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Gong Y, Wang Q, Wei L, Liang W, Wang L, Lv N, Du X, Zhang J, Shen C, Xin Y, Sun L, Xu J. Genome-wide adenine N6-methylation map reveals epigenomic regulation of lipid accumulation in Nannochloropsis. PLANT COMMUNICATIONS 2024; 5:100773. [PMID: 38007614 PMCID: PMC10943562 DOI: 10.1016/j.xplc.2023.100773] [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: 12/28/2022] [Revised: 02/09/2023] [Accepted: 11/23/2023] [Indexed: 11/27/2023]
Abstract
Epigenetic marks on histones and DNA, such as DNA methylation at N6-adenine (6mA), play crucial roles in gene expression and genome maintenance, but their deposition and function in microalgae remain largely uncharacterized. Here, we report a genome-wide 6mA map for the model industrial oleaginous microalga Nannochloropsis oceanica produced by single-molecule real-time sequencing. Found in 0.1% of adenines, 6mA sites are mostly enriched at the AGGYV motif, more abundant in transposons and 3' untranslated regions, and associated with active transcription. Moreover, 6mA gradually increases in abundance along the direction of gene transcription and shows special positional enrichment near splicing donor and transcription termination sites. Highly expressed genes tend to show greater 6mA abundance in the gene body than do poorly expressed genes, indicating a positive interaction between 6mA and general transcription factors. Furthermore, knockout of the putative 6mA methylase NO08G00280 by genome editing leads to changes in methylation patterns that are correlated with changes in the expression of molybdenum cofactor, sulfate transporter, glycosyl transferase, and lipase genes that underlie reductions in biomass and oil productivity. By contrast, knockout of the candidate demethylase NO06G02500 results in increased 6mA levels and reduced growth. Unraveling the epigenomic players and their roles in biomass productivity and lipid metabolism lays a foundation for epigenetic engineering of industrial microalgae.
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Affiliation(s)
- Yanhai Gong
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qintao Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Li Wei
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Wensi Liang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Lianhong Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Nana Lv
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xuefeng Du
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jiashun Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Chen Shen
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yi Xin
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Luyang Sun
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China; Shandong Energy Institute, Qingdao, China; Qingdao New Energy Shandong Laboratory, Qingdao, China; University of Chinese Academy of Sciences, Beijing 100049, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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2
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Diehl N, Li H, Scheschonk L, Burgunter-Delamare B, Niedzwiedz S, Forbord S, Sæther M, Bischof K, Monteiro C. The sugar kelp Saccharina latissima I: recent advances in a changing climate. ANNALS OF BOTANY 2024; 133:183-212. [PMID: 38109285 PMCID: PMC10921839 DOI: 10.1093/aob/mcad173] [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: 07/10/2023] [Revised: 09/26/2023] [Accepted: 11/07/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND The sugar kelp Saccharina latissima is a Laminariales species widely distributed in the Northern Hemisphere. Its physiology and ecology have been studied since the 1960s, given its ecological relevance on western temperate coasts. However, research interest has been rising recently, driven mainly by reports of negative impacts of anthropogenically induced environmental change and by the increased commercial interest in cultivating the species, with several industrial applications for the resulting biomass. SCOPE We used a variety of sources published between 2009 to May 2023 (but including some earlier literature where required), to provide a comprehensive review of the ecology, physiology, biochemical and molecular biology of S. latissima. In so doing we aimed to better understand the species' response to stressors in natural communities, but also inform the sustainable cultivation of the species. CONCLUSION Due to its wide distribution, S. latissima has developed a variety of physiological and biochemical mechanisms to adjust to environmental changes, including adjustments in photosynthetic parameters, modulation of osmolytes and antioxidants, reprogramming of gene expression and epigenetic modifications, among others summarized in this review. This is particularly important because massive changes in the abundance and distribution of S. latissima have already been observed. Namely, presence and abundance of S. latissima has significantly decreased at the rear edges on both sides of the Atlantic, and increased in abundance at the polar regions. These changes were mainly caused by climate change and will therefore be increasingly evident in the future. Recent developments in genomics, transcriptomics and epigenomics have clarified the existence of genetic differentiation along its distributional range with implications in the fitness at some locations. The complex biotic and abiotic interactions unraveled here demonstrated the cascading effects the disappearance of a kelp forest can have in a marine ecosystem. We show how S. latissima is an excellent model to study acclimation and adaptation to environmental variability and how to predict future distribution and persistence under climate change.
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Affiliation(s)
- Nora Diehl
- Marine Botany, Faculty of Biology and Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Huiru Li
- Key Laboratory of Mariculture (Ministry of Education), Fisheries College, Ocean University of China, Qingdao 266003, China
| | | | - Bertille Burgunter-Delamare
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Sarina Niedzwiedz
- Marine Botany, Faculty of Biology and Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Silje Forbord
- Department of Fisheries and New Biomarine Industry, SINTEF Ocean AS, 7465 Trondheim, Norway
| | - Maren Sæther
- Seaweed Solutions AS, Bynesveien 50C, 7018 Trondheim, Norway
| | - Kai Bischof
- Marine Botany, Faculty of Biology and Chemistry, University of Bremen, 28359 Bremen, Germany
| | - Catia Monteiro
- CIBIO, Research Centre in Biodiversity and Genetic Resources – InBIO Associate Laboratory, Campus of Vairão, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus of Vairão, Vairão, Portugal
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Wan J, Zhou Y, Beardall J, Raven JA, Lin J, Huang J, Lu Y, Liang S, Ye M, Xiao M, Zhao JY, Dai X, Xia J, Jin P. DNA methylation and gene transcription act cooperatively in driving the adaptation of a marine diatom to global change. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad150. [PMID: 37100754 DOI: 10.1093/jxb/erad150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Indexed: 06/19/2023]
Abstract
Genetic changes together with epigenetic modifications such as DNA methylation have been demonstrated to regulate many biological processes and thereby govern the response of organisms to environmental changes. However, how DNA methylation might act cooperatively with gene transcription and thereby mediate the long-term adaptive responses of marine microalgae to global change is virtually unknown. Here we performed a transcriptomic analysis, and a whole-genome bisulfite sequencing, along with phenotypic analysis of a model marine diatom Phaeodactylum tricornutum adapted for two years to high CO2 and/or warming conditions. Our results show that the methylated islands (peaks of methylation) mCHH were positively correlated with expression of genes in the sub-region of the gene body when the populations were grown under high CO2 or its combination with warming for ~2 years. We further identified the differentially expressed genes (DEGs) and hence the metabolic pathways in which they function, at the transcriptomics level in differentially methylated regions (DMRs). Although DEGs in DMRs contributed only 18-24% of the total DEGs, we found that those DEGs acted cooperatively with DNA methylation and then regulated key processes such as central carbon metabolism, amino acid metabolism, ribosome biogenesis, terpenoid backbone biosynthesis, and degradation of misfolded proteins. Taken together, by integrating transcriptomic, epigenetic and phenotypic analysis, our study provides evidence for DNA methylation acting cooperatively with gene transcription to contribute to the adaptation of microalgae to global changes.
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Affiliation(s)
- Jiaofeng Wan
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yunyue Zhou
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - John Beardall
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - John A Raven
- Division of Plant Science, University of Dundee at the James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
- School of Biology, University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia
- Climate Change Cluster, University of Technology, Sydney, Ultimo, NSW 2007, Australia
| | - Jiamin Lin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jiali Huang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Yucong Lu
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Shiman Liang
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Mengcheng Ye
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Mengting Xiao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jing Yuan Zhao
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Xiaoying Dai
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Jianrong Xia
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
| | - Peng Jin
- School of Environmental Science and Engineering, Guangzhou University, Guangzhou, 510006, China
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4
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Hoguin A, Yang F, Groisillier A, Bowler C, Genovesio A, Ait-Mohamed O, Vieira FRJ, Tirichine L. The model diatom Phaeodactylum tricornutum provides insights into the diversity and function of microeukaryotic DNA methyltransferases. Commun Biol 2023; 6:253. [PMID: 36894681 PMCID: PMC9998398 DOI: 10.1038/s42003-023-04629-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
Cytosine methylation is an important epigenetic mark involved in the transcriptional control of transposable elements in mammals, plants and fungi. The Stramenopiles-Alveolate-Rhizaria (SAR) lineages are a major group of ecologically important marine microeukaryotes, including the phytoplankton groups diatoms and dinoflagellates. However, little is known about their DNA methyltransferase diversity. Here, we performed an in-silico analysis of DNA methyltransferases found in marine microeukaryotes and showed that they encode divergent DNMT3, DNMT4, DNMT5 and DNMT6 enzymes. Furthermore, we found three classes of enzymes within the DNMT5 family. Using a CRISPR/Cas9 strategy we demonstrated that the loss of the DNMT5a gene correlates with a global depletion of DNA methylation and overexpression of young transposable elements in the model diatom Phaeodactylum tricornutum. The study provides a view of the structure and function of a DNMT family in the SAR supergroup using an attractive model species.
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Affiliation(s)
- Antoine Hoguin
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Feng Yang
- Nantes Université, CNRS, US2B, UMR 6286, F-44000, Nantes, France
| | | | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Auguste Genovesio
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France
| | - Ouardia Ait-Mohamed
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France.
| | - Fabio Rocha Jimenez Vieira
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Université Paris, 75005, Paris, France.
- Laboratory of Computational and Quantitative Biology-LCQB - UMR 7238 CNRS-Sorbonne Université. Institut de Biologie Paris Seine, 75005, Paris, France.
| | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, F-44000, Nantes, France.
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Liu F, Zhang P, Liang Z, Yuan Y, Liu Y, Wu Y. The global dynamic of DNA methylation in response to heat stress revealed epigenetic mechanism of heat acclimation in Saccharina japonica. JOURNAL OF PHYCOLOGY 2023; 59:249-263. [PMID: 36453855 DOI: 10.1111/jpy.13305] [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: 06/19/2022] [Accepted: 11/15/2022] [Indexed: 06/17/2023]
Abstract
Saccharina japonica is an ecologically and economically important kelp in cold-temperate regions. When it is cultivated on a large scale in the temperate and even subtropical zones, heat stress is a frequent abiotic stress. This study is the first attempt to reveal the regulatory mechanism of the response to heat stress from the perspective of DNA methylation in S. japonica. We firstly obtained the characteristics of variation in the methylome under heat stress, and observed that heat stress caused a slight increase in the overall methylation level and methylation rate, especially in the non-coding regions of the genome. Secondly, we noted that methylation was probably one of factors affecting the expression of genes, and that methylation within the gene body was positively correlated with the gene expression (rho = 0.0784). Moreover, it was found that among the differentially expressed genes regulated by methylation, many genes were related to heat stress response, such as HSP gene family, genes of antioxidant enzymes, genes related to proteasome-ubiquitination pathway, and plant cell signaling pathways. This study demonstrated that DNA methylation is involved in regulating the response to heat stress, laying a foundation for studying the acclimation and adaptation of S. japonica to heat stress from an epigenetic perspective.
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Affiliation(s)
- Fuli Liu
- Key Laboratory of Marine Genetics and Breeding, Ministry of Education; College of Marine Life Science, Ocean University of China, Qingdao, China
| | - Pengyan Zhang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Zhourui Liang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yanmin Yuan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yi Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Yukun Wu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
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6
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Scheschonk L, Bischof K, Kopp MEL, Jueterbock A. Differences by origin in methylome suggest eco-phenotypes in the kelp Saccharina latissima. Evol Appl 2023; 16:262-278. [PMID: 36793679 PMCID: PMC9923482 DOI: 10.1111/eva.13382] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 03/25/2022] [Accepted: 03/31/2022] [Indexed: 11/29/2022] Open
Abstract
Most kelp species are of high ecological and economic importance worldwide, but are highly susceptible to rising ocean temperatures due to their sessile lifestyle. Due to interference with reproduction, development and growth, natural kelp forests have vanished in multiple regions after extreme summer heat waves. Furthermore, increasing temperatures are likely to decrease biomass production and, thus, reduce production security of farmed kelp. Epigenetic variation, and cytosine methylation as a heritable epigenetic trait, is a rapid means of acclimation and adaptation to environmental conditions, including temperature. While the first methylome of brown macroalgae has been recently described in the kelp Saccharina japonica, its functional relevance and contribution to environmental acclimation is currently unknown. The main objective of our study was to identify the importance of the methylome in the congener kelp species Saccharina latissima for temperature acclimation. Our study is the first to compare DNA methylation in kelp between wild populations of different latitudinal origin, and the first to investigate the effect of cultivation and rearing temperature on genome-wide cytosine methylation. Origin appears to determine many traits in kelp, but it is unknown to what extent the effects of thermal acclimation may be overruled by lab-related acclimation. Our results suggest that seaweed hatchery conditions have strong effects on the methylome and, thus, putatively on the epigenetically controlled characteristics of young kelp sporophytes. However, culture origin could best explain epigenetic differences in our samples suggesting that epigenetic mechanisms contribute to local adaptation of eco-phenotypes. Our study is a first step to understand whether DNA methylation marks (via their effect on gene regulation) may be used as biological regulators to enhance production security and kelp restoration success under rising temperatures, and highlights the importance to match hatchery conditions to origin.
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Affiliation(s)
| | - Kai Bischof
- Marine Botany & MARUM University of Bremen Bremen Germany
| | | | - Alexander Jueterbock
- Algal and Microbial Biotechnology Division Faculty of Biosciences and Aquaculture Nord University Bodø Norway
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Ferrari M, Muto A, Bruno L, Cozza R. DNA Methylation in Algae and Its Impact on Abiotic Stress Responses. PLANTS (BASEL, SWITZERLAND) 2023; 12:241. [PMID: 36678953 PMCID: PMC9861306 DOI: 10.3390/plants12020241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Epigenetics, referring to heritable gene regulatory information that is independent of changes in DNA sequences, is an important mechanism involved both in organism development and in the response to environmental events. About the epigenetic marks, DNA methylation is one of the most conserved mechanisms, playing a pivotal role in organism response to several biotic and abiotic stressors. Indeed, stress can induce changes in gene expression through hypo- or hyper-methylation of DNA at specific loci and/or in DNA methylation at the genome-wide level, which has an adaptive significance and can direct genome evolution. Exploring DNA methylation in responses to abiotic stress could have important implications for improving stress tolerance in algae. This article summarises the DNA methylation pattern in algae and its impact on abiotic stress, such as heavy metals, nutrients and temperature. Our discussion provides information for further research in algae for a better comprehension of the epigenetic response under abiotic stress, which could favour important implications to sustain algae growth under abiotic stress conditions, often related to high biosynthesis of interesting metabolites.
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Bourdareau S, Godfroy O, Gueno J, Scornet D, Coelho SM, Tirichine L, Cock JM. An Efficient Chromatin Immunoprecipitation Protocol for the Analysis of Histone Modification Distributions in the Brown Alga Ectocarpus. Methods Protoc 2022; 5:mps5030036. [PMID: 35645344 PMCID: PMC9149930 DOI: 10.3390/mps5030036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/16/2022] Open
Abstract
The brown algae are an important but understudied group of multicellular marine organisms. A number of genetic and genomic tools have been developed for the model brown alga Ectocarpus; this includes, most recently, chromatin immunoprecipitation methodology, which allows genome-wide detection and analysis of histone post-translational modifications. Post-translational modifications of histone molecules have been shown to play an important role in gene regulation in organisms from other major eukaryotic lineages, and this methodology will therefore be a very useful tool to investigate genome function in the brown algae. This article provides a detailed, step-by-step description of the Ectocarpus ChIP protocol, which effectively addresses the difficult problem of efficiently extracting chromatin from cells protected by a highly resistant cell wall. The protocol described here will be an essential tool for the future application of chromatin analysis methodologies in brown algal research.
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Affiliation(s)
- Simon Bourdareau
- Algal Genetics Group, Integrative Biology of Marine Models Laboratory, CNRS, Sorbonne Université, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France; (S.B.); (O.G.); (J.G.); (D.S.); (S.M.C.)
| | - Olivier Godfroy
- Algal Genetics Group, Integrative Biology of Marine Models Laboratory, CNRS, Sorbonne Université, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France; (S.B.); (O.G.); (J.G.); (D.S.); (S.M.C.)
| | - Josselin Gueno
- Algal Genetics Group, Integrative Biology of Marine Models Laboratory, CNRS, Sorbonne Université, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France; (S.B.); (O.G.); (J.G.); (D.S.); (S.M.C.)
| | - Delphine Scornet
- Algal Genetics Group, Integrative Biology of Marine Models Laboratory, CNRS, Sorbonne Université, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France; (S.B.); (O.G.); (J.G.); (D.S.); (S.M.C.)
| | - Susana M. Coelho
- Algal Genetics Group, Integrative Biology of Marine Models Laboratory, CNRS, Sorbonne Université, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France; (S.B.); (O.G.); (J.G.); (D.S.); (S.M.C.)
| | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, F-44000 Nantes, France
- Correspondence: (L.T.); (J.M.C.); Tel.: +33-2-98-29-23-60 (J.M.C.)
| | - J. Mark Cock
- Algal Genetics Group, Integrative Biology of Marine Models Laboratory, CNRS, Sorbonne Université, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France; (S.B.); (O.G.); (J.G.); (D.S.); (S.M.C.)
- Correspondence: (L.T.); (J.M.C.); Tel.: +33-2-98-29-23-60 (J.M.C.)
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Dual-color fluorescence in situ hybridization with combinatorial labeling probes enables a detailed karyotype analysis of Saccharina japonica. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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10
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Wei L, Liu B, Liu D, Xu Z, Wang R, Zhang W. Identification and expression analysis of genome-wide long noncoding RNA responsive CO 2 fluctuated environment in marine microalga Nannochloropsis oceanica. MARINE POLLUTION BULLETIN 2022; 176:113419. [PMID: 35152114 DOI: 10.1016/j.marpolbul.2022.113419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/27/2022] [Accepted: 01/30/2022] [Indexed: 06/14/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been demonstrated to participate in plant growth and development as well as response to different biotic and abiotic stresses. However, the knowledge of lncRNA was limited in microalgae. In this study, by RNA deep sequencing, 134 lncRNAs were identified in marine Nannochloropsis oceanica in response to carbon dioxide fluctuation. Among them, there were 51 lncRNAs displayed differentially expressed between low and high CO2 treatments, including 33 upregulation and 18 downregulation lncRNAs. Cellulose metabolic process, glucan metabolic process, polysaccharide metabolic process, and transmembrane transporter activity were functionally enriched. Multiple potential target genes of lncRNA and lncRNA-mRNA co-located gene network were analyzed. Subsequent analysis had demonstrated that lncRNAs would participate in many biological molecular processes, including gene expression, transcriptional regulation, protein expression and epigenetic regulation. In addition, alternative splicing events were firstly analyzed in response to CO2 fluctuation. There were 2051 alternative splicing (AS events) identified, which might be associated with lncRNA. These observations will provide a novel insight into lncRNA function in Nannochloropsis and provide a series of targets for lncRNA-based gene editing in future.
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Affiliation(s)
- Li Wei
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
| | - Bingqing Liu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Danmei Liu
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Zhengru Xu
- College of Foreign Language, Hainan Normal University, Haikou 571157, China
| | - Ruiping Wang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China
| | - Wenfei Zhang
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou 571158, China.
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11
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Vigneau J, Borg M. The epigenetic origin of life history transitions in plants and algae. PLANT REPRODUCTION 2021; 34:267-285. [PMID: 34236522 PMCID: PMC8566409 DOI: 10.1007/s00497-021-00422-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 05/17/2023]
Abstract
Plants and algae have a complex life history that transitions between distinct life forms called the sporophyte and the gametophyte. This phenomenon-called the alternation of generations-has fascinated botanists and phycologists for over 170 years. Despite the mesmerizing array of life histories described in plants and algae, we are only now beginning to learn about the molecular mechanisms controlling them and how they evolved. Epigenetic silencing plays an essential role in regulating gene expression during multicellular development in eukaryotes, raising questions about its impact on the life history strategy of plants and algae. Here, we trace the origin and function of epigenetic mechanisms across the plant kingdom, from unicellular green algae through to angiosperms, and attempt to reconstruct the evolutionary steps that influenced life history transitions during plant evolution. Central to this evolutionary scenario is the adaption of epigenetic silencing from a mechanism of genome defense to the repression and control of alternating generations. We extend our discussion beyond the green lineage and highlight the peculiar case of the brown algae. Unlike their unicellular diatom relatives, brown algae lack epigenetic silencing pathways common to animals and plants yet display complex life histories, hinting at the emergence of novel life history controls during stramenopile evolution.
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Affiliation(s)
- Jérômine Vigneau
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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Yang X, Wang X, Yao J, Duan D. Genome-Wide Mapping of Cytosine Methylation Revealed Dynamic DNA Methylation Patterns Associated with Sporophyte Development of Saccharina japonica. Int J Mol Sci 2021; 22:9877. [PMID: 34576045 PMCID: PMC8472486 DOI: 10.3390/ijms22189877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 09/08/2021] [Indexed: 02/04/2023] Open
Abstract
Cytosine methylation plays vital roles in regulating gene expression and plant development. However, the function of DNA methylation in the development of macroalgae remains unclear. Through the genome-wide bisulfite sequencing of cytosine methylation in holdfast, stipe and blade, we obtained the complete 5-mC methylation landscape of Saccharina japonica sporophyte. Our results revealed that the total DNA methylation level of sporophyte was less than 0.9%, and the content of CHH contexts was dominant. Moreover, the distribution of CHH methylation within the genes exhibited exon-enriched characteristics. Profiling of DNA methylation in three parts revealed the diverse methylation pattern of sporophyte development. These pivotal DMRs were involved in cell motility, cell cycle and cell wall/membrane biogenesis. In comparison with stipe and blade, hypermethylation of mannuronate C5-epimerase in holdfast decreased the transcript abundance, which affected the synthesis of alginate, the key component of cell walls. Additionally, 5-mC modification participated in the regulation of blade and holdfast development by the glutamate content respectively via glutamine synthetase and amidophosphoribosyl transferase, which may act as the epigenetic regulation signal. Overall, our study revealed the global methylation characteristics of the well-defined holdfast, stipe and blade, and provided evidence for epigenetic regulation of sporophyte development in brown macroalgae.
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Affiliation(s)
- Xiaoqi Yang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Y.); (X.W.); (J.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuliang Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Y.); (X.W.); (J.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Jianting Yao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Y.); (X.W.); (J.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
| | - Delin Duan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; (X.Y.); (X.W.); (J.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266071, China
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Molecular and FISH analysis of 45S rDNA on BAC molecule of Saccharina japonica. AQUACULTURE AND FISHERIES 2021. [DOI: 10.1016/j.aaf.2021.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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14
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DNA methylation-mediated modulation of rapid desiccation tolerance acquisition and dehydration stress memory in the resurrection plant Boea hygrometrica. PLoS Genet 2021; 17:e1009549. [PMID: 33930012 PMCID: PMC8115786 DOI: 10.1371/journal.pgen.1009549] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/12/2021] [Accepted: 04/14/2021] [Indexed: 12/02/2022] Open
Abstract
Pre-exposure of plants to various abiotic conditions confers improved tolerance to subsequent stress. Mild drought acclimation induces acquired rapid desiccation tolerance (RDT) in the resurrection plant Boea hygrometrica, but the mechanisms underlying the priming and memory processes remain unclear. In this study, we demonstrated that drought acclimation-induced RDT can be maintained for at least four weeks but was completely erased after 18 weeks based on a combination of the phenotypic and physiological parameters. Global transcriptome analysis identified several RDT-specific rapid dehydration-responsive genes related to cytokinin and phospholipid biosynthesis, nitrogen and carbon metabolism, and epidermal morphogenesis, most of which were pre-induced by drought acclimation. Comparison of whole-genome DNA methylation revealed dehydration stress-responsive hypomethylation in the CG, CHG, and CHH contexts and acclimation-induced hypermethylation in the CHH context of the B. hygrometrica genome, consistent with the transcriptional changes in methylation pathway genes. As expected, the global promoter and gene body methylation levels were negatively correlated with gene expression levels in both acclimated and dehydrated plants but showed no association with transcriptional divergence during the procedure. Nevertheless, the promoter methylation variations in the CG and CHG contexts were significantly associated with the differential expression of genes required for fundamental genetic processes of DNA conformation, RNA splicing, translation, and post-translational protein modification during acclimation, growth, and rapid dehydration stress response. It was also associated with the dehydration stress-induced upregulation of memory genes, including pre-mRNA-splicing factor 38A, vacuolar amino acid transporter 1-like, and UDP-sugar pyrophosphorylase, which may contribute directly or indirectly to the improvement of dehydration tolerance in B. hygrometrica plants. Altogether, our findings demonstrate the potential implications of DNA methylation in dehydration stress memory and, therefore, provide a molecular basis for enhanced dehydration tolerance in plants induced by drought acclimation. Drought is a major adverse environmental condition affecting plant growth and productivity. Although plants can be trained to improved tolerance to the subsequent drought stress, most land plants are unable to recover from severe dehydration when the relative water content in their vegetative tissues drops below 20–30%. However, a small group of angiosperms, termed resurrection plants, can survive extreme water deficiency of their vegetative tissues to an air-dried state and recovered upon rehydration. Understanding the biochemical and molecular basis of desiccation tolerance is valuable for extending our knowledge of the maximum ability of plants to deal with extreme water loss. Boea hygrometrica is a well-characterized resurrection plant that can not only tolerate slow dehydration but also extend its ability to survive rapid dehydration after a priming process of slow dehydration and rehydration. The rapid desiccation tolerance in primed plants can be maintained for at least four weeks. Here, we utilized this system of drought acclimation-induced RDT acquisition, maintenance, and erasing to explore plant phenotypic, physiological, and transcriptional changes, as well as DNA methylation dynamics. The analyses of the effect of DNA methylation on gene expression and promoter methylation changes with differential gene expression revealed the putative epigenetic control of dehydration stress memory in plants.
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Teng L, Han W, Fan X, Zhang X, Xu D, Wang Y, Rahman S, Pellegrini M, Mock T, Ye N. Integrative analysis of chloroplast DNA methylation in a marine alga-Saccharina japonica. PLANT MOLECULAR BIOLOGY 2021; 105:611-623. [PMID: 33528753 DOI: 10.1007/s11103-020-01113-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 12/30/2020] [Indexed: 05/17/2023]
Abstract
KEY MESSAGE We applied an integrative approach using multiple methods to verify cytosine methylation in the chloroplast DNA of the multicellular brown alga Saccharina japonica. Cytosine DNA methylation is a heritable process which plays important roles in regulating development throughout the life cycle of an organism. Although methylation of nuclear DNA has been studied extensively, little is known about the state and role of DNA methylation in chloroplast genomes, especially in marine algae. Here, we have applied an integrated approach encompassing whole-genome bisulfite sequencing, methylated DNA immunoprecipitation, gene co-expression networks and photophysiological analyses to provide evidence for the role of chloroplast DNA methylation in a marine alga, the multicellular brown alga Saccharina japonica. Although the overall methylation level was relatively low in the chloroplast genome of S. japonica, gametophytes exhibited higher methylation levels than sporophytes. Gene-specific bisulfite-cloning sequencing provided additional evidence for the methylation of key photosynthetic genes. Many of them were highly expressed in sporophytes whereas genes involved in transcription, translation and biosynthesis were strongly expressed in gametophytes. Nucleus-encoded photosynthesis genes were co-expressed with their chloroplast-encoded counterparts potentially contributing to the higher photosynthetic performance in sporophytes compared to gametophytes where these co-expression networks were less pronounced. A nucleus-encoded DNA methyltransferase of the DNMT2 family is assumed to be responsible for the methylation of the chloroplast genome because it is predicted to possess a plastid transit peptide.
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Affiliation(s)
- Linhong Teng
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
- College of Life Science, Dezhou University, Dezhou, 253023, China
| | - Wentao Han
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Xiao Fan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Xiaowen Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Dong Xu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Yitao Wang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Sadequr Rahman
- Tropical Medicine and Biology Platform and School of Science, Monash University Malaysia, Jalan Lagoon Selatan, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, Institute for Genomics and Proteomics, University of California, Los Angeles, CA, 90095, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Naihao Ye
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
- Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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16
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Ferrari M, Torelli A, Marieschi M, Cozza R. Role of DNA methylation in the chromium tolerance of Scenedesmus acutus (Chlorophyceae) and its impact on the sulfate pathway regulation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 301:110680. [PMID: 33218643 DOI: 10.1016/j.plantsci.2020.110680] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 09/11/2020] [Accepted: 09/13/2020] [Indexed: 06/11/2023]
Abstract
DNA methylation is a very important epigenetic modification that participates in many biological functions. Although many researches on DNA methylation have been reported in various plant species, few studies have assessed the global DNA methylation pattern in algae. Even more the complex mechanisms by which DNA methylation modulates stress in algae are yet largely unresolved, mainly with respect to heavy metal stress, for which in plants, metal- and species- specific responses were instead evidenced. In this work, we performed a comparative Whole-Genome Bisulfite Sequencing (WGBS) on two strains of the green alga Scenedesmus acutus with different Cr(VI) sensitivity. The pattern of distribution of 5-mC showed significant differences between the two strains concerning both differentially methylated local contexts (CG, CHG and CHH) and Differentially Methylated Regions (DMRs) as well. We also demonstrated that DNA methylation plays an important role in modulating some genes for sulfate uptake/assimilation confirming the involvement of the sulfate pathway in the Cr-tolerance. Our results suggest that DNA methylation may be of particular importance in defining signal specificity associated with Cr-tolerance and in establishing new epigenetic marks which contribute to the adaptation to metal stress and also to transmit the epigenomic traits to the progeny.
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Affiliation(s)
- Michele Ferrari
- Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci - 87036, Arcavacata di Rende, Cosenza, Italy.
| | - Anna Torelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale delle Scienze 11/A - 43124, Parma, Italy.
| | - Matteo Marieschi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Viale delle Scienze 11/A - 43124, Parma, Italy.
| | - Radiana Cozza
- Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci - 87036, Arcavacata di Rende, Cosenza, Italy.
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Abstract
Model organisms are extensively used in research as accessible and convenient systems for studying a particular area or question in biology. Traditionally, only a limited number of organisms have been studied in detail, but modern genomic tools are enabling researchers to extend beyond the set of classical model organisms to include novel species from less-studied phylogenetic groups. This review focuses on model species for an important group of multicellular organisms, the brown algae. The development of genetic and genomic tools for the filamentous brown alga Ectocarpus has led to it emerging as a general model system for this group, but additional models, such as Fucus or Dictyota dichotoma, remain of interest for specific biological questions. In addition, Saccharina japonica has emerged as a model system to directly address applied questions related to algal aquaculture. We discuss the past, present, and future of brown algal model organisms in relation to the opportunities and challenges in brown algal research.
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Affiliation(s)
- Susana M Coelho
- Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), CNRS, Sorbonne Université, 29680 Roscoff, France;
- Current affiliation: Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
| | - J Mark Cock
- Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), CNRS, Sorbonne Université, 29680 Roscoff, France;
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Gahlaut V, Samtani H, Khurana P. Genome-wide identification and expression profiling of cytosine-5 DNA methyltransferases during drought and heat stress in wheat (Triticum aestivum). Genomics 2020; 112:4796-4807. [PMID: 32890700 DOI: 10.1016/j.ygeno.2020.08.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/17/2020] [Accepted: 08/25/2020] [Indexed: 01/25/2023]
Abstract
DNA methylation is a potential epigenetic mechanism that regulates genome stability, development, and stress mitigation in plants. It is mediated by cytosine-5 DNA methyltransferases (C5-MTases). We identified 52 wheat C5-MTases; and based on domain structure and phylogenetics, these 52 C5-MTases were classified into four sub-families including MET, CMT, DRM and DNMT2; and were distributed on 18 chromosomes. Cis-acting regulatory elements analysis identified abiotic stress-responsive, phytohormone-responsive, development-related and light-related elements in the promoters of TaC5-MTases. We also examined the transcript abundance of TaC5-MTases in different tissues, developmental stages and under abiotic stresses. Notably, most of the TaC5-MTases (TaCMT2, TaCMT3b, TaCMT3c, TaMET1, TaDRM10, TaDNMT2) showed differential regulation of their transcript abundance during drought and heat stress. Overall, the above results provide significant insights into the expression and the probable functions of TaC5-MTases and will also expedite future research programs to explore the mechanisms of epigenetic regulation in wheat.
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Affiliation(s)
- Vijay Gahlaut
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
| | - Harsha Samtani
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
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