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Ford SA, Craig RJ, Ness RW. A novel method for identifying Chlamydomonas reinhardtii (Chlorophyta) and closely related species from nature. JOURNAL OF PHYCOLOGY 2023; 59:281-288. [PMID: 36453860 DOI: 10.1111/jpy.13306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Here, we introduce a new method for efficiently sampling Chlamydomonas reinhardtii and closely related species using a colony PCR-based screen with novel primer sets designed to specifically detect these important model microalgae. To demonstrate the utility of our new method, we collected 130 soil samples from a wide range of habitats in Ontario, Canada and identified 33 candidate algae, which were barcoded by sequencing a region of the rbcL plastid gene. For select isolates, 18S rRNA gene and YPT4 nuclear markers were also sequenced. Based on phylogenetic and haplotype network analyses of these three loci, seven novel isolates were identified as C. reinhardtii, and one additional isolate appeared to be more closely related to C. reinhardtii than any other known species. All seven new C. reinhardtii strains were interfertile with previously collected C. reinhardtii field isolates, validating the effectiveness of our molecular screen.
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Affiliation(s)
- Scott A Ford
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario, M5S 3G5, Canada
| | - Rory J Craig
- California Institute for Quantitative Biosciences, University of California, Berkeley, 174 Stanley Hall, Berkeley, California, 94720-3220, USA
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario, L5L 1C6, Canada
- Department of Cell & Systems Biology, University of Toronto, 25 Harbord Street, Toronto, Ontario, M5S 3G5, Canada
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario, M5S 3B2, Canada
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2
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López-Cortegano E, Craig RJ, Chebib J, Samuels T, Morgan AD, Kraemer SA, Böndel KB, Ness RW, Colegrave N, Keightley PD. De Novo Mutation Rate Variation and Its Determinants in Chlamydomonas. Mol Biol Evol 2021; 38:3709-3723. [PMID: 33950243 PMCID: PMC8383909 DOI: 10.1093/molbev/msab140] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
De novo mutations are central for evolution, since they provide the raw material for natural selection by regenerating genetic variation. However, studying de novo mutations is challenging and is generally restricted to model species, so we have a limited understanding of the evolution of the mutation rate and spectrum between closely related species. Here, we present a mutation accumulation (MA) experiment to study de novo mutation in the unicellular green alga Chlamydomonas incerta and perform comparative analyses with its closest known relative, Chlamydomonas reinhardtii. Using whole-genome sequencing data, we estimate that the median single nucleotide mutation (SNM) rate in C. incerta is μ = 7.6 × 10-10, and is highly variable between MA lines, ranging from μ = 0.35 × 10-10 to μ = 131.7 × 10-10. The SNM rate is strongly positively correlated with the mutation rate for insertions and deletions between lines (r > 0.97). We infer that the genomic factors associated with variation in the mutation rate are similar to those in C. reinhardtii, allowing for cross-prediction between species. Among these genomic factors, sequence context and complexity are more important than GC content. With the exception of a remarkably high C→T bias, the SNM spectrum differs markedly between the two Chlamydomonas species. Our results suggest that similar genomic and biological characteristics may result in a similar mutation rate in the two species, whereas the SNM spectrum has more freedom to diverge.
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Affiliation(s)
- Eugenio López-Cortegano
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Rory J Craig
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jobran Chebib
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Toby Samuels
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew D Morgan
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Katharina B Böndel
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Nick Colegrave
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter D Keightley
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
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Craig RJ, Hasan AR, Ness RW, Keightley PD. Comparative genomics of Chlamydomonas. THE PLANT CELL 2021; 33:1016-1041. [PMID: 33793842 PMCID: PMC8226300 DOI: 10.1093/plcell/koab026] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 01/22/2021] [Indexed: 05/06/2023]
Abstract
Despite its role as a reference organism in the plant sciences, the green alga Chlamydomonas reinhardtii entirely lacks genomic resources from closely related species. We present highly contiguous and well-annotated genome assemblies for three unicellular C. reinhardtii relatives: Chlamydomonas incerta, Chlamydomonas schloesseri, and the more distantly related Edaphochlamys debaryana. The three Chlamydomonas genomes are highly syntenous with similar gene contents, although the 129.2 Mb C. incerta and 130.2 Mb C. schloesseri assemblies are more repeat-rich than the 111.1 Mb C. reinhardtii genome. We identify the major centromeric repeat in C. reinhardtii as a LINE transposable element homologous to Zepp (the centromeric repeat in Coccomyxa subellipsoidea) and infer that centromere locations and structure are likely conserved in C. incerta and C. schloesseri. We report extensive rearrangements, but limited gene turnover, between the minus mating type loci of these Chlamydomonas species. We produce an eight-species core-Reinhardtinia whole-genome alignment, which we use to identify several hundred false positive and missing genes in the C. reinhardtii annotation and >260,000 evolutionarily conserved elements in the C. reinhardtii genome. In summary, these resources will enable comparative genomics analyses for C. reinhardtii, significantly extending the analytical toolkit for this emerging model system.
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Affiliation(s)
| | - Ahmed R Hasan
- Department of Biology, University of Toronto Mississauga, Mississauga, Onatrio, Canada L5L 1C6
| | - Rob W Ness
- Department of Biology, University of Toronto Mississauga, Mississauga, Onatrio, Canada L5L 1C6
| | - Peter D Keightley
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, EH9 3FL Edinburgh, UK
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4
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Maltsev Y, Maltseva I, Maltseva S, Kociolek JP, Kulikovskiy M. A New Species of Freshwater Algae Nephrochlamys yushanlensis sp. nov. (Selenastraceae, Sphaeropleales) and Its Lipid Accumulation during Nitrogen and Phosphorus Starvation. JOURNAL OF PHYCOLOGY 2021; 57:606-618. [PMID: 33296071 DOI: 10.1111/jpy.13116] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 10/17/2020] [Accepted: 10/28/2020] [Indexed: 06/12/2023]
Abstract
The new species Nephrochlamys yushanlensis sp. nov. is described from a freshwater plankton sample. A comparison of morphology, 18S rDNA gene and ITS2 sequences, and fatty acid profiles showed that the novel strain represents a new lineage within the genus Nephrochlamys. For the first time with a member of the Selenastraceae, experiments with phosphate and nitrate deprivation were conducted to evaluate changes in biomass, lipid and triacylglycerol (TAGs) accumulation, and composition of fatty acids. Biomass dry weight under simultaneous nitrogen and phosphorus depletion was 1.73 g · L-1 , which is significantly lower than the 2.41 g · L-1 observed in the control. All conditions of nutrient restriction significantly increased the lipid content in comparison with the control. The largest increase in the total lipid content, reaching 58.64% DW per cell at the end of cultivation, occurred with nitrogen deficiency. Significant increases in TAGs content (to 23.69% and 21.74%, respectively) occurred in phosphorus- and nitrogen-depleted conditions in comparison to the control (16.90%). Oleic (49.8-64.1%), palmitic (21.1-22.7%), and linoleic (8.6-10.3%) acids were the dominant fatty acids when cultured on standard BBM medium, as well as with the shortage of nutrients. Phosphorus deprivation as well as absence of both nitrogen and phosphorus led to the appearance of FAMEs α-linolenic (1.5-4.1%) and stearidonic (1.0-1.8%) acids. In general, FAME profiles revealed that the relative percentage of saturated and monounsaturated fatty acids increased (88.9% of total fatty acids) in nitrogen-depletion conditions, suggesting this strain may be suitable for biodiesel production.
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Affiliation(s)
- Yevhen Maltsev
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
| | - Irina Maltseva
- Bohdan Khmelnytskyi Melitopol State Pedagogical University, 72312, Melitopol, Ukraine
| | - Svetlana Maltseva
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
| | - John Patrick Kociolek
- Museum of Natural History and Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USA
| | - Maxim Kulikovskiy
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
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Matsuzaki R, Suzuki S, Yamaguchi H, Kawachi M, Kanesaki Y, Yoshikawa H, Mori T, Nozaki H. The Rubisco small subunits in the green algal genus Chloromonas provide insights into evolutionary loss of the eukaryotic carbon-concentrating organelle, the pyrenoid. BMC Ecol Evol 2021; 21:11. [PMID: 33514317 PMCID: PMC7853309 DOI: 10.1186/s12862-020-01733-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 12/10/2020] [Indexed: 12/14/2022] Open
Abstract
Background Pyrenoids are protein microcompartments composed mainly of Rubisco that are localized in the chloroplasts of many photosynthetic organisms. Pyrenoids contribute to the CO2-concentrating mechanism. This organelle has been lost many times during algal/plant evolution, including with the origin of land plants. The molecular basis of the evolutionary loss of pyrenoids is a major topic in evolutionary biology. Recently, it was hypothesized that pyrenoid formation is controlled by the hydrophobicity of the two helices on the surface of the Rubisco small subunit (RBCS), but the relationship between hydrophobicity and pyrenoid loss during the evolution of closely related algal/plant lineages has not been examined. Here, we focused on, the Reticulata group of the unicellular green algal genus Chloromonas, within which pyrenoids are present in some species, although they are absent in the closely related species. Results Based on de novo transcriptome analysis and Sanger sequencing of cloned reverse transcription-polymerase chain reaction products, rbcS sequences were determined from 11 strains of two pyrenoid-lacking and three pyrenoid-containing species of the Reticulata group. We found that the hydrophobicity of the RBCS helices was roughly correlated with the presence or absence of pyrenoids within the Reticulata group and that a decrease in the hydrophobicity of the RBCS helices may have primarily caused pyrenoid loss during the evolution of this group. Conclusions Although we suggest that the observed correlation may only exist for the Reticulata group, this is still an interesting study that provides novel insight into a potential mechanism determining initial evolutionary steps of gain and loss of the pyrenoid.
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Affiliation(s)
- Ryo Matsuzaki
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Shigekatsu Suzuki
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Haruyo Yamaguchi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Yu Kanesaki
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, 422-8529, Japan.,NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, 156-8502, Japan
| | - Toshiyuki Mori
- Department of Tropical Medicine and Parasitology, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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Sexual reproduction of the snow alga Chloromonas fukushimae (Volvocales, Chlorophyceae) induced using cultured materials. PLoS One 2020; 15:e0238265. [PMID: 32845939 PMCID: PMC7449499 DOI: 10.1371/journal.pone.0238265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/12/2020] [Indexed: 11/19/2022] Open
Abstract
Snow algae are microalgae, growing in melting snowpacks, and are thought to act as primary producers in the snow ecosystem. Chloromonas (Volvocales, Chlorophyceae) contains more than 15 snow-inhabiting species. Although vegetative cells and zygotes, or asexual cysts, of snow species of the genus are frequently collected in the field, sexual reproduction and zygote formation in culture have only been induced in C. tughillensis. Here we describe the sexual reproduction of another snow-inhabiting species, C. fukushimae, which was induced using both previously examined and newly established Japanese strains. Mating of isogamous gametes began after mixing two different strains, implying that C. fukushimae is an outcrossing species. Motile and nonmotile zygotes of the species were also described in this report. The nonmotile zygote of C. fukushimae was distinguishable from those of the other snow-inhabiting species of Chloromonas, based on the zygote shape and the presence of several large lipid bodies within the cell. In addition, C. fukushimae carried out sexual reproduction and produced zygotes even under the nitrogen-sufficient condition.
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Maltsev Y, Maltseva I, Maltseva S, Kociolek JP, Kulikovskiy M. Fatty Acid Content and Profile of the Novel Strain of Coccomyxa elongata (Trebouxiophyceae, Chlorophyta) Cultivated at Reduced Nitrogen and Phosphorus Concentrations. JOURNAL OF PHYCOLOGY 2019; 55:1154-1165. [PMID: 31318981 DOI: 10.1111/jpy.12903] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/01/2019] [Indexed: 06/10/2023]
Abstract
A novel freshwater strain of Coccomyxa elongata (MZ-Ch64) was isolated from the Zaporizhia region, Ukraine. The identification was based on the phylogenetic analysis of SSU rDNA gene and ITS1-5.8S rDNA-ITS2 region and predicted secondary structure of the ITS2. Phylogenetic analysis placed this strain in the Coccomyxa group, within the class Trebouxiophyceae. The novel strain MZ-Ch64 formed a strongly supported lineage closest with C. elongata. The MZ-Ch64 strain differed from the morphological description of the species by the size of vegetative cells and absence of small mucilaginous caps at one end of the cell. A number of experiments with different concentrations of phosphate and nitrate were conducted to evaluate changes in the resulting fatty acid profiles and biomass productivity. The fatty acid profile and total fatty acids varied significantly under different nutrient deficiencies. The dominant fatty acid during cultivation on standard BBM medium, as well as in phosphorus-depleted conditions, was oleic acid (to 48.0%-54.6% of total fatty acids). Absence of nitrogen alone, and absence of both nitrogen and phosphorus, led to an increase of palmitic acid (to 24.7%-25.6%), cis-7-hexadecenoic acid (to 14.8%) and α-linolenic acid (to 9.1%-10.1%) in comparison with the control sample. The greatest variation was found for oleic acid (31.9%-54.6%). Thus, this strain can be considered as a potential producer of oleic acid or cis-7-hexadecenoic and α-linolenic acids for biotechnological applications.
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Affiliation(s)
- Yevhen Maltsev
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
| | - Irina Maltseva
- Bohdan Khmelnytskyi Melitopol State Pedagogical University, 72312, Melitopol, Ukraine
| | - Svetlana Maltseva
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
| | - John Patrick Kociolek
- Museum of Natural History and Department of Ecology and Evolutionary Biology, University of Colorado, 80309, Boulder, Colorado, USA
| | - Maxim Kulikovskiy
- К.A. Timiryazev Institute of Plant Physiology RAS, IPP RAS, Moscow, 127276, Russia
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Craig RJ, Böndel KB, Arakawa K, Nakada T, Ito T, Bell G, Colegrave N, Keightley PD, Ness RW. Patterns of population structure and complex haplotype sharing among field isolates of the green algaChlamydomonas reinhardtii. Mol Ecol 2019; 28:3977-3993. [DOI: 10.1111/mec.15193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 07/05/2019] [Accepted: 07/17/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Rory J. Craig
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
- Department of Biology University of Toronto Mississauga Mississauga ON Canada
| | - Katharina B. Böndel
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
- Institute of Plant Breeding, Seed Science and Population Genetics University of Hohenheim Stuttgart Germany
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences Keio University Tsuruoka Japan
- Systems Biology Program Graduate School of Media and Governance Keio University Fujisawa Japan
| | - Takashi Nakada
- Institute for Advanced Biosciences Keio University Tsuruoka Japan
- Systems Biology Program Graduate School of Media and Governance Keio University Fujisawa Japan
- Faculty of Environment and Information Sciences Yokohama National University Yokohama Japan
| | - Takuro Ito
- Institute for Advanced Biosciences Keio University Tsuruoka Japan
- Systems Biology Program Graduate School of Media and Governance Keio University Fujisawa Japan
| | - Graham Bell
- Department of Biology McGill University Montreal QC Canada
| | - Nick Colegrave
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Peter D. Keightley
- Institute of Evolutionary Biology School of Biological Sciences University of Edinburgh Edinburgh UK
| | - Rob W. Ness
- Department of Biology University of Toronto Mississauga Mississauga ON Canada
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Matsuzaki R, Nozaki H, Takeuchi N, Hara Y, Kawachi M. Taxonomic re-examination of "Chloromonas nivalis (Volvocales, Chlorophyceae) zygotes" from Japan and description of C. muramotoi sp. nov. PLoS One 2019; 14:e0210986. [PMID: 30677063 PMCID: PMC6345437 DOI: 10.1371/journal.pone.0210986] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/06/2019] [Indexed: 11/19/2022] Open
Abstract
Recent molecular data has strongly suggested that field-collected cysts of snow algae that are morphologically identifiable as the zygotes of Chloromonas nivalis are composed of multiple species. Motile vegetative cells, however, have not been directly obtained from these cysts because of the difficulties involved in inducing their germination. Recently, our comparative molecular analyses, using both field-collected and cultured materials, demonstrated that one Japanese lineage of "C. nivalis zygotes" belongs to C. miwae. Herein, we examined another Japanese lineage of field-collected "C. nivalis zygotes" and a new strain originating from Japan. Our molecular data demonstrated that these two different life cycle stages are conspecific, and that they represent a new species that we herein describe as C. muramotoi sp. nov., based on the vegetative and asexual morphological characteristics of the strain. Multigene phylogenetic analyses showed that this new species was sister to C. miwae. Scanning electron microscopy demonstrated that the cysts of C. muramotoi are different from those of C. miwae, based on the arrangement of the flanges developing on the cell wall.
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Affiliation(s)
- Ryo Matsuzaki
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Nozomu Takeuchi
- Department of Earth Sciences, Graduate School of Science, Chiba University, Yayoicho, Inage ward, Chiba, Chiba, Japan
| | - Yoshiaki Hara
- Institute of Arts and Sciences, Yamagata University, Kojirakawa, Yamagata, Yamagata, Japan
| | - Masanobu Kawachi
- Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, Japan
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Young R, Purton S. CITRIC: cold-inducible translational readthrough in the chloroplast of Chlamydomonas reinhardtii using a novel temperature-sensitive transfer RNA. Microb Cell Fact 2018; 17:186. [PMID: 30474564 PMCID: PMC6260665 DOI: 10.1186/s12934-018-1033-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/16/2018] [Indexed: 01/17/2023] Open
Abstract
Background The chloroplast of eukaryotic microalgae such as Chlamydomonas reinhardtii is a potential platform for metabolic engineering and the production of recombinant proteins. In industrial biotechnology, inducible expression is often used so that the translation or function of the heterologous protein does not interfere with biomass accumulation during the growth stage. However, the existing systems used in bacterial or fungal platforms do not transfer well to the microalgal chloroplast. We sought to develop a simple inducible expression system for the microalgal chloroplast, exploiting an unused stop codon (TGA) in the plastid genome. We have previously shown that this codon can be translated as tryptophan when we introduce into the chloroplast genome a trnWUCA gene encoding a plastidial transfer RNA with a modified anticodon sequence, UCA. Results A mutated version of our trnWUCA gene was developed that encodes a temperature-sensitive variant of the tRNA. This allows transgenes that have been modified to contain one or more internal TGA codons to be translated differentially according to the culture temperature, with a gradient of recombinant protein accumulation from 35 °C (low/off) to 15 °C (high). We have named this the CITRIC system, an acronym for cold-inducible translational readthrough in chloroplasts. The exact induction behaviour can be tailored by altering the number of TGA codons within the transgene. Conclusions CITRIC adds to the suite of genetic engineering tools available for the microalgal chloroplast, allowing a greater degree of control over the timing of heterologous protein expression. It could also be used as a heat-repressible system for studying the function of essential native genes in the chloroplast. The genetic components of CITRIC are entirely plastid-based, so no engineering of the nuclear genome is required. Electronic supplementary material The online version of this article (10.1186/s12934-018-1033-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rosanna Young
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.,Department of Medicine, Sir Alexander Fleming Building, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Saul Purton
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.
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11
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Sasso S, Stibor H, Mittag M, Grossman AR. From molecular manipulation of domesticated Chlamydomonas reinhardtii to survival in nature. eLife 2018; 7:39233. [PMID: 30382941 PMCID: PMC6211829 DOI: 10.7554/elife.39233] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/12/2018] [Indexed: 01/19/2023] Open
Abstract
In the mid-20th century, the unicellular and genetically tractable green alga Chlamydomonas reinhardtii was first developed as a model organism to elucidate fundamental cellular processes such as photosynthesis, light perception and the structure, function and biogenesis of cilia. Various studies of C. reinhardtii have profoundly advanced plant and cell biology, and have also impacted algal biotechnology and our understanding of human disease. However, the 'real' life of C. reinhardtii in the natural environment has largely been neglected. To extend our understanding of the biology of C. reinhardtii, it will be rewarding to explore its behavior in its natural habitats, learning more about its abundance and life cycle, its genetic and physiological diversity, and its biotic and abiotic interactions.
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Affiliation(s)
- Severin Sasso
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, Germany
| | - Herwig Stibor
- Department Biology II, Ludwig Maximilian University, Munich, Germany
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, Germany
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Improved taxon sampling and multigene phylogeny of unicellular chlamydomonads closely related to the colonial volvocalean lineage Tetrabaenaceae-Goniaceae-Volvocaceae (Volvocales, Chlorophyceae). Mol Phylogenet Evol 2018; 130:1-8. [PMID: 30266459 DOI: 10.1016/j.ympev.2018.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 09/13/2018] [Accepted: 09/21/2018] [Indexed: 11/23/2022]
Abstract
In the green algal order Volvocales (Chlorophyceae), flagellate colonial forms have evolved at least four times. One of these colonial lineages, Tetrabaenaceae-Goniaceae-Volvocaceae (TGV), which belongs to the clade Reinhardtinia, is closely related to several unicellular chlamydomonads in the genera Chlamydomonas and Vitreochlamys. However, the unicellular sister of TGV has not been specified. Here, the largest ever 18S rRNA phylogenetic tree of Reinhardtinia was constructed including several newly isolated chlamydomonads, and a clade (core-Reinhardtinia) including 32 unicellular lineages and three colonial families were recognized. Interrelationships within core-Reinhardtinia were barely resolved in the tree, and therefore combined 18S-atpB-psaA-psaB-psbC-rbcL gene phylogenetic analyses were performed with selected representatives of 29 of the 32 unicellular lineages and three colonial families. The 29 unicellular lineages were clustered into five metaclades and an unassigned lineage; the metaclade that includes Chlamydomonas pila was resolved, with moderate support, as the sister clade to TGV. To examine possible biases from specific gene(s), long-branch taxa, and the heterogeneous base composition, phylogenetic analyses using several smaller data sets were also performed. Light microscopy of C. pila and its relatives indicated that any early steps towards colony evolution appeared after divergence of TGV from the C. pila lineage.
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Maltsev Y, Gusev E, Maltseva I, Kulikovskiy M, Namsaraev Z, Petrushkina M, Filimonova A, Sorokin B, Golubeva A, Butaeva G, Khrushchev A, Zotko N, Kuzmin D. Description of a new species of soil algae, Parietochloris grandis sp. nov., and study of its fatty acid profiles under different culturing conditions. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.06.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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14
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Phylogeny of the egg-loving green alga Oophila amblystomatis (Chlamydomonadales) and its response to the herbicides atrazine and 2,4-D. Symbiosis 2018. [DOI: 10.1007/s13199-018-0564-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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15
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Geng S, Miyagi A, Umen JG. Evolutionary divergence of the sex-determining gene MID uncoupled from the transition to anisogamy in volvocine algae. Development 2018; 145:dev.162537. [PMID: 29549112 DOI: 10.1242/dev.162537] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 03/13/2018] [Indexed: 12/28/2022]
Abstract
Volvocine algae constitute a unique comparative model for investigating the evolution of oogamy from isogamous mating types. The sex- or mating type-determining gene MID encodes a conserved RWP-RK transcription factor found in either the MT- or male mating locus of dioecious volvocine species. We previously found that MID from the isogamous species Chlamydomonas reinhardtii (CrMID) could not induce ectopic spermatogenesis when expressed heterologously in Volvox carteri females, suggesting coevolution of Mid function with gamete dimorphism. Here we found that ectopic expression of MID from the anisogamous species Pleodorina starrii (PsMID) could efficiently induce spermatogenesis when expressed in V. carteri females and, unexpectedly, that GpMID from the isogamous species Gonium pectorale was also able to induce V. carteri spermatogenesis. Neither VcMID nor GpMID could complement a C. reinhardtii mid mutant, at least partly owing to instability of heterologous Mid proteins. Our data show that Mid divergence was not a major contributor to the transition between isogamy and anisogamy/oogamy in volvocine algae, and instead implicate changes in cis-regulatory interactions and/or trans-acting factors of the Mid network in the evolution of sexual dimorphism.
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Affiliation(s)
- Sa Geng
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA
| | - Ayano Miyagi
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA
| | - James G Umen
- Donald Danforth Plant Science Center, 975 N. Warson Rd., St. Louis, MO 63132, USA
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16
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Procházková L, Remias D, Řezanka T, Nedbalová L. Chloromonas nivalis subsp. tatrae, subsp. nov. (Chlamydomonadales, Chlorophyta): re-examination of a snow alga from the High Tatra Mountains (Slovakia). FOTTEA (PRAHA) 2018; 18:1-18. [PMID: 30976329 PMCID: PMC6456015 DOI: 10.5507/fot.2017.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Melting snow fields populated by aplanozygotes of the genus Chloromonas (Chlamydomonadales, Chlorophyta) are found in polar and alpine habitats. In the High Tatra Mountains (Slovakia), cells causing blooms of brownish-red snow designated as Scotiella tatrae kol turned out to be genetically (18S, ITS1 and ITS2 rDNA, rbcL) very closely related to Chloromonas nivalis (Chodat) Hoham et Mullet from the Austrian Alps. Therefore, Sc. tatrae is transferred into the latter taxon and reduced to a subspecies as Cr. nivalis subsp. tatrae. Both exhibit a similar photosynthetic performance, thrive in similar habitats at open sites above timberline, but differ in astaxanthin accumulation and number of aplanozygote cell wall flanges. In a field sample of Cr. nivalis subsp. tatrae, polyunsaturated fatty acids formed nearly 50 % of total lipids, dominating in phospholipids and glycolipids. Cr. nivalis subsp. tatrae represents likely a variation of a common cryoflora species with distinct morphology.
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Affiliation(s)
- Lenka Procházková
- Charles University, Faculty of Science, Department of Ecology, Viničná 7, CZ–128 44 Prague, Czech Republic
- Corresponding author
| | - Daniel Remias
- University of Applied Sciences Upper Austria, Stelzhamerstraße 23, A–4600 Wels, Austria
| | - Tomáš Řezanka
- Institute of Microbiology CAS, Vídeňská 1083, CZ–142 20 Prague, Czech Republic
| | - Linda Nedbalová
- Charles University, Faculty of Science, Department of Ecology, Viničná 7, CZ–128 44 Prague, Czech Republic
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17
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Simon N, Foulon E, Grulois D, Six C, Desdevises Y, Latimier M, Le Gall F, Tragin M, Houdan A, Derelle E, Jouenne F, Marie D, Le Panse S, Vaulot D, Marin B. Revision of the Genus Micromonas Manton et Parke (Chlorophyta, Mamiellophyceae), of the Type Species M. pusilla (Butcher) Manton & Parke and of the Species M. commoda van Baren, Bachy and Worden and Description of Two New Species Based on the Genetic and Phenotypic Characterization of Cultured Isolates. Protist 2017; 168:612-635. [PMID: 29028580 DOI: 10.1016/j.protis.2017.09.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 08/31/2017] [Accepted: 09/06/2017] [Indexed: 11/30/2022]
Abstract
The green picoalgal genus Micromonas is broadly distributed in estuaries, coastal marine habitats and open oceans, from the equator to the poles. Phylogenetic, ecological and genomic analyses of culture strains and natural populations have suggested that this cosmopolitan genus is composed of several cryptic species corresponding to genetic lineages. We performed a detailed analysis of variations in morphology, pigment content, and sequences of the nuclear-encoded small-subunit rRNA gene and the second internal transcribed spacer (ITS2) from strains isolated worldwide. A new morphological feature of the genus, the presence of tip hairs at the extremity of the hair point, was discovered and subtle differences in hair point length were detected between clades. Clear non-homoplasious synapomorphies were identified in the small-subunit rRNA gene and ITS2 spacer sequences of five genetic lineages. These findings lead us to provide emended descriptions of the genus Micromonas, of the type species M. pusilla, and of the recently described species M. commoda, as well as to describe 2 new species, M. bravo and M. polaris. By clarifying the status of the genetic lineages identified within Micromonas, these formal descriptions will facilitate further interpretations of large-scale analyses investigating ecological trends in time and space for this widespread picoplankter.
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Affiliation(s)
- Nathalie Simon
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France.
| | - Elodie Foulon
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Daphné Grulois
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Christophe Six
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Yves Desdevises
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7232, BIOM, Observatoire Océanologique, 66650 Banyuls/Mer, France
| | - Marie Latimier
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Florence Le Gall
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Margot Tragin
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Aude Houdan
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Evelyne Derelle
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7232, BIOM, Observatoire Océanologique, 66650 Banyuls/Mer, France
| | - Fabien Jouenne
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Dominique Marie
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Sophie Le Panse
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), FR2424, Imaging Core Facility, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Daniel Vaulot
- Sorbonne Universités, Université Pierre et Marie Curie - Paris 06 and Centre National de la recherche Scientifique (CNRS), UMR 7144, Laboratoire Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Place Georges Teissier, 29680 Roscoff, France
| | - Birger Marin
- Botanisches Institut, Biozentrum Köln, Universität zu Köln, Zülpicher Str. 47b, 50674 Köln, Germany
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18
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19
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Adaptation of phytoplankton to a decade of experimental warming linked to increased photosynthesis. Nat Ecol Evol 2017; 1:94. [PMID: 28812653 DOI: 10.1038/s41559-017-0094] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 01/19/2017] [Indexed: 11/08/2022]
Abstract
Phytoplankton photosynthesis is a critical flux in the carbon cycle, accounting for approximately 40% of the carbon dioxide fixed globally on an annual basis and fuelling the productivity of aquatic food webs. However, rapid evolutionary responses of phytoplankton to warming remain largely unexplored, particularly outside the laboratory, where multiple selection pressures can modify adaptation to environmental change. Here, we use a decade-long experiment in outdoor mesocosms to investigate mechanisms of adaptation to warming (+4 °C above ambient temperature) in the green alga Chlamydomonas reinhardtii, in naturally assembled communities. Isolates from warmed mesocosms had higher optimal growth temperatures than their counterparts from ambient treatments. Consequently, warm-adapted isolates were stronger competitors at elevated temperature and experienced a decline in competitive fitness in ambient conditions, indicating adaptation to local thermal regimes. Higher competitive fitness in the warmed isolates was linked to greater photosynthetic capacity and reduced susceptibility to photoinhibition. These findings suggest that adaptive responses to warming in phytoplankton could help to mitigate projected declines in aquatic net primary production by increasing rates of cellular net photosynthesis.
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20
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Nakada T, Tomita M. Morphology and phylogeny of a new wall-less freshwater volvocalean flagellate, Hapalochloris nozakii gen. et sp. nov. (Volvocales, Chlorophyceae). JOURNAL OF PHYCOLOGY 2017; 53:108-117. [PMID: 27767210 DOI: 10.1111/jpy.12484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 09/13/2016] [Indexed: 06/06/2023]
Abstract
New strains of a wall-less unicellular volvocalean flagellate were isolated from a freshwater environment in Japan. Observations of the alga, described here as Hapalochloris nozakii Nakada, gen. et sp. nov., were made using light, fluorescence, and electron microscopy. Each vegetative cell had two flagella, four contractile vacuoles, and a spirally furrowed cup-shaped chloroplast with an axial pyrenoid, and mitochondria located in the furrows. Based on the morphology, H. nozakii was distinguished from other known wall-less volvocalean flagellates. Under electron microscopy, fibrous material, instead of a cell wall and dense cortical microtubules, was observed outside and inside the cell membrane, respectively. Based on the phylogenetic analyses of 18S rRNA gene sequences, H. nozakii was found to be closely related to Asterococcus, Oogamochlamys, Rhysamphichloris, and "Dunaliella" lateralis and was separated from other known wall-less flagellate volvocaleans, indicating independent secondary loss of the cell wall in H. nozakii. In the combined 18S rRNA and chloroplast gene tree, H. nozakii was sister to Lobochlamys.
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Affiliation(s)
- Takashi Nakada
- Institute for Advanced Biosciences, Keio University, Kakuganji, Tsuruoka 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Kakuganji, Tsuruoka 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa 252-0882, Japan
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21
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Nakada T, Tomita M, Wu JT, Nozaki H. Taxonomic revision of Chlamydomonas subg. Amphichloris (Volvocales, Chlorophyceae), with resurrection of the genus Dangeardinia and descriptions of Ixipapillifera gen. nov. and Rhysamphichloris gen. nov. JOURNAL OF PHYCOLOGY 2016; 52:283-304. [PMID: 27037593 DOI: 10.1111/jpy.12397] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 12/17/2015] [Indexed: 06/05/2023]
Abstract
Chlamydomonas (Cd.) is one of the largest but most polyphyletic genera of freshwater unicellular green algae. It consists of 400-600 morphological species and requires taxonomic revision. Toward reclassification, each morphologically defined classical subgenus (or subgroup) should be examined using culture strains. Chlamydomonas subg. Amphichloris is characterized by a central nucleus between two axial pyrenoids, however, the phylogenetic structure of this subgenus has yet to be examined using molecular data. Here, we examined 12 strains including six newly isolated strains, morphologically identified as Chlamydomonas subg. Amphichloris, using 18S rRNA gene phylogeny, light microscopy, and mitochondria fluorescent microscopy. Molecular phylogenetic analyses revealed three independent lineages of the subgenus, separated from the type species of Chlamydomonas, Cd. reinhardtii. These three lineages were further distinguished from each other by light and fluorescent microscopy-in particular by the morphology of the papillae, chloroplast surface, stigmata, and mitochondria-and are here assigned to three genera: Dangeardinia emend., Ixipapillifera gen. nov., and Rhysamphichloris gen. nov. Based on the molecular and morphological data, two to three species were recognized in each genus, including one new species, I. pauromitos. In addition, Cd. deasonii, which was previously assigned to subgroup "Pleiochloris," was included in the genus Ixipapillifera as I. deasonii comb. nov.
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Affiliation(s)
- Takashi Nakada
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
- Institute for Advanced Biosciences, Keio University, Kakuganji, Tsuruoka, 997-0052, Japan
| | - Masaru Tomita
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
- Institute for Advanced Biosciences, Keio University, Kakuganji, Tsuruoka, 997-0052, Japan
| | - Jiunn-Tzong Wu
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bukyo-ku, Tokyo, 113-0033, Japan
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22
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Munakata H, Nakada T, Nakahigashi K, Nozaki H, Tomita M. Phylogenetic Position and Molecular Chronology of a Colonial Green Flagellate, Stephanosphaera pluvialis
(Volvocales, Chlorophyceae), among Unicellular Algae. J Eukaryot Microbiol 2015; 63:340-8. [DOI: 10.1111/jeu.12283] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 11/10/2015] [Accepted: 11/13/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Hidehito Munakata
- Systems Biology Program; Graduate School of Media and Governance; Keio University; Fujisawa 252-0882 Japan
- Institute for Advanced Biosciences; Keio University; Kakuganji Tsuruoka 997-0052 Japan
| | - Takashi Nakada
- Systems Biology Program; Graduate School of Media and Governance; Keio University; Fujisawa 252-0882 Japan
- Institute for Advanced Biosciences; Keio University; Kakuganji Tsuruoka 997-0052 Japan
| | - Kenji Nakahigashi
- Systems Biology Program; Graduate School of Media and Governance; Keio University; Fujisawa 252-0882 Japan
- Institute for Advanced Biosciences; Keio University; Kakuganji Tsuruoka 997-0052 Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences; Graduate School of Science; University of Tokyo; 7-3-1 Hongo, Bunkyo Tokyo 113-0033 Japan
| | - Masaru Tomita
- Systems Biology Program; Graduate School of Media and Governance; Keio University; Fujisawa 252-0882 Japan
- Institute for Advanced Biosciences; Keio University; Kakuganji Tsuruoka 997-0052 Japan
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Kawasaki Y, Nakada T, Tomita M. Taxonomic revision of oil-producing green algae, Chlorococcum oleofaciens (Volvocales, Chlorophyceae), and its relatives. JOURNAL OF PHYCOLOGY 2015; 51:1000-1016. [PMID: 26986894 DOI: 10.1111/jpy.12343] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 07/13/2015] [Indexed: 06/05/2023]
Abstract
Historically, species in Volvocales were classified based primarily on morphology. Although the taxonomy of Chlamydomonas has been re-examined using a polyphasic approach including molecular phylogeny, that of Chlorococcum (Cc.), the largest coccoid genus in Volvocales, has yet to be reexamined. Six species thought to be synonymous with the oil-producing alga Cc. oleofaciens were previously not confirmed by molecular phylogeny. In this study, seven authentic strains of Cc. oleofaciens and its putative synonyms, along with 11 relatives, were examined based on the phylogeny of the 18S ribosomal RNA (rRNA) gene, comparisons of secondary structures of internal transcribed spacer 1 (ITS1) and ITS2 rDNA, and morphological observations by light microscopy. Seven 18S rRNA types were recognized among these strains and three were distantly related to Cc. oleofaciens. Comparisons of ITS rDNA structures suggested possible separation of the remaining four types into different species. Shapes of vegetative cells, thickness of the cell walls in old cultures, the size of cells in old cultures, and stigma morphology of zoospores also supported the 18S rRNA grouping. Based on these results, the 18 strains examined were reclassified into seven species. Among the putative synonyms, synonymy of Cc. oleofaciens, Cc. croceum, and Cc. granulosum was confirmed, and Cc. microstigmatum, Cc. rugosum, Cc. aquaticum, and Cc. nivale were distinguished from Cc. oleofaciens. Furthermore, another related strain is described as a new species, Macrochloris rubrioleum sp. nov.
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Affiliation(s)
- Yuriko Kawasaki
- Institute for Advanced Biosciences, Keio University, Kakuganji, Tsuruoka, 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
| | - Takashi Nakada
- Institute for Advanced Biosciences, Keio University, Kakuganji, Tsuruoka, 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Kakuganji, Tsuruoka, 997-0052, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-0882, Japan
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Geng S, De Hoff P, Umen JG. Evolution of sexes from an ancestral mating-type specification pathway. PLoS Biol 2014; 12:e1001904. [PMID: 25003332 PMCID: PMC4086717 DOI: 10.1371/journal.pbio.1001904] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/30/2014] [Indexed: 01/20/2023] Open
Abstract
Male and female sexes have evolved repeatedly in eukaryotes but the origins of dimorphic sexes and their relationship to mating types in unicellular species are not understood. Volvocine algae include isogamous species such as Chlamydomonas reinhardtii, with two equal-sized mating types, and oogamous multicellular species such as Volvox carteri with sperm-producing males and egg-producing females. Theoretical work predicts genetic linkage of a gamete cell-size regulatory gene(s) to an ancestral mating-type locus as a possible step in the evolution of dimorphic gametes, but this idea has not been tested. Here we show that, contrary to predictions, a single conserved mating locus (MT) gene in volvocine algae-MID, which encodes a RWP-RK domain transcription factor-evolved from its ancestral role in C. reinhardtii as a mating-type specifier, to become a determinant of sperm and egg development in V. carteri. Transgenic female V. carteri expressing male MID produced functional sperm packets during sexual development. Transgenic male V. carteri with RNA interference (RNAi)-mediated knockdowns of VcMID produced functional eggs, or self-fertile hermaphrodites. Post-transcriptional controls were found to regulate cell-type-limited expression and nuclear localization of VcMid protein that restricted its activity to nuclei of developing male germ cells and sperm. Crosses with sex-reversed strains uncoupled sex determination from sex chromosome identity and revealed gender-specific roles for male and female mating locus genes in sexual development, gamete fitness and reproductive success. Our data show genetic continuity between the mating-type specification and sex determination pathways of volvocine algae, and reveal evidence for gender-specific adaptations in the male and female mating locus haplotypes of Volvox. These findings will enable a deeper understanding of how a master regulator of mating-type determination in an ancestral unicellular species was reprogrammed to control sexually dimorphic gamete development in a multicellular descendant.
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Affiliation(s)
- Sa Geng
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
| | - Peter De Hoff
- The Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - James G. Umen
- Donald Danforth Plant Science Center, St. Louis, Missouri, United States of America
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Hamaji T, Ferris PJ, Nishii I, Nishimura Y, Nozaki H. Distribution of the sex-determining gene MID and molecular correspondence of mating types within the isogamous genus Gonium (Volvocales, Chlorophyta). PLoS One 2013; 8:e64385. [PMID: 23696888 PMCID: PMC3655996 DOI: 10.1371/journal.pone.0064385] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Accepted: 04/12/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Isogamous organisms lack obvious cytological differences in the gametes of the two complementary mating types. Consequently, it is difficult to ascertain which of the two mating types are homologous when comparing related but sexual isolated strains or species. The colonial volvocalean algal genus Gonium consists of such isogamous organisms with heterothallic mating types designated arbitrarily as plus or minus in addition to homothallic strains. Homologous molecular markers among lineages may provide an "objective" framework to assign heterothallic mating types. METHODOLOGY/PRINCIPAL FINDINGS Using degenerate primers designed based on previously reported MID orthologs, the "master regulator" of mating types/sexes in the colonial Volvocales, MID homologs were identified and their presence/absence was examined in nine strains of four species of Gonium. Only one of the two complementary mating types in each of the four heterothallic species has a MID homolog. In addition to heterothallic strains, a homothallic strain of G. multicoccum has MID. Molecular evolutionary analysis suggests that MID of this homothallic strain retains functional constraint comparable to that of the heterothallic strains. CONCLUSION/SIGNIFICANCE We coordinated mating genotypes based on presence or absence of a MID homolog, respectively, in heterothallic species. This scheme should be applicable to heterothallic species of other isogamous colonial Volvocales including Pandorina and Yamagishiella. Homothallism emerged polyphyletically in the colonial Volvocales, although its mechanism remains unknown. Our identification of a MID homolog for a homothallic strain of G. multicoccum suggests a MID-dependent mechanism is involved in the sexual developmental program of this homothallic species.
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Affiliation(s)
- Takashi Hamaji
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Japan.
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Hamaji T, Smith DR, Noguchi H, Toyoda A, Suzuki M, Kawai-Toyooka H, Fujiyama A, Nishii I, Marriage T, Olson BJSC, Nozaki H. Mitochondrial and plastid genomes of the colonial green alga Gonium pectorale give insights into the origins of organelle DNA architecture within the volvocales. PLoS One 2013; 8:e57177. [PMID: 23468928 PMCID: PMC3582580 DOI: 10.1371/journal.pone.0057177] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 01/18/2013] [Indexed: 02/07/2023] Open
Abstract
Volvocalean green algae have among the most diverse mitochondrial and plastid DNAs (mtDNAs and ptDNAs) from the eukaryotic domain. However, nearly all of the organelle genome data from this group are restricted to unicellular species, like Chlamydomonas reinhardtii, and presently only one multicellular species, the ∼4,000-celled Volvox carteri, has had its organelle DNAs sequenced. The V. carteri organelle genomes are repeat rich, and the ptDNA is the largest plastome ever sequenced. Here, we present the complete mtDNA and ptDNA of the colonial volvocalean Gonium pectorale, which is comprised of ∼16 cells and occupies a phylogenetic position closer to that of V. carteri than C. reinhardtii within the volvocine line. The mtDNA and ptDNA of G. pectorale are circular-mapping AT-rich molecules with respective lengths and coding densities of 16 and 222.6 kilobases and 73 and 44%. They share some features with the organelle DNAs of V. carteri, including palindromic repeats within the plastid compartment, but show more similarities with those of C. reinhardtii, such as a compact mtDNA architecture and relatively low organelle DNA intron contents. Overall, the G. pectorale organelle genomes raise several interesting questions about the origin of linear mitochondrial chromosomes within the Volvocales and the relationship between multicellularity and organelle genome expansion.
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Affiliation(s)
- Takashi Hamaji
- Department of Botany, Graduate School of Science, Kyoto University, Oiwake-cho, Kita-shirakawa, Sakyo-ku, Kyoto, Japan
| | - David R. Smith
- Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hideki Noguchi
- Center for Advanced Genomics, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Atsushi Toyoda
- Center for Advanced Genomics, National Institute of Genetics, Mishima, Shizuoka, Japan
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Masahiro Suzuki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Hiroko Kawai-Toyooka
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Asao Fujiyama
- Center for Advanced Genomics, National Institute of Genetics, Mishima, Shizuoka, Japan
- Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Ichiro Nishii
- Temasek Life Sciences Laboratory, The National University of Singapore, Singapore, Singapore
| | - Tara Marriage
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - Bradley J. S. C. Olson
- Division of Biology, Kansas State University, Manhattan, Kansas, United States of America
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
- * E-mail:
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Lerche K, Hallmann A. Stable nuclear transformation of Eudorina elegans. BMC Biotechnol 2013; 13:11. [PMID: 23402598 PMCID: PMC3576287 DOI: 10.1186/1472-6750-13-11] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 02/08/2013] [Indexed: 05/16/2023] Open
Abstract
Background A fundamental step in evolution was the transition from unicellular to differentiated, multicellular organisms. Volvocine algae have been used for several decades as a model lineage to investigate the evolutionary aspects of multicellularity and cellular differentiation. There are two well-studied volvocine species, a unicellular alga (Chlamydomonas reinhardtii) and a multicellular alga with differentiated cell types (Volvox carteri). Species with intermediate characteristics also exist, which blur the boundaries between unicellularity and differentiated multicellularity. These species include the globular alga Eudorina elegans, which is composed of 16–32 cells. However, detailed molecular analyses of E. elegans require genetic manipulation. Unfortunately, genetic engineering has not yet been established for Eudorina, and only limited DNA and/or protein sequence information is available. Results Here, we describe the stable nuclear transformation of E. elegans by particle bombardment using both a chimeric selectable marker and reporter genes from different heterologous sources. Transgenic algae resistant to paromomycin were achieved using the aminoglycoside 3′-phosphotransferase VIII (aphVIII) gene of Streptomyces rimosus, an actinobacterium, under the control of an artificial promoter consisting of two V. carteri promoters in tandem. Transformants exhibited an increase in resistance to paromomycin by up to 333-fold. Co-transformation with non-selectable plasmids was achieved with a rate of 50 - 100%. The luciferase (gluc) gene from the marine copepod Gaussia princeps, which previously was engineered to match the codon usage of C. reinhardtii, was used as a reporter gene. The expression of gluc was mediated by promoters from C. reinhardtii and V. carteri. Heterologous heat shock promoters induced an increase in luciferase activity (up to 600-fold) at elevated temperatures. Long-term stability and both constitutive and inducible expression of the co-bombarded gluc gene was demonstrated by transcription analysis and bioluminescence assays. Conclusions Heterologous flanking sequences, including promoters, work in E. elegans and permit both constitutive and inducible expression of heterologous genes. Stable nuclear transformation of E. elegans is now routine. Thus, we show that genetic engineering of a species is possible even without the resources of endogenous genes and promoters.
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Affiliation(s)
- Kai Lerche
- Department of Cellular and Developmental Biology of Plants, University of Bielefeld, Bielefeld, Germany
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Ratha SK, Prasanna R, Gupta V, Dhar DW, Saxena AK. Bioprospecting and indexing the microalgal diversity of different ecological habitats of India. World J Microbiol Biotechnol 2011; 28:1657-67. [PMID: 22805948 DOI: 10.1007/s11274-011-0973-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 12/02/2011] [Indexed: 11/29/2022]
Abstract
Our study reports the collection, biodiversity analyses, isolation and identification of microalgae from different habitats of India. Cyanophyceae and Chlorophyceae were the most dominant algal groups recorded, with the highest number being recorded for non-heterocystous cyanobacteria (48), followed by 44 unicellular forms. Sagar Island, Sunderbans recorded the greatest number of algae, and unicellular/colonial green algae were present in all the samples. Shannon's Diversity Index was highest in Koikhali, Sunderbans, followed by Rushikulya River, Odisha. Selective enrichment, purification through serial dilution followed by plating and regular observations led to the isolation of sixteen strains. Identification was done by using microscopic observations, supported with standard monographs and classified as belonging to seven genera (Chlorella, Chlorococcum, Kirchneria, Scenedesmus, Chlamydomonas, Tetracystis and Ulothrix). 18S rDNA sequencing was undertaken for four strains. The set of sixteen strains were screened under standard cultural conditions for their growth kinetics and Chlorella sorokiniana MIC-G5, followed by Chlorella sp. MIC-G4 exhibited the highest growth rates. The strain Chlorococcum sp. MIC-G2 recorded highest chlorophyll, while MIC-G3 ranked highest for carbohydrates. The study aided in identifying the dominant microalgae in the diverse habitats and characterizing their growth rate and carbohydrate content, providing a valuable germplasm for further utilization in agriculture and industry.
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Affiliation(s)
- Sachitra Kumar Ratha
- Division of Microbiology, Indian Agricultural Research Institute, New Delhi, 110012, India
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Setohigashi Y, Hamaji T, Hayama M, Matsuzaki R, Nozaki H. Uniparental inheritance of chloroplast DNA is strict in the isogamous volvocalean Gonium. PLoS One 2011; 6:e19545. [PMID: 21559302 PMCID: PMC3085477 DOI: 10.1371/journal.pone.0019545] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2011] [Accepted: 03/31/2011] [Indexed: 11/19/2022] Open
Abstract
Background A problem has remained unresolved regarding the exceptions to the unilateral inheritance of chloroplast DNA (cpDNA) from MT+/female in Chlamydomonas and other volvocaleans demonstrated by the previous genetic analyses. For identification of the parental types of cpDNA, these studies used parents that have differences in restriction fragment length polymorphisms and exhibit partial sexual incompatibility. Methodology/Principal Findings In the present study, we used sexually compatible parents of the isogamous colonial volvocalean Gonium maiaprilis that seemed an ideal species to identify the pattern of cpDNA inheritance based on the length difference in the putative group I intron interrupted in the Rubisco large subunit gene and objective identification of mating types by the presence or absence of the minus-dominance (MID) gene. We examined patterns of inheritance of cpDNA and presence/absence of a MID ortholog (GmMID) in 107 F1 progeny of G. maiaprilis that were obtained by inducing germination of separated single zygotes. The results demonstrated no exception of the uniparental inheritance of cpDNA from the MT+ parent (lacking GmMID) in sexually compatible or genetically less divergent strains of G. maiaprilis. Conclusions/Significance The present data suggest that the uniparental inheritance of cpDNA is likely more strict in crossings of less diverged strains or sexually compatible parental volvocaleans, and some genetic inconsistency between the parents may cause exceptional uniparental inheritance of cpDNA.
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Affiliation(s)
- Yuka Setohigashi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Takashi Hamaji
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Mahoko Hayama
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Ryo Matsuzaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo, Japan
- * E-mail:
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