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Takahashi K, Suzuki S, Kawai-Toyooka H, Yamamoto K, Hamaji T, Ootsuki R, Yamaguchi H, Kawachi M, Higashiyama T, Nozaki H. Reorganization of the ancestral sex-determining regions during the evolution of trioecy in Pleodorina starrii. Commun Biol 2023; 6:590. [PMID: 37296191 PMCID: PMC10256686 DOI: 10.1038/s42003-023-04949-1] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/17/2023] [Indexed: 06/12/2023] Open
Abstract
The coexistence of three sexual phenotypes (male, female and bisexual) in a single species, 'trioecy', is rarely found in diploid organisms such as flowering plants and invertebrates. However, trioecy in haploid organisms has only recently been reported in a green algal species, Pleodorina starrii. Here, we generated whole-genome data of the three sex phenotypes of P. starrii to reveal a reorganization of the ancestral sex-determining regions (SDRs) in the sex chromosomes: the male and bisexual phenotypes had the same "male SDR" with paralogous gene expansions of the male-determining gene MID, whereas the female phenotype had a "female SDR" with transposition of the female-specific gene FUS1 to autosomal regions. Although the male and bisexual sex phenotypes had the identical male SDR and harbored autosomal FUS1, MID and FUS1 expression during sexual reproduction differed between them. Thus, the coexistence of three sex phenotypes in P. starrii is possible.
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Affiliation(s)
- Kohei Takahashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Shigekatsu Suzuki
- Biodiversity Division, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Hiroko Kawai-Toyooka
- Department of Frontier Bioscience, Hosei University, Kajino-cho, Koganei, Tokyo, 184-8584, Japan
| | - Kayoko Yamamoto
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Takashi Hamaji
- Research and Development Initiative, Chuo University, Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan
| | - Ryo Ootsuki
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Bunkyo-ku, Tokyo, 112-8681, Japan
- Department of Natural Sciences, Faculty of Arts and Sciences, Komazawa University, Komazawa, Setagaya-ku, Tokyo, 154-8525, Japan
| | - Haruyo Yamaguchi
- Biodiversity Division, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Masanobu Kawachi
- Biodiversity Division, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
| | - Tetsuya Higashiyama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
- Biodiversity Division, National Institute for Environmental Studies, Onogawa, Tsukuba, Ibaraki, 305-8506, Japan.
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Sekimoto H, Komiya A, Tsuyuki N, Kawai J, Kanda N, Ootsuki R, Suzuki Y, Toyoda A, Fujiyama A, Kasahara M, Abe J, Tsuchikane Y, Nishiyama T. A divergent RWP-RK transcription factor determines mating type in heterothallic Closterium. New Phytol 2023; 237:1636-1651. [PMID: 36533897 DOI: 10.1111/nph.18662] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
The Closterium peracerosum-strigosum-littorale complex (Closterium, Zygnematophyceae) has an isogamous mating system. Members of the Zygnematophyceae are the closest relatives to extant land plants and are distantly related to chlorophytic models, for which a genetic basis of mating type (MT) determination has been reported. We thus investigated MT determination in Closterium. We sequenced genomes representing the two MTs, mt+ and mt-, in Closterium and identified CpMinus1, a gene linked to the mt- phenotype. We analyzed its function using reverse genetics methods. CpMinus1 encodes a divergent RWP-RK domain-containing-like transcription factor and is specifically expressed during gamete differentiation. Introduction of CpMinus1 into an mt+ strain was sufficient to convert it to a phenotypically mt- strain, while CpMinus1-knockout mt- strains were phenotypically mt+. We propose that CpMinus1 is the major MT determinant that acts by evoking the mt- phenotype and suppressing the mt+ phenotype in heterothallic Closterium. CpMinus1 likely evolved independently in the Zygnematophyceae lineage, which lost an egg-sperm anisogamous mating system. mt- specific regions possibly constitute an MT locus flanked by common sequences that undergo some recombination.
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Affiliation(s)
- Hiroyuki Sekimoto
- Division of Material and Biological Sciences, Graduate School of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Ayumi Komiya
- Division of Material and Biological Sciences, Graduate School of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Natsumi Tsuyuki
- Division of Material and Biological Sciences, Graduate School of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Junko Kawai
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Naho Kanda
- Division of Material and Biological Sciences, Graduate School of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Ryo Ootsuki
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8568, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Masahiro Kasahara
- Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8568, Japan
| | - Jun Abe
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Yuki Tsuchikane
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kakumacho, Kanazawa, Ishikawa, 920-1192, Japan
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Takahashi K, Kawai-Toyooka H, Ootsuki R, Hamaji T, Tsuchikane Y, Sekimoto H, Higashiyama T, Nozaki H. Three sex phenotypes in a haploid algal species give insights into the evolutionary transition to a self-compatible mating system. Evolution 2021; 75:2984-2993. [PMID: 34250602 PMCID: PMC9291101 DOI: 10.1111/evo.14306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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] [Received: 03/11/2021] [Revised: 05/17/2021] [Accepted: 06/01/2021] [Indexed: 01/01/2023]
Abstract
Mating systems of haploid species such as fungi, algae, and bryophytes are either heterothallic (self‐incompatible) with two sex phenotypes (male and female, or mating type minus and plus in isogamous species) or homothallic (self‐compatible) with only a bisexual phenotype producing zygotes within a clone. The anisogamous volvocine green alga Pleodorina starrii is a haploid species previously reported to have a heterothallic mating system. Here, we found that two additional culture strains originating from the same water system of P. starrii were taxonomically identified as P. starrii and produced male and female gametes and zygotes within a clone (bisexual). Sequences of rapidly evolving plastid genome regions were identical between the bisexual and unisexual (male or female) P. starrii strains. Intercrossings between the bisexual and unisexual strains demonstrated normal thick‐walled zygotes and high survivability of F1 strains. Thus, these strains belong to the same biological species. Pleodorina starrii has a new haploid mating system that is unique in having three sex phenotypes, namely, male, female, and bisexual. Genetic analyses suggested the existence of autosomal “bisexual factor” locus independent of volvocine male and female determining regions. The present findings increase our understanding of the initial evolutionary step of transition from heterothallism to homothallism.
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Affiliation(s)
- Kohei Takahashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiroko Kawai-Toyooka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.,Current Address: Department of Frontier Bioscience, Faculty of Bioscience and Applied Chemistry, Hosei University, Kajinocho, Koganei-shi, Tokyo, 184-8584, Japan
| | - Ryo Ootsuki
- Department of Natural Sciences, Faculty of Arts and Sciences, Komazawa University, Tokyo, 154-8525, Japan.,Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo, 112-8681, Japan
| | - Takashi Hamaji
- Research and Development Initiative, Chuo University, Tokyo, 112-8551, Japan
| | - Yuki Tsuchikane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.,Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo, 112-8681, Japan
| | - Hiroyuki Sekimoto
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Tokyo, 112-8681, Japan
| | - Tetsuya Higashiyama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.,Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan.,Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
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Imai R, Tsuda Y, Ebihara A, Matsumoto S, Tezuka A, Nagano AJ, Ootsuki R, Watano Y. Mating system evolution and genetic structure of diploid sexual populations of Cyrtomium falcatum in Japan. Sci Rep 2021; 11:3124. [PMID: 33542454 PMCID: PMC7862634 DOI: 10.1038/s41598-021-82731-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 01/12/2021] [Indexed: 11/09/2022] Open
Abstract
Evolution of mating systems has become one of the most important research areas in evolutionary biology. Cyrtomium falcatum is a homosporous fern species native to eastern Asia. Two subspecies belonging to a sexual diploid race of C. falcatum are recognized: subsp. littorale and subsp. australe. Subspecies littorale shows intermediate selfing rates, while subsp. australe is an obligate outcrosser. We aimed to evaluate the process of mating system evolution and divergence for the two subspecies using restriction site associated DNA sequencing (RAD-seq). The results showed that subsp. littorale had lower genetic diversity and stronger genetic drift than subsp. australe. Fluctuations in the effective population size over time were evaluated by extended Bayesian skyline plot and Stairway plot analyses, both of which revealed a severe population bottleneck about 20,000 years ago in subsp. littorale. This bottleneck and the subsequent range expansion after the LGM appear to have played an important role in the divergence of the two subspecies and the evolution of selfing in subsp. littorale. These results shed new light on the relationship between mating system evolution and past demographic change in fern species.
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Affiliation(s)
- Ryosuke Imai
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda , Nagano, 386-2204, Japan.
| | - Yoshiaki Tsuda
- Sugadaira Research Station, Mountain Science Center, University of Tsukuba, Sugadaira, Ueda , Nagano, 386-2204, Japan
| | - Atsushi Ebihara
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan
| | - Sadamu Matsumoto
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki, 305-0005, Japan
| | - Ayumi Tezuka
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
| | - Ryo Ootsuki
- Department of Natural Sciences, Faculty of Arts and Sciences, Komazawa University, 1-23-1 Komazawa, Setagaya-ku, Tokyo, 154-8525, Japan
| | - Yasuyuki Watano
- Department of Biology, Graduate School of Science, Chiba University, Inage, Chiba, Chiba, 263-8522, Japan
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Miyoshi S, Kimura S, Ootsuki R, Higaki T, Nakamasu A. Developmental analyses of divarications in leaves of an aquatic fern Microsorum pteropus and its varieties. PLoS One 2019; 14:e0210141. [PMID: 30682033 PMCID: PMC6347172 DOI: 10.1371/journal.pone.0210141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/18/2018] [Indexed: 11/18/2022] Open
Abstract
Plant leaves occur in diverse shapes. Divarication patterns that develop during early growths are one of key factors that determine leaf shapes. We utilized leaves of Microsorum pteropus, a semi-aquatic fern, and closely related varieties to analyze a variation in the divarication patterns. The leaves exhibited three major types of divarication: no lobes, bifurcation, and trifurcation (i.e., monopodial branching). Our investigation of their developmental processes, using time-lapse imaging, revealed localized growths and dissections of blades near each leaf apex. Restricted cell divisions responsible for the apical growths were confirmed using a pulse-chase strategy for EdU labeling assays.
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Affiliation(s)
- Saori Miyoshi
- Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Seisuke Kimura
- Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
- Center for Ecological Evolutionary Developmental Biology, Kyoto Sangyo University, Kyoto, Japan
| | - Ryo Ootsuki
- Department of Natural Sciences, Faculty of Arts and Sciences, Komazawa University, Tokyo, Japan
- Faculty of Chemical and Biological Sciences, Japan Women's University, Tokyo, Japan
| | - Takumi Higaki
- International Research Organization for Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
| | - Akiko Nakamasu
- Department of Bioresource and Environmental Sciences, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
- International Research Organization for Advanced Science and Technology, Kumamoto University, Kumamoto, Japan
- Meiji Institute for Advanced Study of Mathematical Sciences, Meiji University, Tokyo, Japan
- * E-mail:
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Misawa K, Ootsuki R. PAFFT: A new homology search algorithm for third-generation sequencers. Genomics 2015; 106:265-7. [PMID: 26387926 DOI: 10.1016/j.ygeno.2015.09.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 04/29/2015] [Revised: 09/02/2015] [Accepted: 09/14/2015] [Indexed: 11/24/2022]
Abstract
DNA sequencers that can conduct real-time sequencing from a single polymerase molecule are known as third-generation sequencers. Third-generation sequencers enable sequencing of reads that are several kilobases long. However, the raw data generated from third-generation sequencers are known to be error-prone. Because of sequencing errors, it is difficult to identify which genes are homologous to the reads obtained using third-generation sequencers. In this study, a new method for homology search algorithm, PAFFT, is developed. This method is the extension of the MAFFT algorithm which was used for multiple alignments. PAFFT detects global homology rather than local homology so that homologous regions can be detected even when the error rate of sequencing is high. PAFFT will boost application of third-generation sequencers.
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Affiliation(s)
- Kazuharu Misawa
- Advanced Center for Computing and Communication, RIKEN, Hirosawa 2-1, Wako, Saitama 351-0198, Japan.
| | - Ryo Ootsuki
- Faculty of Chemical and Biological Sciences, Japan Women's University, Tokyo, Japan; Department of Natural Sciences, Faculty of Arts and Sciences, Komazawa University, 1-23-1 Komazawa, Setagaya-ku, Tokyo 154-8525, Japan
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Sugita N, Ootsuki R, Fujita T, Murakami N, Ueda K. Possible Spore Dispersal of a Bird-Nest FernAsplenium setoiby Bonin flying foxesPteropus pselaphon. Mammal Study 2013. [DOI: 10.3106/041.038.0301] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Ootsuki R, Sato H, Nakato N, Murakami N. Evidence of genetic segregation in the apogamous fern species Cyrtomium fortunei (Dryopteridaceae). J Plant Res 2012; 125:605-612. [PMID: 22392021 DOI: 10.1007/s10265-012-0483-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 02/13/2012] [Indexed: 05/31/2023]
Abstract
In apogamous ferns, all offspring from a parent are expected to be clonal. However, apogamous 'species' frequently demonstrate a large amount of morphological and genetic variations. Cyrtomium fortunei composed of four varieties (C. fortunei var. fortunei, var. clivicola, var. intermedium, and var. atropunctatum), is all reported to be apogamous triploids, but demonstrates large and continuous morphological variation. In previous studies, we showed that considerable genetic diversity was observed in many local populations of the apogamous fern 'species'. We hypothesized that genetic segregation has occurred, because neither sexual type nor intraspecific polyploidy have been observed in C. fortunei in Japan. Of 732 progeny examined (250 gametophytes and 482 sporophytes), obtained from a parental sporophyte whose pgiC genotype was estimated as aab, 11 (4.4%) gametophytes and 8 (1.7%) sporophytes showed a different genotype (aaa) from that of the parent sporophyte. We showed that genetic segregation occurs in apogamous C. fortunei in relatively high frequency. Moreover, we could first show that the segregation frequency in gametophytes is significantly higher than that in sporophytes of the next generation (χ² = 4.90, P = 0.027). It may suggest the existence of deleterious genes, which are expressed during the morphogenesis and growth of sporophytes.
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Affiliation(s)
- Ryo Ootsuki
- Makino Herbarium, Tokyo Metropolitan University, 1-1 Minamiosawa, Hachioji, Tokyo 192-0397, Japan.
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Nakato N, Ootsuki R, Murakami N, Masuyama S. Two types of partial fertility in a diploid population of the fern Thelypteris decursive-pinnata (Thelypteridaceae). J Plant Res 2012; 125:465-474. [PMID: 22038490 DOI: 10.1007/s10265-011-0461-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 10/12/2011] [Indexed: 05/31/2023]
Abstract
Two types of abnormal sporophytes were observed in a population of diploid Thelypteris decursive-pinnata. Most sporophytes in this population exhibited regular chromosome pairing, resulting in the formation of 30 bivalents in meiosis I; however, they produced abortive spores to various degrees. Some formed large globose spores at low frequencies, most likely to be unreduced diplospores. The other type of abnormal sporophyte underwent synaptic failure to form 60 univalents at meiosis I, but produced fertile spores, mostly large globose ones at low frequencies. The globose spores were considered unreduced diplospores because the gametophytes arising from them produced tetraploid sporophytes by gametophytic selfing. One tetraploid formed only univalents at meiosis I. Allozyme variation was not detected in this population, although neighboring ordinary diploid populations exhibited it to a certain degree. The sympatric occurrence and allozyme uniformity of the two groups suggest that both are offspring of a founder sporophyte, which may have possessed two types of mutated recessive genes responsible for the spore sterility and the synaptic failure in meiosis. Unreduced spores formed by these two types may play an important role in the polyploid speciation of this species.
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Nakano K, Yamashiro K, Ikemura Y, Washio S, Ootsuki R. [Clinical experience with a new glucose solution, Trelan G50 for glucose tolerance test--with special reference to the comparison of the clinical results of Trelan G50 and glucose]. Nihon Rinsho 1972; 30:1413-8. [PMID: 4672543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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