1
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López ME, Denoyes B, Bucher E. Epigenomic and transcriptomic persistence of heat stress memory in strawberry (Fragaria vesca). BMC PLANT BIOLOGY 2024; 24:405. [PMID: 38750420 PMCID: PMC11096098 DOI: 10.1186/s12870-024-05093-6] [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: 03/22/2024] [Accepted: 05/02/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND In plants, epigenetic stress memory has so far been found to be largely transient. Here, we wanted to assess the heritability of heat stress-induced epigenetic and transcriptomic changes following woodland strawberry (Fragaria vesca) reproduction. Strawberry is an ideal model to study epigenetic inheritance because it presents two modes of reproduction: sexual (self-pollinated plants) and asexual (clonally propagated plants named daughter plants). Taking advantage of this model, we investigated whether heat stress-induced DNA methylation changes can be transmitted via asexual reproduction. RESULTS Our genome-wide study provides evidence for stress memory acquisition and maintenance in F. vesca. We found that specific DNA methylation marks or epimutations are stably transmitted over at least three asexual generations. Some of the epimutations were associated with transcriptional changes after heat stress. CONCLUSION Our findings show that the strawberry methylome and transcriptome respond with a high level of flexibility to heat stress. Notably, independent plants acquired the same epimutations and those were inherited by their asexual progenies. Overall, the asexual progenies can retain some information in the genome of past stresses encountered by their progenitors. This molecular memory, also documented at the transcriptional level, might be involved in functional plasticity and stress adaptation. Finally, these findings may contribute to novel breeding approaches for climate-ready plants.
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Affiliation(s)
- María-Estefanía López
- Crop Genome Dynamics Group, Agroscope, Nyon, 1260, Switzerland
- Department of Botany and Plant Biology, Faculty of Sciences, University of Geneva, Geneva, 1205, Switzerland
| | - Béatrice Denoyes
- INRAE, Biologie du Fruit et Pathologie, Univ. Bordeaux, Villenave d'Ornon, F-33140, France
| | - Etienne Bucher
- Crop Genome Dynamics Group, Agroscope, Nyon, 1260, Switzerland.
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2
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Provera I, Martinez M, Zenone A, Giacalone VM, D'Anna G, Badalamenti F, Marín-Guirao L, Procaccini G. Exploring priming strategies to improve stress resilience of Posidonia oceanica seedlings. MARINE POLLUTION BULLETIN 2024; 200:116057. [PMID: 38301434 DOI: 10.1016/j.marpolbul.2024.116057] [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: 12/06/2023] [Revised: 01/12/2024] [Accepted: 01/14/2024] [Indexed: 02/03/2024]
Abstract
Seagrasses' ability to store information after exposure to stress (i.e. stress memory) and to better respond to further stress (i.e. priming) have recently been observed, although the temporal persistence of the memory and the mechanisms for priming induction remain to be defined. Here, we explored three priming strategies in Posidonia oceanica seedlings, each inducing a different level of stress, for temperature and salinity. We investigated changes in morphometry, growth rate and biomass between primed and non-primed seedlings. The results showed similar behaviour of seedlings when exposed to an acute stress event, regardless of whether they had been primed or not and of the priming strategy received. This opens the debate on the level of stress necessary for inducing a priming status and the persistence of the stress memory in P. oceanica seedlings. Although no priming-induced stress resistance was observed, seedlings showed unexpectedly high resilience to extreme levels of both abiotic stressors.
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Affiliation(s)
- I Provera
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy.
| | - M Martinez
- Institute of Anthropic Impacts and Sustainability in Marine Environment, National Research Council (IAS-CNR), Lungomare Cristoforo Colombo n. 4521 (ex complesso Roosevelt), Località Addaura, 90149 Palermo, Italy
| | - A Zenone
- Stazione Zoologica Anton Dohrn, Lungomare Cristoforo Colombo 4521, 90149 Palermo, Italy; National Biodiversity Future Centre (NBFC), Palermo, Italy
| | - V M Giacalone
- Institute of Anthropic Impacts and Sustainability in Marine Environment, National Research Council (IAS-CNR), Via del Mare 3, 91021 Torretta Granitola, Italy; National Biodiversity Future Centre (NBFC), Palermo, Italy
| | - G D'Anna
- Institute of Anthropic Impacts and Sustainability in Marine Environment, National Research Council (IAS-CNR), via Giovanni da Verrazzano 17, 91014 Castellammare del Golfo, Italy; National Biodiversity Future Centre (NBFC), Palermo, Italy
| | - F Badalamenti
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; Institute of Anthropic Impacts and Sustainability in Marine Environment, National Research Council (IAS-CNR), Lungomare Cristoforo Colombo n. 4521 (ex complesso Roosevelt), Località Addaura, 90149 Palermo, Italy; National Biodiversity Future Centre (NBFC), Palermo, Italy
| | - L Marín-Guirao
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; Centro Oceanográfico de Murcia (IEO-CSIC), Varadero 1, 30740 San Pedro del Pinatar, Spain
| | - G Procaccini
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy; National Biodiversity Future Centre (NBFC), Palermo, Italy
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3
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Swaegers J, De Cupere S, Gaens N, Lancaster LT, Carbonell JA, Sánchez Guillén RA, Stoks R. Plasticity and associated epigenetic mechanisms play a role in thermal evolution during range expansion. Evol Lett 2024; 8:76-88. [PMID: 38370551 PMCID: PMC10872138 DOI: 10.1093/evlett/qrac007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/06/2022] [Accepted: 12/28/2022] [Indexed: 02/20/2024] Open
Abstract
Due to global change, many species are shifting their distribution and are thereby confronted with novel thermal conditions at the moving range edges. Especially during the initial phases of exposure to a new environment, it has been hypothesized that plasticity and associated epigenetic mechanisms enable species to cope with environmental change. We tested this idea by capitalizing on the well-documented southward range expansion of the damselfly Ischnura elegans from France into Spain where the species invaded warmer regions in the 1950s in eastern Spain (old edge region) and in the 2010s in central Spain (new edge region). Using a common garden experiment at rearing temperatures matching the ancestral and invaded thermal regimes, we tested for evolutionary changes in (thermal plasticity in) larval life history and heat tolerance in these expansion zones. Through the use of de- and hypermethylating agents, we tested whether epigenetic mechanisms play a role in enabling heat tolerance during expansion. We used the phenotype of the native sister species in Spain, I. graellsii, as proxy for the locally adapted phenotype. New edge populations converged toward the phenotype of the native species through plastic thermal responses in life history and heat tolerance while old edge populations (partly) constitutively evolved a faster life history and higher heat tolerance than the core populations, thereby matching the native species. Only the heat tolerance of new edge populations increased significantly when exposed to the hypermethylating agent. This suggests that the DNA methylation machinery is more amenable to perturbation at the new edge and shows it is able to play a role in achieving a higher heat tolerance. Our results show that both (evolved) plasticity as well as associated epigenetic mechanisms are initially important when facing new thermal regimes but that their importance diminishes with time.
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Affiliation(s)
- Janne Swaegers
- Laboratory of Evolutionary Stress Ecology and Ecotoxicology, University of Leuven, Leuven, Belgium
| | - Simon De Cupere
- Laboratory of Evolutionary Stress Ecology and Ecotoxicology, University of Leuven, Leuven, Belgium
| | - Noah Gaens
- Laboratory of Evolutionary Stress Ecology and Ecotoxicology, University of Leuven, Leuven, Belgium
| | - Lesley T Lancaster
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - José A Carbonell
- Department of Zoology, Faculty of Biology, University of Seville, Seville, Spain
| | | | - Robby Stoks
- Laboratory of Evolutionary Stress Ecology and Ecotoxicology, University of Leuven, Leuven, Belgium
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4
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Ashey J, McKelvie H, Freeman J, Shpilker P, Zane LH, Becker DM, Cowen L, Richmond RH, Paul VJ, Seneca FO, Putnam HM. Characterizing transcriptomic responses to sediment stress across location and morphology in reef-building corals. PeerJ 2024; 12:e16654. [PMID: 38313033 PMCID: PMC10836209 DOI: 10.7717/peerj.16654] [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: 04/20/2023] [Accepted: 11/20/2023] [Indexed: 02/06/2024] Open
Abstract
Anthropogenic activities increase sediment suspended in the water column and deposition on reefs can be largely dependent on colony morphology. Massive and plating corals have a high capacity to trap sediments, and active removal mechanisms can be energetically costly. Branching corals trap less sediment but are more susceptible to light limitation caused by suspended sediment. Despite deleterious effects of sediments on corals, few studies have examined the molecular response of corals with different morphological characteristics to sediment stress. To address this knowledge gap, this study assessed the transcriptomic responses of branching and massive corals in Florida and Hawai'i to varying levels of sediment exposure. Gene expression analysis revealed a molecular responsiveness to sediments across species and sites. Differential Gene Expression followed by Gene Ontology (GO) enrichment analysis identified that branching corals had the largest transcriptomic response to sediments, in developmental processes and metabolism, while significantly enriched GO terms were highly variable between massive corals, despite similar morphologies. Comparison of DEGs within orthogroups revealed that while all corals had DEGs in response to sediment, there was not a concerted gene set response by morphology or location. These findings illuminate the species specificity and genetic basis underlying coral susceptibility to sediments.
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Affiliation(s)
- Jill Ashey
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States
| | - Hailey McKelvie
- Department of Computer Science, Tufts University, Medford, Massachusetts, United States
| | - John Freeman
- Department of Computer Science, Tufts University, Medford, Massachusetts, United States
| | - Polina Shpilker
- Department of Computer Science, Tufts University, Medford, Massachusetts, United States
| | - Lauren H. Zane
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States
| | - Danielle M. Becker
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States
| | - Lenore Cowen
- Department of Computer Science, Tufts University, Medford, Massachusetts, United States
| | - Robert H. Richmond
- Kewalo Marine Lab, University of Hawaii at Manoa, Honolulu, Hawaii, United States
| | - Valerie J. Paul
- Smithsonian Marine Station, Smithsonian, Fort Pierce, Florida, United States
| | | | - Hollie M. Putnam
- Department of Biological Sciences, University of Rhode Island, Kingston, Rhode Island, United States
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5
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Williams CJ, Dai D, Tran KA, Monroe JG, Williams BP. Dynamic DNA methylation turnover in gene bodies is associated with enhanced gene expression plasticity in plants. Genome Biol 2023; 24:227. [PMID: 37828516 PMCID: PMC10571256 DOI: 10.1186/s13059-023-03059-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 09/14/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND In several eukaryotes, DNA methylation occurs within the coding regions of many genes, termed gene body methylation (GbM). Whereas the role of DNA methylation on the silencing of transposons and repetitive DNA is well understood, gene body methylation is not associated with transcriptional repression, and its biological importance remains unclear. RESULTS We report a newly discovered type of GbM in plants, which is under constitutive addition and removal by dynamic methylation modifiers in all cells, including the germline. Methylation at Dynamic GbM genes is removed by the DRDD demethylation pathway and added by an unknown source of de novo methylation, most likely the maintenance methyltransferase MET1. We show that the Dynamic GbM state is present at homologous genes across divergent lineages spanning over 100 million years, indicating evolutionary conservation. We demonstrate that Dynamic GbM is tightly associated with the presence of a promoter or regulatory chromatin state within the gene body, in contrast to other gene body methylated genes. We find Dynamic GbM is associated with enhanced gene expression plasticity across development and diverse physiological conditions, whereas stably methylated GbM genes exhibit reduced plasticity. Dynamic GbM genes exhibit reduced dynamic range in drdd mutants, indicating a causal link between DNA demethylation and enhanced gene expression plasticity. CONCLUSIONS We propose a new model for GbM in regulating gene expression plasticity, including a novel type of GbM in which increased gene expression plasticity is associated with the activity of DNA methylation writers and erasers and the enrichment of a regulatory chromatin state.
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Affiliation(s)
- Clara J Williams
- Department of Plant & Microbial Biology, University of California, Berkeley, USA
| | - Dawei Dai
- Department of Plant & Microbial Biology, University of California, Berkeley, USA
| | - Kevin A Tran
- Department of Plant & Microbial Biology, University of California, Berkeley, USA
| | - J Grey Monroe
- Department of Plant Sciences, University of California, Davis, USA
| | - Ben P Williams
- Department of Plant & Microbial Biology, University of California, Berkeley, USA.
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6
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Rehman S, Ahmad Z, Ramakrishnan M, Kalendar R, Zhuge Q. Regulation of plant epigenetic memory in response to cold and heat stress: towards climate resilient agriculture. Funct Integr Genomics 2023; 23:298. [PMID: 37700098 DOI: 10.1007/s10142-023-01219-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 09/14/2023]
Abstract
Plants have evolved to adapt and grow in hot and cold climatic conditions. Some also adapt to daily and seasonal temperature changes. Epigenetic modifications play an important role in regulating plant tolerance under such conditions. DNA methylation and post-translational modifications of histone proteins influence gene expression during plant developmental stages and under stress conditions, including cold and heat stress. While short-term modifications are common, some modifications may persist and result in stress memory that can be inherited by subsequent generations. Understanding the mechanisms of epigenomes responding to stress and the factors that trigger stress memory is crucial for developing climate-resilient agriculture, but such an integrated view is currently limited. This review focuses on the plant epigenetic stress memory during cold and heat stress. It also discusses the potential of machine learning to modify stress memory through epigenetics to develop climate-resilient crops.
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Affiliation(s)
- Shamsur Rehman
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, China
| | - Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, China
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, Viikinkaari 1, FI-00014 University of Helsinki, Helsinki, Finland.
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan.
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China.
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7
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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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8
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Pazzaglia J, Dattolo E, Ruocco M, Santillán-Sarmiento A, Marin-Guirao L, Procaccini G. DNA methylation dynamics in a coastal foundation seagrass species under abiotic stressors. Proc Biol Sci 2023; 290:20222197. [PMID: 36651048 PMCID: PMC9845983 DOI: 10.1098/rspb.2022.2197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/19/2022] [Indexed: 01/19/2023] Open
Abstract
DNA methylation (DNAm) has been intensively studied in terrestrial plants in response to environmental changes, but its dynamic changes in a temporal scale remain unexplored in marine plants. The seagrass Posidonia oceanica ranks among the slowest-growing and longest-living plants on Earth, and is particularly vulnerable to sea warming and local anthropogenic pressures. Here, we analysed the dynamics of DNAm changes in plants collected from coastal areas differentially impacted by eutrophication (i.e. oligotrophic, Ol; eutrophic, Eu) and exposed to abiotic stressors (nutrients, temperature increase and their combination). Levels of global DNAm (% 5-mC) and the expression of key genes involved in DNAm were assessed after one, two and five weeks of exposure. Results revealed a clear differentiation between plants, depending on environmental stimuli, time of exposure and plants' origin. % 5-mC levels were higher during the initial stress exposure especially in Ol plants, which upregulated almost all genes involved in DNAm. Contrarily, Eu plants showed lower expression levels, which increased under chronic exposure to stressors, particularly to temperature. These findings show that DNAm is dynamic in P. oceanica during stress exposure and underlined that environmental epigenetic variations could be implicated in the regulation of acclimation and phenotypic differences depending on local conditions.
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Affiliation(s)
- Jessica Pazzaglia
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy
| | - Emanuela Dattolo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy
| | - Miriam Ruocco
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy
| | - Alex Santillán-Sarmiento
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy
- Faculty of Engineering, National University of Chimborazo, Riobamba, Ecuador
| | - Lazaro Marin-Guirao
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy
- Seagrass Ecology Group, Oceanographic Centre of Murcia, Spanish Institute of Oceanography, Murcia, Spain
| | - Gabriele Procaccini
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, 80121 Naples, Italy
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9
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Sandoval-Gil JM, Ruiz JM, Marín-Guirao L. Advances in understanding multilevel responses of seagrasses to hypersalinity. MARINE ENVIRONMENTAL RESEARCH 2023; 183:105809. [PMID: 36435174 DOI: 10.1016/j.marenvres.2022.105809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Human- and nature-induced hypersaline conditions in coastal systems can lead to profound alterations of the structure and vitality of seagrass meadows and their socio-ecological benefits. In the last two decades, recent research efforts (>50 publications) have contributed significantly to unravel the physiological basis underlying the seagrass-hypersalinity interactions, although most (∼70%) are limited to few species (e.g. Posidonia oceanica, Zostera marina, Thalassia testudinum, Cymodocea nodosa). Variables related to photosynthesis and carbon metabolism are among the most prevalent in the literature, although other key metabolic processes such as plant water relations and responses at molecular (i.e. gene expression) and ultrastructure level are attracting attention. This review emphasises all these latest insights, offering an integrative perspective on the interplay among biological responses across different functional levels (from molecular to clonal structure), and their interaction with biotic/abiotic factors including those related to climate change. Other issues such as the role of salinity in driving the evolutionary trajectory of seagrasses, their acclimation mechanisms to withstand salinity increases or even the adaptive properties of populations that have historically lived under hypersaline conditions are also included. The pivotal role of the costs and limits of phenotypic plasticity in the successful acclimation of marine plants to hypersalinity is also discussed. Finally, some lines of research are proposed to fill the remaining knowledge gaps.
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Affiliation(s)
- Jose Miguel Sandoval-Gil
- Universidad Autónoma de Baja California (UABC), Instituto de Investigaciones Oceanológicas (IIO), Marine Botany Research Group, Ensenada, Baja California, 22860, Mexico
| | - Juan M Ruiz
- Seagrass Ecology Group, Spanish Institute of Oceanography (IEO-CSIC), C/ Varadero s/n, 30740 San Pedro del Pinatar, Murcia, Spain
| | - Lázaro Marín-Guirao
- Seagrass Ecology Group, Spanish Institute of Oceanography (IEO-CSIC), C/ Varadero s/n, 30740 San Pedro del Pinatar, Murcia, Spain.
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10
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López ME, Roquis D, Becker C, Denoyes B, Bucher E. DNA methylation dynamics during stress response in woodland strawberry ( Fragaria vesca). HORTICULTURE RESEARCH 2022; 9:uhac174. [PMID: 36204205 PMCID: PMC9533225 DOI: 10.1093/hr/uhac174] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 07/27/2022] [Indexed: 05/29/2023]
Abstract
Environmental stresses can result in a wide range of physiological and molecular responses in plants. These responses can also impact epigenetic information in genomes, especially at the level of DNA methylation (5-methylcytosine). DNA methylation is the hallmark heritable epigenetic modification and plays a key role in silencing transposable elements (TEs). Although DNA methylation is an essential epigenetic mechanism, fundamental aspects of its contribution to stress responses and adaptation remain obscure. We investigated epigenome dynamics of wild strawberry (Fragaria vesca) in response to variable ecologically relevant environmental conditions at the DNA methylation level. F. vesca methylome responded with great plasticity to ecologically relevant abiotic and hormonal stresses. Thermal stress resulted in substantial genome-wide loss of DNA methylation. Notably, all tested stress conditions resulted in marked hot spots of differential DNA methylation near centromeric or pericentromeric regions, particularly in the non-symmetrical DNA methylation context. Additionally, we identified differentially methylated regions (DMRs) within promoter regions of transcription factor (TF) superfamilies involved in plant stress-response and assessed the effects of these changes on gene expression. These findings improve our understanding on stress-response at the epigenome level by highlighting the correlation between DNA methylation, TEs and gene expression regulation in plants subjected to a broad range of environmental stresses.
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Affiliation(s)
- María-Estefanía López
- Crop Genome Dynamics Group, Agroscope, 1260 Nyon, Switzerland
- Department of Botany and Plant Biology, Faculty of Sciences, University of Geneva, 1205 Geneva, Switzerland
| | - David Roquis
- Crop Genome Dynamics Group, Agroscope, 1260 Nyon, Switzerland
| | - Claude Becker
- LMU BioCenter, Faculty of Biology, Ludwig-Maximilians-University Munich, D-82152 Martinsried, Germany
| | - Béatrice Denoyes
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, F-33140 Villenave d’Ornon, France
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11
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Ruocco M, Jahnke M, Silva J, Procaccini G, Dattolo E. 2b-RAD Genotyping of the Seagrass Cymodocea nodosa Along a Latitudinal Cline Identifies Candidate Genes for Environmental Adaptation. Front Genet 2022; 13:866758. [PMID: 35651946 PMCID: PMC9149362 DOI: 10.3389/fgene.2022.866758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/19/2022] [Indexed: 11/18/2022] Open
Abstract
Plant populations distributed along broad latitudinal gradients often show patterns of clinal variation in genotype and phenotype. Differences in photoperiod and temperature cues across latitudes influence major phenological events, such as timing of flowering or seed dormancy. Here, we used an array of 4,941 SNPs derived from 2b-RAD genotyping to characterize population differentiation and levels of genetic and genotypic diversity of three populations of the seagrass Cymodocea nodosa along a latitudinal gradient extending across the Atlantic-Mediterranean boundary (i.e., Gran Canaria—Canary Islands, Faro—Portugal, and Ebro Delta—Spain). Our main goal was to search for potential outlier loci that could underlie adaptive differentiation of populations across the latitudinal distribution of the species. We hypothesized that such polymorphisms could be related to variation in photoperiod-temperature regime occurring across latitudes. The three populations were clearly differentiated and exhibited diverse levels of clonality and genetic diversity. Cymodocea nodosa from the Mediterranean displayed the highest genotypic richness, while the Portuguese population had the highest clonality values. Gran Canaria exhibited the lowest genetic diversity (as observed heterozygosity). Nine SNPs were reliably identified as outliers across the three sites by two different methods (i.e., BayeScan and pcadapt), and three SNPs could be associated to specific protein-coding genes by screening available C. nodosa transcriptomes. Two SNPs-carrying contigs encoded for transcription factors, while the other one encoded for an enzyme specifically involved in the regulation of flowering time, namely Lysine-specific histone demethylase 1 homolog 2. When analyzing biological processes enriched within the whole dataset of outlier SNPs identified by at least one method, “regulation of transcription” and “signalling” were among the most represented. Our results highlight the fundamental importance signal integration and gene-regulatory networks, as well as epigenetic regulation via DNA (de)methylation, could have for enabling adaptation of seagrass populations along environmental gradients.
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Affiliation(s)
| | - Marlene Jahnke
- Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Gothenburg, Sweden
| | - João Silva
- Centre of Marine Sciences, University of Algarve, Faro, Portugal
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12
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Nanni AV, Morse AM, Newman JRB, Choquette NE, Wedow JM, Liu Z, Leakey ADB, Conesa A, Ainsworth EA, McIntyre LM. Variation in leaf transcriptome responses to elevated ozone corresponds with physiological sensitivity to ozone across maize inbred lines. Genetics 2022; 221:6586798. [PMID: 35579358 DOI: 10.1093/genetics/iyac080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
We examine the impact of sustained elevated ozone concentration on the leaf transcriptome of 5 diverse maize inbred genotypes, which vary in physiological sensitivity to ozone (B73, Mo17, Hp301, C123, NC338), using long reads to assemble transcripts and short reads to quantify expression of these transcripts. More than 99% of the long reads, 99% of the assembled transcripts, and 97% of the short reads map to both B73 and Mo17 reference genomes. Approximately 95% of the genes with assembled transcripts belong to known B73-Mo17 syntenic loci and 94% of genes with assembled transcripts are present in all temperate lines in the NAM pan-genome. While there is limited evidence for alternative splicing in response to ozone stress, there is a difference in the magnitude of differential expression among the 5 genotypes. The transcriptional response to sustained ozone stress in the ozone resistant B73 genotype (151 genes) was modest, while more than 3,300 genes were significantly differentially expressed in the more sensitive NC338 genotype. There is the potential for tandem duplication in 30% of genes with assembled transcripts, but there is no obvious association between potential tandem duplication and differential expression. Genes with a common response across the 5 genotypes (83 genes) were associated with photosynthesis, in particular photosystem I. The functional annotation of genes not differentially expressed in B73 but responsive in the other 4 genotypes (789) identifies reactive oxygen species. This suggests that B73 has a different response to long term ozone exposure than the other 4 genotypes. The relative magnitude of the genotypic response to ozone, and the enrichment analyses are consistent regardless of whether aligning short reads to: long read assembled transcripts; the B73 reference; the Mo17 reference. We find that prolonged ozone exposure directly impacts the photosynthetic machinery of the leaf.
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Affiliation(s)
- Adalena V Nanni
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32611, USA.,Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Alison M Morse
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32611, USA.,Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Jeremy R B Newman
- Department of Pathology, University of Florida, Gainesville, Florida 32611, USA.,Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Nicole E Choquette
- Carl R. Woese Institute for Genomic Biology, Department of Plant Biology, and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jessica M Wedow
- Carl R. Woese Institute for Genomic Biology, Department of Plant Biology, and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Zihao Liu
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32611, USA.,Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
| | - Andrew D B Leakey
- Carl R. Woese Institute for Genomic Biology, Department of Plant Biology, and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ana Conesa
- Department of Cell and Microbial Sciences, University of Florida, Gainesville, Florida 32611, USA.,Institute for Integrative Systems Biology, Spanish National Research Council, 46980 Paterna, Spain
| | - Elizabeth A Ainsworth
- Carl R. Woese Institute for Genomic Biology, Department of Plant Biology, and Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.,USDA ARS Global Change and Photosynthesis Research Unit, Urbana, IL 61801, USA
| | - Lauren M McIntyre
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, Florida 32611, USA.,Genetics Institute, University of Florida, Gainesville, Florida 32611, USA
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