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Kamakura S, Bilcke G, Sato S. Transcriptional responses to salinity-induced changes in cell wall morphology of the euryhaline diatom Pleurosira laevis. JOURNAL OF PHYCOLOGY 2024; 60:308-326. [PMID: 38446079 DOI: 10.1111/jpy.13437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/23/2024] [Accepted: 02/05/2024] [Indexed: 03/07/2024]
Abstract
Diatoms are unicellular algae with morphologically diverse silica cell walls, which are called frustules. The mechanism of frustule morphogenesis has attracted attention in biology and nanomaterials engineering. However, the genetic regulation of the morphology remains unclear. We therefore used transcriptome sequencing to search for genes involved in frustule morphology in the centric diatom Pleurosira laevis, which exhibits morphological plasticity between flat and domed valve faces in salinity 2 and 7, respectively. We observed differential expression of transposable elements (TEs) and transporters, likely due to osmotic response. Up-regulation of mechanosensitive ion channels and down-regulation of Ca2+-ATPases in cells with flat valves suggested that cytosolic Ca2+ levels were changed between the morphologies. Calcium signaling could be a mechanism for detecting osmotic pressure changes and triggering morphological shifts. We also observed an up-regulation of ARPC1 and annexin, involved in the regulation of actin filament dynamics known to affect frustule morphology, as well as the up-regulation of genes encoding frustule-related proteins such as BacSETs and frustulin. Taken together, we propose a model in which salinity-induced morphogenetic changes are driven by upstream responses, such as the regulation of cytosolic Ca2+ levels, and downstream responses, such as Ca2+-dependent regulation of actin dynamics and frustule-related proteins. This study highlights the sensitivity of euryhaline diatoms to environmental salinity and the role of active cellular processes in controlling gross valve morphology under different osmotic pressures.
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Affiliation(s)
- Shiho Kamakura
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, Obama, Fukui, Japan
| | - Gust Bilcke
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Protistology and Aquatic Ecology, Department of Biology, Ghent University, Ghent, Belgium
| | - Shinya Sato
- Faculty of Marine Science and Technology, Fukui Prefectural University, Obama, Fukui, Japan
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2
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Ji N, Wang J, Huang W, Huang J, Cai Y, Sun S, Shen X, Liang Y. Transcriptome analysis of the harmful alga Heterosigma akashiwo under a 24-hour light-dark cycle. HARMFUL ALGAE 2024; 133:102601. [PMID: 38485440 DOI: 10.1016/j.hal.2024.102601] [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: 09/12/2023] [Revised: 01/29/2024] [Accepted: 02/05/2024] [Indexed: 03/19/2024]
Abstract
The photoperiod, which is defined as the period of time within a 24-hour time frame that light is available, is an important environmental regulator of several physiological processes in phytoplankton, including harmful bloom-forming phytoplankton. The ichthyotoxic raphidophyte Heterosigma akashiwo is a globally distributed bloom-forming phytoplankton. Despite extensive studies on the ecological impact of H. akashiwo, the influence of the photoperiod on crucial biological processes of this species remains unclear. In this study, gene expression in H. akashiwo was analyzed over a 24-hour light-dark (14:10) treatment period. Approximately 36 % of unigenes in H. akashiwo were differentially expressed during this 24-hour treatment period, which is indicative of their involvement in the response to light-dark variation. Notably, the number of differentially expressed genes exhibited an initial increase followed by a subsequent decrease as the sampling time progressed (T0 vs. other time points). Unigenes associated with photosynthesis and photoprotection reached their peak expression levels after 2-4 h of illumination (T12-T14). In contrast, the expression of unigenes associated with DNA replication peaked at the starting point of the dark period (T0). Furthermore, although several unigenes annotated to photoreceptors displayed potential diel periodicity, genes from various photoreceptor families (such as phytochrome and cryptochrome) showed unique expression patterns. Collectively, our findings offer novel perspectives on the response of H. akashiwo to the light-dark cycle, serving as a valuable resource for investigating the physiology and ecology of this species.
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Affiliation(s)
- Nanjing Ji
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China; Jiangsu Marine Resources Development Research Institute, Lianyungang 222005, China; CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
| | - Junyue Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Wencong Huang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Jinwang Huang
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yuefeng Cai
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Song Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Xin Shen
- Jiangsu Key Laboratory of Marine Bioresources and Environment/Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222005, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yue Liang
- Center of Deep Sea Research, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China.
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Liu X, Chen J, Du H, Liu Z, Du H, Rashid A, Wang Y, Ma W, Wang S. Resolving the dynamics of chrysolaminarin regulation in a marine diatom: A physiological and transcriptomic study. Int J Biol Macromol 2023; 252:126361. [PMID: 37591430 DOI: 10.1016/j.ijbiomac.2023.126361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 08/01/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023]
Abstract
Diatom containing different active biological macromolecules are thought to be an excellent microbial cell factory. Phaeodactylum tricornutum, a model diatom, is a superb chassis organism accumulating chrysolaminarin with important bioactivities. However, the characteristic of chrysolaminarin accumulation and molecular mechanism of the fluctuated chrysolaminarin in diatom are still unknown. In this study, physiological data and transcriptomic analysis were carried out to clarify the mechanism involved in chrysolaminarin fluctuation. The results showed that chrysolaminarin content fluctuated, from 7.41 % dry weight (DW) to 40.01 % DW during one light/dark cycle, increase by day and decrease by night. The similar fluctuated characteristic was also observed in neutral lipid content. Genes related to the biosynthesis of chrysolaminarin and neutral lipid were up-regulated at the beginning of light-phase, explaining the accumulation of these biological macromolecules. Furthermore, genes involved in carbohydrate degradation, cell cycle, DNA replication and mitochondria-localized β-oxidation were up-regulated at the end of light phase and at the beginning of dark phase hinting an energy transition of carbohydrate to cell division during the dark period. Totally, our findings provide important information for the regulatory mechanism in the diurnal fluctuation of chrysolaminarin. It would also be of great help for the mass production of economical chrysolaminarin in marine diatom.
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Affiliation(s)
- Xiaojuan Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou 515063, Guangdong, China
| | - Jichen Chen
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou 515063, Guangdong, China
| | - Hong Du
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou 515063, Guangdong, China.
| | - Zidong Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou 515063, Guangdong, China
| | - Hua Du
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou 515063, Guangdong, China
| | - Azhar Rashid
- Department of Environmental Sciences, The University of Haripur, Haripur 22620, Pakistan
| | - Yuwen Wang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou 515063, Guangdong, China
| | - Wanying Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou 515063, Guangdong, China
| | - Shuqi Wang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Guangdong Provincial Key Laboratory of Marine Disaster Prediction and Prevention, STU-UNIVPM Joint Algal Research Center, College of Sciences, Shantou University, Shantou 515063, Guangdong, China
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Liu Z, Liu W, Wang Z, Qi K, Xie Z, Zhang S, Wu J, Wang P. Diurnal transcriptome dynamics reveal the photoperiod response of Pyrus. PHYSIOLOGIA PLANTARUM 2023; 175:e13893. [PMID: 36929905 DOI: 10.1111/ppl.13893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/15/2023] [Accepted: 03/14/2023] [Indexed: 06/18/2023]
Abstract
Photoperiod provides a key environmental signal that controls plant growth. Plants have evolved an integrated mechanism for sensing photoperiods with internal clocks to orchestrate physiological events. This mechanism has been identified to enable timely plant growth and improve fitness. Although the components and pathways underlying photoperiod regulation have been described in many species, diurnal patterns of gene expression at the genome-wide level under different photoperiods are rarely reported in perennial fruit trees. To explore the global gene expression in response to photoperiod, pear plants were cultured under long-day (LD) and short-day (SD) conditions. A time-series transcriptomic study was implemented using LD and SD samples collected at 4 h intervals over 2 days. We identified 13,677 rhythmic genes, of which 7639 were identified under LD and 10,557 under SD conditions. Additionally, 4674 genes were differentially expressed in response to photoperiod change. We also characterized the candidate homologs of clock-associated genes in pear. Clock genes were involved in the regulation of many processes throughout the day, including photosynthesis, stress response, hormone dynamics, and secondary metabolism. Strikingly, genes within photosynthesis-related pathways were enriched in both the rhythmic and differential expression analyses. Several key candidate genes were identified to be associated with regulating photosynthesis and improving productivity under different photoperiods. The results suggest that temporal variation in gene expression should not be ignored in pear gene function research. Overall, our work expands the understanding of photoperiod regulation of plant growth, particularly by extending the research to non-model trees.
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Affiliation(s)
- Zhe Liu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
- Department of Pharmacy, Changzhi Medical College, Changzhi, 046000, China
| | - Weijuan Liu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhangqing Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Kaijie Qi
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhihua Xie
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Shaoling Zhang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Juyou Wu
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
| | - Peng Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, 210095, Nanjing, China
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Debit A, Charton F, Pierre-Elies P, Bowler C, Cruz de Carvalho H. Differential expression patterns of long noncoding RNAs in a pleiomorphic diatom and relation to hyposalinity. Sci Rep 2023; 13:2440. [PMID: 36765079 PMCID: PMC9918465 DOI: 10.1038/s41598-023-29489-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Long non-coding (lnc)RNAs have been shown to have central roles in stress responses, cell identity and developmental processes in multicellular organisms as well as in unicellular fungi. Previous works have shown the occurrence of lncRNAs in diatoms, namely in Phaeodactylum tricornutum, many of which being expressed under specific stress conditions. Interestingly, P. tricornutum is the only known diatom that has a demonstrated morphological plasticity, occurring in three distinct morphotypes: fusiform, triradiate and oval. Although the morphotypes are interchangeable, the fusiform is the dominant one while both the triradiate and the oval forms are less common, the latter often being associated with stress conditions such as low salinity and solid culture media, amongst others. Nonetheless, the molecular basis underpinning morphotype identity in P. tricornutum remains elusive. Using twelve previously published transcriptomic datasets originating from the three morphotypes of P. tricornutum, we sought to investigate the expression patterns of lncRNAs (lincRNAs and NATs) in these distinct morphotypes, using pairwise comparisons, in order to explore the putative involvement of these noncoding molecules in morphotype identity. We found that differentially expressed lncRNAs cluster according to morphotype, indicating that lncRNAs are not randomly expressed, but rather seem to provide a specific (noncoding) transcriptomic signature of the morphotype. We also present evidence to suggest that the major differences in DE genes (both noncoding and coding) between the stress related oval morphotype and the most common fusiform morphotype could be due, to a large extent, to the hyposaline culture conditions rather than to the morphotype itself. However, several lncRNAs associated to each one of the three morphotypes were identified, which could have a potential role in morphotype (or cell) identity in P. tricornutum, similar to what has been found in both animals and plant development.
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Affiliation(s)
- Ahmed Debit
- Institut de Biologie de L'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Florent Charton
- Institut de Biologie de L'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Priscillia Pierre-Elies
- Institut de Biologie de L'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Chris Bowler
- Institut de Biologie de L'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Helena Cruz de Carvalho
- Institut de Biologie de L'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France.
- Faculté des Sciences et Technologie, Université Paris Est-Créteil (UPEC), 61, Avenue du Général De Gaulle, 94000, Créteil, France.
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Häfker NS, Andreatta G, Manzotti A, Falciatore A, Raible F, Tessmar-Raible K. Rhythms and Clocks in Marine Organisms. ANNUAL REVIEW OF MARINE SCIENCE 2023; 15:509-538. [PMID: 36028229 DOI: 10.1146/annurev-marine-030422-113038] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The regular movements of waves and tides are obvious representations of the oceans' rhythmicity. But the rhythms of marine life span across ecological niches and timescales, including short (in the range of hours) and long (in the range of days and months) periods. These rhythms regulate the physiology and behavior of individuals, as well as their interactions with each other and with the environment. This review highlights examples of rhythmicity in marine animals and algae that represent important groups of marine life across different habitats. The examples cover ecologically highly relevant species and a growing number of laboratory model systems that are used to disentangle key mechanistic principles. The review introduces fundamental concepts of chronobiology, such as the distinction between rhythmic and endogenous oscillator-driven processes. It also addresses the relevance of studying diverse rhythms and oscillators, as well as their interconnection, for making better predictions of how species will respond to environmental perturbations, including climate change. As the review aims to address scientists from the diverse fields of marine biology, ecology, and molecular chronobiology, all of which have their own scientific terms, we provide definitions of key terms throughout the article.
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Affiliation(s)
- N Sören Häfker
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria; ,
- Research Platform "Rhythms of Life," University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Gabriele Andreatta
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria; ,
- Research Platform "Rhythms of Life," University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Alessandro Manzotti
- Laboratoire de Biologie du Chloroplaste et Perception de la Lumière chez les Microalgues, UMR 7141, CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France;
| | - Angela Falciatore
- Laboratoire de Biologie du Chloroplaste et Perception de la Lumière chez les Microalgues, UMR 7141, CNRS, Sorbonne Université, Institut de Biologie Physico-Chimique, Paris, France;
| | - Florian Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria; ,
- Research Platform "Rhythms of Life," University of Vienna, Vienna BioCenter, Vienna, Austria
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria; ,
- Research Platform "Rhythms of Life," University of Vienna, Vienna BioCenter, Vienna, Austria
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
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Light intensity and spectral composition drive reproductive success in the marine benthic diatom Seminavis robusta. Sci Rep 2021; 11:17560. [PMID: 34475415 PMCID: PMC8413402 DOI: 10.1038/s41598-021-92838-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/09/2021] [Indexed: 12/13/2022] Open
Abstract
The properties of incident light play a crucial role in the mating process of diatoms, a group of ecologically important microalgae. While species-specific requirements for light intensity and photoperiod have been observed in several diatom species, little is known about the light spectrum that allows sexual reproduction. Here, we study the effects of spectral properties and light intensity on the initiation and progression of sexual reproduction in the model benthic diatom Seminavis robusta. We found that distinct stages of the mating process have different requirements for light. Vigorous mating pair formation occurred under a broad range of light intensities, ranging from 10 to 81 µE m−2 s−1, while gametogenesis and subsequent stages were strongly affected by moderate light intensities of 27 µE m−2 s−1 and up. In addition, light of blue or blue–green wavelengths was required for the formation of mating pairs. Combining flow cytometric analysis with expression profiling of the diatom-specific cyclin dsCyc2 suggests that progression through a blue light-dependent checkpoint in the G1 cell cycle phase is essential for induction of sexual reproduction. Taken together, we expand the current model of mating in benthic pennate diatoms, which relies on the interplay between light, cell cycle and sex pheromone signaling.
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