotrophic heterokonts Bicosoecida, Blastocystis and Labyrinthulida (Bigyra) as the earliest diverging lineages. A separate analysis of the phototrophic lineages, by adding the rbcL gene, further resolved the Ochrophyta lineages by increased support for several important nodes. Except for the positioning of Chrysophyceae, Eustigmatophyceae, Raphidophyceae and Pinguiophyceae, all main branches of Ochrophyta were resolved. Our results support the transfer of classes Dictyochophyceae and Pelagophyceae from subphylum Phaeista to Khakista. Based on all our trees, in combination with current knowledge about ultrastructure of heterokonts we suggest that a more advanced flagellar apparatus originated at one occasion in the ancestor of Phaeista whereas, Khakista independently reduced their flagellar apparatus and gained chlorophyll c(3).
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Affiliation(s)
- Ingvild Riisberg
- Marine Biology, Department of Biology, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
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