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Wisecaver JH, Auber RP, Pendleton AL, Watervoort NF, Fallon TR, Riedling OL, Manning SR, Moore BS, Driscoll WW. Extreme genome diversity and cryptic speciation in a harmful algal-bloom-forming eukaryote. Curr Biol 2023; 33:2246-2259.e8. [PMID: 37224809 PMCID: PMC10247466 DOI: 10.1016/j.cub.2023.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/14/2023] [Accepted: 05/02/2023] [Indexed: 05/26/2023]
Abstract
Harmful algal blooms of the toxic haptophyte Prymnesium parvum are a recurrent problem in many inland and estuarine waters around the world. Strains of P. parvum vary in the toxins they produce and in other physiological traits associated with harmful algal blooms, but the genetic basis for this variation is unknown. To investigate genome diversity in this morphospecies, we generated genome assemblies for 15 phylogenetically and geographically diverse strains of P. parvum, including Hi-C guided, near-chromosome-level assemblies for two strains. Comparative analysis revealed considerable DNA content variation between strains, ranging from 115 to 845 Mbp. Strains included haploids, diploids, and polyploids, but not all differences in DNA content were due to variation in genome copy number. Haploid genome size between strains of different chemotypes differed by as much as 243 Mbp. Syntenic and phylogenetic analyses indicate that UTEX 2797, a common laboratory strain from Texas, is a hybrid that retains two phylogenetically distinct haplotypes. Investigation of gene families variably present across the strains identified several functional categories associated with metabolic and genome size variation in P. parvum, including genes for the biosynthesis of toxic metabolites and proliferation of transposable elements. Together, our results indicate that P. parvum comprises multiple cryptic species. These genomes provide a robust phylogenetic and genomic framework for investigations into the eco-physiological consequences of the intra- and inter-specific genetic variation present in P. parvum and demonstrate the need for similar resources for other harmful algal-bloom-forming morphospecies.
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Affiliation(s)
- Jennifer H Wisecaver
- Department of Biochemistry, Purdue University, 175 S University St, West Lafayette, IN 47907, USA; Purdue Center for Plant Biology, Purdue University, 175 S University St, West Lafayette, IN 47907, USA.
| | - Robert P Auber
- Department of Biochemistry, Purdue University, 175 S University St, West Lafayette, IN 47907, USA; Purdue Center for Plant Biology, Purdue University, 175 S University St, West Lafayette, IN 47907, USA
| | - Amanda L Pendleton
- Department of Biochemistry, Purdue University, 175 S University St, West Lafayette, IN 47907, USA; Purdue Center for Plant Biology, Purdue University, 175 S University St, West Lafayette, IN 47907, USA
| | - Nathan F Watervoort
- Department of Biochemistry, Purdue University, 175 S University St, West Lafayette, IN 47907, USA; Purdue Center for Plant Biology, Purdue University, 175 S University St, West Lafayette, IN 47907, USA
| | - Timothy R Fallon
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and University of California San Diego, 9500 Gilman Dr #0204, La Jolla, CA 92093, USA
| | - Olivia L Riedling
- Department of Biochemistry, Purdue University, 175 S University St, West Lafayette, IN 47907, USA; Purdue Center for Plant Biology, Purdue University, 175 S University St, West Lafayette, IN 47907, USA
| | - Schonna R Manning
- Department of Biological Sciences, Institute of Environment, Florida International University, 3000 NE 151st Street, MSB 250B, North Miami, FL 33181, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography and University of California San Diego, 9500 Gilman Dr #0204, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Dr #0204, La Jolla, CA 92093, USA
| | - William W Driscoll
- Department of Biology, Penn State Harrisburg, 777 W. Harrisburg Pike, Middletown, PA 17057, USA
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Okada R, Inui T, Iguchi Y, Kitagawa T, Takata K, Kitagawa T. Molecular and morphological analyses revealed a cryptic species of dojo loach Misgurnus anguillicaudatus (Cypriniformes: Cobitidae) in Japan. JOURNAL OF FISH BIOLOGY 2017; 91:989-996. [PMID: 28868749 DOI: 10.1111/jfb.13393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Accepted: 06/29/2017] [Indexed: 06/07/2023]
Abstract
Although it has been reported that populations of the Japanese dojo loach Misgurnus anguillicaudatus (Cypriniformes: Cobitidae) belong to two distinct mitochondrial (mt)DNA (Type I and Type II), the taxonomic status of the species remains unresolved. To address this question, nuclear DNA and morphological analyses were performed on M. anguillicaudatus population in the Nakaikemi Wetland, where Type I and Type II lineages are sympatric. Results suggest the existence of a cryptic species (Type I) within the Japanese dojo loach.
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Affiliation(s)
- R Okada
- Program in Environmental Management, Graduate School of Agriculture, Kindai University, Nara 3327-204, Japan
| | - T Inui
- Program in Environmental Management, Graduate School of Agriculture, Kindai University, Nara 3327-204, Japan
| | - Y Iguchi
- Program in Environmental Management, Graduate School of Agriculture, Kindai University, Nara 3327-204, Japan
| | - T Kitagawa
- Program in Environmental Management, Graduate School of Agriculture, Kindai University, Nara 3327-204, Japan
| | - K Takata
- Department of Biology, Faculty of Science, Shinshu University, Matsumoto 3-1-1, Japan
| | - T Kitagawa
- Program in Environmental Management, Graduate School of Agriculture, Kindai University, Nara 3327-204, Japan
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Dia A, Guillou L, Mauger S, Bigeard E, Marie D, Valero M, Destombe C. Spatiotemporal changes in the genetic diversity of harmful algal blooms caused by the toxic dinoflagellateAlexandrium minutum. Mol Ecol 2014; 23:549-60. [DOI: 10.1111/mec.12617] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 11/08/2013] [Accepted: 11/19/2013] [Indexed: 11/28/2022]
Affiliation(s)
- A. Dia
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7144; Adaptation et diversité en milieu marin; Station Biologique de Roscoff; Place Georges Teissier CS 90074 29688 Roscoff France
- CNRS; UMR 7144; Adaptation et diversité en milieu marin; Station Biologique de Roscoff; Place Georges Teissier CS 90074 29688 Roscoff France
| | - L. Guillou
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7144; Adaptation et diversité en milieu marin; Station Biologique de Roscoff; Place Georges Teissier CS 90074 29688 Roscoff France
- CNRS; UMR 7144; Adaptation et diversité en milieu marin; Station Biologique de Roscoff; Place Georges Teissier CS 90074 29688 Roscoff France
| | - S. Mauger
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7144; Adaptation et diversité en milieu marin; Station Biologique de Roscoff; Place Georges Teissier CS 90074 29688 Roscoff France
- CNRS; UMR 7144; Adaptation et diversité en milieu marin; Station Biologique de Roscoff; Place Georges Teissier CS 90074 29688 Roscoff France
| | - E. Bigeard
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7144; Adaptation et diversité en milieu marin; Station Biologique de Roscoff; Place Georges Teissier CS 90074 29688 Roscoff France
- CNRS; UMR 7144; Adaptation et diversité en milieu marin; Station Biologique de Roscoff; Place Georges Teissier CS 90074 29688 Roscoff France
| | - D. Marie
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7144; Adaptation et diversité en milieu marin; Station Biologique de Roscoff; Place Georges Teissier CS 90074 29688 Roscoff France
- CNRS; UMR 7144; Adaptation et diversité en milieu marin; Station Biologique de Roscoff; Place Georges Teissier CS 90074 29688 Roscoff France
| | - M. Valero
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7144; Adaptation et diversité en milieu marin; Station Biologique de Roscoff; Place Georges Teissier CS 90074 29688 Roscoff France
- CNRS; UMR 7144; Adaptation et diversité en milieu marin; Station Biologique de Roscoff; Place Georges Teissier CS 90074 29688 Roscoff France
| | - C. Destombe
- Sorbonne Universités; UPMC Univ Paris 06; UMR 7144; Adaptation et diversité en milieu marin; Station Biologique de Roscoff; Place Georges Teissier CS 90074 29688 Roscoff France
- CNRS; UMR 7144; Adaptation et diversité en milieu marin; Station Biologique de Roscoff; Place Georges Teissier CS 90074 29688 Roscoff France
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Herrera-Sepúlveda A, Hernandez-Saavedra NY, Medlin LK, West N. Capillary electrophoresis finger print technique (CE-SSCP): an alternative tool for the monitoring activities of HAB species in Baja California Sur Costal. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:6863-6871. [PMID: 22744160 DOI: 10.1007/s11356-012-1033-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Accepted: 06/07/2012] [Indexed: 05/28/2023]
Abstract
In Mexican waters, there is no a formal and well-established monitoring program of harmful algal blooms (HAB) events. Until now, most of the work has been focused on the characterization of organisms present in certain communities. Therefore, the development of new techniques for the rapid detection of HAB species is necessary. Capillary electrophoresis finger print technique (CE-SSCP) is a fingerprinting technique based on the identification of different conformers dependent of its base composition. This technique, coupled with capillary electrophoresis, has been used to compare and identify different conformers. The aim of this study was to determine if CE-SSCP analysis of ribosomal RNA (rRNA) gene fragments could be used for a rapid identification of toxic and harmful HAB species to improve monitoring activities along the coasts of Baja California Sur, Mexico.Three different highly variable regions of the 18S and 28S rRNA genes were chosen and their suitability for the discrimination of different dinoflagellate species was assessed by CE-SSCP.The CE-SSCP results obtained for the LSU D7 fragment has demonstrated that this technique with this gene region could be useful for the identification of the ten dinoflagellates species of different genera.We have shown that this method can be used to discriminate species and the next step will be to apply it to natural samples to achieve our goal of molecular monitoring for toxic algae in Mexican waters. This strategy will offer an option to improve an early warning system of HAB events for coastal BCS, allowing the possible implementation of mitigation strategies. A monitoring program of HAB species using molecular methods will permit the analysis of several samples in a short period of time, without the pressure of counting with a taxonomic expert in phytoplankton taxonomy.
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Affiliation(s)
- Angélica Herrera-Sepúlveda
- Centro de Investigaciones Biológicas del Noroeste S. C., Instituto Politécnico Nacional No. 195, La Paz, BCS 23090, Mexico
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