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Agius DR, Kapazoglou A, Avramidou E, Baranek M, Carneros E, Caro E, Castiglione S, Cicatelli A, Radanovic A, Ebejer JP, Gackowski D, Guarino F, Gulyás A, Hidvégi N, Hoenicka H, Inácio V, Johannes F, Karalija E, Lieberman-Lazarovich M, Martinelli F, Maury S, Mladenov V, Morais-Cecílio L, Pecinka A, Tani E, Testillano PS, Todorov D, Valledor L, Vassileva V. Exploring the crop epigenome: a comparison of DNA methylation profiling techniques. FRONTIERS IN PLANT SCIENCE 2023; 14:1181039. [PMID: 37389288 PMCID: PMC10306282 DOI: 10.3389/fpls.2023.1181039] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/27/2023] [Indexed: 07/01/2023]
Abstract
Epigenetic modifications play a vital role in the preservation of genome integrity and in the regulation of gene expression. DNA methylation, one of the key mechanisms of epigenetic control, impacts growth, development, stress response and adaptability of all organisms, including plants. The detection of DNA methylation marks is crucial for understanding the mechanisms underlying these processes and for developing strategies to improve productivity and stress resistance of crop plants. There are different methods for detecting plant DNA methylation, such as bisulfite sequencing, methylation-sensitive amplified polymorphism, genome-wide DNA methylation analysis, methylated DNA immunoprecipitation sequencing, reduced representation bisulfite sequencing, MS and immuno-based techniques. These profiling approaches vary in many aspects, including DNA input, resolution, genomic region coverage, and bioinformatics analysis. Selecting an appropriate methylation screening approach requires an understanding of all these techniques. This review provides an overview of DNA methylation profiling methods in crop plants, along with comparisons of the efficacy of these techniques between model and crop plants. The strengths and limitations of each methodological approach are outlined, and the importance of considering both technical and biological factors are highlighted. Additionally, methods for modulating DNA methylation in model and crop species are presented. Overall, this review will assist scientists in making informed decisions when selecting an appropriate DNA methylation profiling method.
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Affiliation(s)
- Dolores Rita Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
- Biology Department, Ġ.F.Abela Junior College, Msida, Malta
| | - Aliki Kapazoglou
- Department of Vitis, Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Evangelia Avramidou
- Laboratory of Forest Genetics and Biotechnology, Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organization-DIMITRA (ELGO-DIMITRA), Athens, Greece
| | - Miroslav Baranek
- Mendeleum-Insitute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czechia
| | - Elena Carneros
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Stefano Castiglione
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Angela Cicatelli
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Aleksandra Radanovic
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
| | - Jean-Paul Ebejer
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Francesco Guarino
- Department of Chemistry and Biology ‘A. Zambelli’, University of Salerno, Fisciano, Italy
| | - Andrea Gulyás
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Norbert Hidvégi
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Nyíregyháza, Hungary
| | - Hans Hoenicka
- Genomic Research Department, Thünen Institute of Forest Genetics, Grosshansdorf, Germany
| | - Vera Inácio
- BioISI – BioSystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Frank Johannes
- Plant Epigenomics, Technical University of Munich (TUM), Freising, Germany
| | - Erna Karalija
- Faculty of Science, University of Sarajevo, Sarajevo, Bosnia and Herzegovina
| | - Michal Lieberman-Lazarovich
- Department of Vegetables and Field Crops, Agricultural Research Organization, Volcani Center, Institute of Plant Sciences, Rishon LeZion, Israel
| | | | - Stéphane Maury
- Laboratoire de Biologie des Ligneux et des Grandes Cultures EA1207 USC1328, INRAE, Université d’Orléans, Orléans, France
| | - Velimir Mladenov
- Faculty of Agriculture, University of Novi Sad, Novi Sad, Serbia
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| | - Pilar S. Testillano
- Center for Biological Research (CIB) of the Spanish National Research Council (CSIC), Madrid, Spain
| | - Dimitar Todorov
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology and University Institute of Biotechnology of Asturias, University of Oviedo, Oviedo, Spain
| | - Valya Vassileva
- Department of Molecular Biology and Genetics, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
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Kumar P, Kaplan Y, Endelman JB, Ginzberg I. Epigenetic Modifications Related to Potato Skin Russeting. PLANTS (BASEL, SWITZERLAND) 2023; 12:2057. [PMID: 37653974 PMCID: PMC10222780 DOI: 10.3390/plants12102057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/17/2023] [Accepted: 05/18/2023] [Indexed: 09/02/2023]
Abstract
Potato tuber skin is a protective corky tissue consisting of suberized phellem cells. Smooth-skinned varieties are characterized by a clean, shiny appearance compared to the darker hue of russeted potatoes. The rough skin of russeted cultivars is a desired, genetically inherited characteristic; however, unwanted russeting of smooth-skinned cultivars often occurs under suboptimal growth conditions. The involvement of epigenetic modifiers in regulating the smooth skin russeting disorder was tested. We used smooth-skin commercial cultivars with and without the russeting disorder and three lines from a breeding population segregating for russeting. Anatomically, the russet skin showed similar characteristics, whether the cause was environmentally triggered or genetically determined. The old outer layers of the corky phellem remain attached to the newly formed phellem layers instead of being sloughed off. Global DNA methylation analysis indicated a significant reduction in the percentage of 5-methylcytosine in mature vs. immature skin and russet vs. smooth skin. This was true for both the smooth-skin commercial cultivars and the russeted lines. The expression level of selected DNA methyltransferases was reduced in accordance. DNA demethylase expression did not change between the skin types and age. Hence, the reduced DNA methylation in mature and russet skin is more likely to be achieved through passive DNA demethylation and loss of methyltransferase activity.
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Affiliation(s)
- Pawan Kumar
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Institute, 68 HaMacabim Road, P.O. Box 15159, Rishon LeZion 7505101, Israel; (P.K.); (Y.K.)
| | - Yulia Kaplan
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Institute, 68 HaMacabim Road, P.O. Box 15159, Rishon LeZion 7505101, Israel; (P.K.); (Y.K.)
| | - Jeffrey B. Endelman
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Idit Ginzberg
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Institute, 68 HaMacabim Road, P.O. Box 15159, Rishon LeZion 7505101, Israel; (P.K.); (Y.K.)
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Teixeira RT. Cork Development: What Lies Within. PLANTS (BASEL, SWITZERLAND) 2022; 11:2671. [PMID: 36297695 PMCID: PMC9611905 DOI: 10.3390/plants11202671] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/16/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
The cork layer present in all dicotyledonous plant species with radial growth is the result of the phellogen activity, a secondary meristem that produces phellem (cork) to the outside and phelloderm inwards. These three different tissues form the periderm, an efficient protective tissue working as a barrier against external factors such as environmental aggressions and pathogen attacks. The protective function offered by cork cells is mainly due to the abundance of suberin in their cell walls. Chemically, suberin is a complex aliphatic network of long chain fatty acids and alcohols with glycerol together with aromatic units. In most woody species growing in temperate climates, the first periderm is replaced by a new functional periderm upon a few years after being formed. One exception to this bark development can be found in cork oak (Quercus suber) which display a single periderm that grows continuously. Quercus suber stands by its thick cork layer development with continuous seasonal growth. Cork raw material has been exploited by man for centuries, especially in Portugal and Spain. Nowadays, its applications have widened vastly, from the most known product, stoppers, to purses or insulating materials used in so many industries, such as construction and car production. Research on how cork develops, and the effect environmental factors on cork oak trees is extremely important to maintain production of good-quality cork, and, by maintaining cork oak stands wealthy, we are preserving a very important ecosystem both by its biodiversity and its vital social and economic role in areas already showing a population declination.
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Affiliation(s)
- Rita Teresa Teixeira
- BioISI-Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016 Lisboa, Portugal
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Maldonado-Alconada AM, Castillejo MÁ, Rey MD, Labella-Ortega M, Tienda-Parrilla M, Hernández-Lao T, Honrubia-Gómez I, Ramírez-García J, Guerrero-Sanchez VM, López-Hidalgo C, Valledor L, Navarro-Cerrillo RM, Jorrin-Novo JV. Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How. Int J Mol Sci 2022; 23:9980. [PMID: 36077370 PMCID: PMC9456323 DOI: 10.3390/ijms23179980] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, "dehesa." It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors' group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.
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Affiliation(s)
- Ana María Maldonado-Alconada
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - María Ángeles Castillejo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - María-Dolores Rey
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Mónica Labella-Ortega
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Marta Tienda-Parrilla
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Tamara Hernández-Lao
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Irene Honrubia-Gómez
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Javier Ramírez-García
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Víctor M. Guerrero-Sanchez
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Cristina López-Hidalgo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
- Plant Physiology, Department of Organisms and Systems Biology, University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, 33006 Asturias, Spain
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology, University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, 33006 Asturias, Spain
| | - Rafael M. Navarro-Cerrillo
- Evaluation and Restoration of Agronomic and Forest Systems ERSAF, Department of Forest Engineering, University of Córdoba, 14014 Cordoba, Spain
| | - Jesús V. Jorrin-Novo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
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Alves S, Braga Â, Parreira D, Alhinho AT, Silva H, Ramos MJN, Costa MMR, Morais‐Cecílio L. Genome-wide identification, phylogeny, and gene duplication of the epigenetic regulators in Fagaceae. PHYSIOLOGIA PLANTARUM 2022; 174:e13788. [PMID: 36169620 PMCID: PMC9828519 DOI: 10.1111/ppl.13788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 09/16/2022] [Accepted: 09/21/2022] [Indexed: 05/04/2023]
Abstract
Epigenetic regulators are proteins involved in controlling gene expression. Information about the epigenetic regulators within the Fagaceae, a relevant family of trees and shrubs of the northern hemisphere ecosystems, is scarce. With the intent to characterize these proteins in Fagaceae, we searched for orthologs of DNA methyltransferases (DNMTs) and demethylases (DDMEs) and Histone modifiers involved in acetylation (HATs), deacetylation (HDACs), methylation (HMTs), and demethylation (HDMTs) in Fagus, Quercus, and Castanea genera. Blast searches were performed in the available genomes, and freely available RNA-seq data were used to de novo assemble transcriptomes. We identified homologs of seven DNMTs, three DDMEs, six HATs, 11 HDACs, 32 HMTs, and 21 HDMTs proteins. Protein analysis showed that most of them have the putative characteristic domains found in these protein families, which suggests their conserved function. Additionally, to elucidate the evolutionary history of these genes within Fagaceae, paralogs were identified, and phylogenetic analyses were performed with DNA and histone modifiers. We detected duplication events in all species analyzed with higher frequency in Quercus and Castanea and discuss the evidence of transposable elements adjacent to paralogs and their involvement in gene duplication. The knowledge gathered from this work is a steppingstone to upcoming studies concerning epigenetic regulation in this economically important family of Fagaceae.
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Affiliation(s)
- Sofia Alves
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, University of LisbonLisboaPortugal
| | - Ângelo Braga
- Instituto Superior de Agronomia, University of LisbonLisboaPortugal
| | - Denise Parreira
- Instituto Superior de Agronomia, University of LisbonLisboaPortugal
| | - Ana Teresa Alhinho
- Centre of Molecular and Environmental Biology (CBMA)University of MinhoBragaPortugal
| | - Helena Silva
- Centre of Molecular and Environmental Biology (CBMA)University of MinhoBragaPortugal
| | - Miguel Jesus Nunes Ramos
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, University of LisbonLisboaPortugal
- Present address:
GenoMed, Diagnósticos de Medicina MolecularLisboaPortugal
| | | | - Leonor Morais‐Cecílio
- LEAF—Linking Landscape, Environment, Agriculture and FoodInstituto Superior de Agronomia, University of LisbonLisboaPortugal
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Kumar P, Ginzberg I. Potato Periderm Development and Tuber Skin Quality. PLANTS 2022; 11:plants11162099. [PMID: 36015402 PMCID: PMC9415511 DOI: 10.3390/plants11162099] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022]
Abstract
The periderm is a corky tissue that replaces the epidermis when the latter is damaged, and is critical for preventing pathogen invasion and water loss. The periderm is formed through the meristematic activity of phellogen cells (cork cambium). The potato skin (phellem cells) composes the outer layers of the tuber periderm and is a model for studying cork development. Early in tuber development and following tuber expansion, the phellogen becomes active and produces the skin. New skin layers are continuously added by division of the phellogen cells until tuber maturation. Some physiological disorders of the potato tuber are related to abnormal development of the skin, including skinning injuries and russeting of smooth-skinned potatoes. Thus, characterizing the potato periderm contributes to modeling cork development in plants and helps to resolve critical agricultural problems. Here, we summarize the data available on potato periderm formation, highlighting tissue characteristics rather than the suberization processes.
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Inácio V, Santos R, Prazeres R, Graça J, Miguel CM, Morais-Cecílio L. Epigenetics at the crossroads of secondary growth regulation. FRONTIERS IN PLANT SCIENCE 2022; 13:970342. [PMID: 35991449 PMCID: PMC9389228 DOI: 10.3389/fpls.2022.970342] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/18/2022] [Indexed: 05/20/2023]
Abstract
The development of plant tissues and organs during post-embryonic growth occurs through the activity of both primary and secondary meristems. While primary meristems (root and shoot apical meristems) promote axial plant growth, secondary meristems (vascular and cork cambium or phellogen) promote radial thickening and plant axes strengthening. The vascular cambium forms the secondary xylem and phloem, whereas the cork cambium gives rise to the periderm that envelops stems and roots. Periderm takes on an increasingly important role in plant survival under climate change scenarios, but it is also a forest product with unique features, constituting the basis of a sustainable and profitable cork industry. There is established evidence that epigenetic mechanisms involving histone post-translational modifications, DNA methylation, and small RNAs play important roles in the activity of primary meristem cells, their maintenance, and differentiation of progeny cells. Here, we review the current knowledge on the epigenetic regulation of secondary meristems, particularly focusing on the phellogen activity. We also discuss the possible involvement of DNA methylation in the regulation of periderm contrasting phenotypes, given the potential impact of translating this knowledge into innovative breeding programs.
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Affiliation(s)
- Vera Inácio
- BioISI – Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- *Correspondence: Vera Inácio,
| | - Raquel Santos
- BioISI – Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Rafael Prazeres
- BioISI – Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - José Graça
- Forest Research Centre (CEF), Institute of Agronomy, Universidade de Lisboa, Lisbon, Portugal
| | - Célia M. Miguel
- BioISI – Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, Associated Laboratory TERRA, Universidade de Lisboa, Lisbon, Portugal
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Abstract
Quercus species (oaks) have been an integral part of the landscape in the northern hemisphere for millions of years. Their ability to adapt and spread across different environments and their contributions to many ecosystem services is well documented. Human activity has placed many oak species in peril by eliminating or adversely modifying habitats through exploitative land usage and by practices that have exacerbated climate change. The goal of this review is to compile a list of oak species of conservation concern, evaluate the genetic data that is available for these species, and to highlight the gaps that exist. We compiled a list of 124 Oaks of Concern based on the Red List of Oaks 2020 and the Conservation Gap Analysis for Native U.S. Oaks and their evaluations of each species. Of these, 57% have been the subject of some genetic analysis, but for most threatened species (72%), the only genetic analysis was done as part of a phylogenetic study. While nearly half (49%) of published genetic studies involved population genetic analysis, only 16 species of concern (13%) have been the subject of these studies. This is a critical gap considering that analysis of intraspecific genetic variability and genetic structure are essential for designing conservation management strategies. We review the published population genetic studies to highlight their application to conservation. Finally, we discuss future directions in Quercus conservation genetics and genomics.
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Molecular Research on Stress Responses in Quercus spp.: From Classical Biochemistry to Systems Biology through Omics Analysis. FORESTS 2021. [DOI: 10.3390/f12030364] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The genus Quercus (oak), family Fagaceae, comprises around 500 species, being one of the most important and dominant woody angiosperms in the Northern Hemisphere. Nowadays, it is threatened by environmental cues, which are either of biotic or abiotic origin. This causes tree decline, dieback, and deforestation, which can worsen in a climate change scenario. In the 21st century, biotechnology should take a pivotal role in facing this problem and proposing sustainable management and conservation strategies for forests. As a non-domesticated, long-lived species, the only plausible approach for tree breeding is exploiting the natural diversity present in this species and the selection of elite, more resilient genotypes, based on molecular markers. In this direction, it is important to investigate the molecular mechanisms of the tolerance or resistance to stresses, and the identification of genes, gene products, and metabolites related to this phenotype. This research is being performed by using classical biochemistry or the most recent omics (genomics, epigenomics, transcriptomics, proteomics, and metabolomics) approaches, which should be integrated with other physiological and morphological techniques in the Systems Biology direction. This review is focused on the current state-of-the-art of such approaches for describing and integrating the latest knowledge on biotic and abiotic stress responses in Quercus spp., with special reference to Quercus ilex, the system on which the authors have been working for the last 15 years. While biotic stress factors mainly include fungi and insects such as Phytophthora cinnamomi, Cerambyx welensii, and Operophtera brumata, abiotic stress factors include salinity, drought, waterlogging, soil pollutants, cold, heat, carbon dioxide, ozone, and ultraviolet radiation. The review is structured following the Central Dogma of Molecular Biology and the omic cascade, from DNA (genomics, epigenomics, and DNA-based markers) to metabolites (metabolomics), through mRNA (transcriptomics) and proteins (proteomics). An integrated view of the different approaches, challenges, and future directions is critically discussed.
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10
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Papoutsoglou EA, Faria D, Arend D, Arnaud E, Athanasiadis IN, Chaves I, Coppens F, Cornut G, Costa BV, Ćwiek-Kupczyńska H, Droesbeke B, Finkers R, Gruden K, Junker A, King GJ, Krajewski P, Lange M, Laporte MA, Michotey C, Oppermann M, Ostler R, Poorter H, Ramı Rez-Gonzalez R, Ramšak Ž, Reif JC, Rocca-Serra P, Sansone SA, Scholz U, Tardieu F, Uauy C, Usadel B, Visser RGF, Weise S, Kersey PJ, Miguel CM, Adam-Blondon AF, Pommier C. Enabling reusability of plant phenomic datasets with MIAPPE 1.1. THE NEW PHYTOLOGIST 2020. [PMID: 32171029 DOI: 10.15454/1yxvzv] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity. We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples. We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0. MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.
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Affiliation(s)
- Evangelia A Papoutsoglou
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Daniel Faria
- BioData.pt, Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
- INESC-ID, 1000-029, Lisboa, Portugal
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Elizabeth Arnaud
- Bioversity International, Parc Scientifique Agropolis II, Montpellier Cedex 5, 34397, France
| | - Ioannis N Athanasiadis
- Geo-Information Science and Remote Sensing Laboratory, Wageningen University, Droevendaalsesteeg 3, Wageningen, 6708PB, the Netherlands
| | - Inês Chaves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Frederik Coppens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | | | - Bruno V Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, 1749-016, Portugal
| | - Hanna Ćwiek-Kupczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Bert Droesbeke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Richard Finkers
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI1000, Ljubljana, Slovenia
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2577, Australia
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Marie-Angélique Laporte
- Bioversity International, Parc Scientifique Agropolis II, Montpellier Cedex 5, 34397, France
| | - Célia Michotey
- Université Paris-Saclay, INRAE, URGI, Versailles, 78026, France
| | - Markus Oppermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Richard Ostler
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | | | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI1000, Ljubljana, Slovenia
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - François Tardieu
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, UMR759, Montpellier, 34060, France
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - Björn Usadel
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Institute for Biology I, BioSC, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Stephan Weise
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | | | - Célia M Miguel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, 1749-016, Portugal
| | | | - Cyril Pommier
- Université Paris-Saclay, INRAE, URGI, Versailles, 78026, France
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11
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Papoutsoglou EA, Faria D, Arend D, Arnaud E, Athanasiadis IN, Chaves I, Coppens F, Cornut G, Costa BV, Ćwiek‐Kupczyńska H, Droesbeke B, Finkers R, Gruden K, Junker A, King GJ, Krajewski P, Lange M, Laporte M, Michotey C, Oppermann M, Ostler R, Poorter H, Ramírez‐Gonzalez R, Ramšak Ž, Reif JC, Rocca‐Serra P, Sansone S, Scholz U, Tardieu F, Uauy C, Usadel B, Visser RGF, Weise S, Kersey PJ, Miguel CM, Adam‐Blondon A, Pommier C. Enabling reusability of plant phenomic datasets with MIAPPE 1.1. THE NEW PHYTOLOGIST 2020; 227:260-273. [PMID: 32171029 PMCID: PMC7317793 DOI: 10.1111/nph.16544] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/24/2020] [Indexed: 05/21/2023]
Abstract
Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity. We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples. We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0. MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.
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12
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Papoutsoglou EA, Faria D, Arend D, Arnaud E, Athanasiadis IN, Chaves I, Coppens F, Cornut G, Costa BV, Ćwiek-Kupczyńska H, Droesbeke B, Finkers R, Gruden K, Junker A, King GJ, Krajewski P, Lange M, Laporte MA, Michotey C, Oppermann M, Ostler R, Poorter H, Ramı Rez-Gonzalez R, Ramšak Ž, Reif JC, Rocca-Serra P, Sansone SA, Scholz U, Tardieu F, Uauy C, Usadel B, Visser RGF, Weise S, Kersey PJ, Miguel CM, Adam-Blondon AF, Pommier C. Enabling reusability of plant phenomic datasets with MIAPPE 1.1. THE NEW PHYTOLOGIST 2020. [PMID: 32171029 DOI: 10.15454/ah6u4a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity. We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples. We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0. MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.
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Affiliation(s)
- Evangelia A Papoutsoglou
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Daniel Faria
- BioData.pt, Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
- INESC-ID, 1000-029, Lisboa, Portugal
| | - Daniel Arend
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Elizabeth Arnaud
- Bioversity International, Parc Scientifique Agropolis II, Montpellier Cedex 5, 34397, France
| | - Ioannis N Athanasiadis
- Geo-Information Science and Remote Sensing Laboratory, Wageningen University, Droevendaalsesteeg 3, Wageningen, 6708PB, the Netherlands
| | - Inês Chaves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- Instituto de Biologia Experimental e Tecnológica (iBET), 2780-157, Oeiras, Portugal
| | - Frederik Coppens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | | | - Bruno V Costa
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, 1749-016, Portugal
| | - Hanna Ćwiek-Kupczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Bert Droesbeke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Richard Finkers
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI1000, Ljubljana, Slovenia
| | - Astrid Junker
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2577, Australia
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, ul. Strzeszyńska 34, 60-479, Poznań, Poland
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Marie-Angélique Laporte
- Bioversity International, Parc Scientifique Agropolis II, Montpellier Cedex 5, 34397, France
| | - Célia Michotey
- Université Paris-Saclay, INRAE, URGI, Versailles, 78026, France
| | - Markus Oppermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Richard Ostler
- Computational and Analytical Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Hendrik Poorter
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | | | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, SI1000, Ljubljana, Slovenia
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Philippe Rocca-Serra
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Susanna-Assunta Sansone
- Oxford e-Research Centre, Department of Engineering Science, University of Oxford, 7 Keble Road, Oxford, OX1 3QG, UK
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - François Tardieu
- INRA, Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux, UMR759, Montpellier, 34060, France
| | - Cristobal Uauy
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Colney, Norwich, NR4 7UH, UK
| | - Björn Usadel
- Plant Sciences (IBG-2), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
- Institute for Biology I, BioSC, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, PO Box 386, Wageningen, 6700AJ, the Netherlands
| | - Stephan Weise
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | | | - Célia M Miguel
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA) Avenida da República, 2780-157, Oeiras, Portugal
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, 1749-016, Portugal
| | | | - Cyril Pommier
- Université Paris-Saclay, INRAE, URGI, Versailles, 78026, France
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13
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Genome-Wide Identification of Epigenetic Regulators in Quercus suber L. Int J Mol Sci 2020; 21:ijms21113783. [PMID: 32471127 PMCID: PMC7313042 DOI: 10.3390/ijms21113783] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/12/2022] Open
Abstract
Modifications of DNA and histones, including methylation and acetylation, are critical for the epigenetic regulation of gene expression during plant development, particularly during environmental adaptation processes. However, information on the enzymes catalyzing all these modifications in trees, such as Quercus suber L., is still not available. In this study, eight DNA methyltransferases (DNA Mtases) and three DNA demethylases (DDMEs) were identified in Q. suber. Histone modifiers involved in methylation (35), demethylation (26), acetylation (8), and deacetylation (22) were also identified in Q. suber. In silico analysis showed that some Q. suber DNA Mtases, DDMEs and histone modifiers have the typical domains found in the plant model Arabidopsis, which might suggest a conserved functional role. Additional phylogenetic analyses of the DNA and histone modifier proteins were performed using several plant species homologs, enabling the classification of the Q. suber proteins. A link between the expression levels of each gene in different Q. suber tissues (buds, flowers, acorns, embryos, cork, and roots) with the functions already known for their closest homologs in other species was also established. Therefore, the data generated here will be important for future studies exploring the role of epigenetic regulators in this economically important species.
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14
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Lopes ST, Sobral D, Costa B, Perdiguero P, Chaves I, Costa A, Miguel CM. Phellem versus xylem: genome-wide transcriptomic analysis reveals novel regulators of cork formation in cork oak. TREE PHYSIOLOGY 2020; 40:129-141. [PMID: 31860724 DOI: 10.1093/treephys/tpz118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/15/2019] [Indexed: 05/23/2023]
Abstract
Cork cambium (or phellogen) is a secondary meristem responsible for the formation of phelloderm and phellem/cork, which together compose the periderm. In Quercus suber L., the phellogen is active throughout the entire life of the tree, producing a continuous and renewable outer bark of cork. To identify specific candidate genes associated with cork cambium activity and phellem differentiation, we performed a comparative transcriptomic study of Q. suber secondary growth tissues (xylem and phellogen/phellem) using RNA-seq. The present work provides a high-resolution map of all the transcripts identified in the phellogen/phellem tissues. A total of 6013 differentially expressed genes were identified, with 2875 of the transcripts being specifically enriched during the cork formation process versus secondary xylem formation. Furthermore, cork samples originating from the original phellogen (`virgin' cork) and from a traumatic phellogen (`amadia' cork) were also compared. Our results point to a shortlist of potentially relevant candidate genes regulating phellogen activity and phellem differentiation, including novel genes involved in the suberization process, as well as genes associated to ethylene and jasmonate signaling and to meristem function. The future functional characterization of some of the identified candidate genes will help to elucidate the molecular mechanisms underlying cork cambium activity and phellem differentiation.
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Affiliation(s)
- Susana T Lopes
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Daniel Sobral
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 2780-156 Oeiras, Portugal
| | - Bruno Costa
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Pedro Perdiguero
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
| | - Inês Chaves
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | - Augusta Costa
- Instituto Nacional de Investigação Agrária e Veterinária, Avenida da República, Quinta do Marquês 2780-157 Oeiras, Portugal
| | - Célia M Miguel
- Instituto de Biologia Experimental e Tecnológica, Avenida da República, Quinta do Marquês, 2780-157 Oeiras, Portugal
- Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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15
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Pinheiro C, Wienkoop S, de Almeida JF, Brunetti C, Zarrouk O, Planchon S, Gori A, Tattini M, Ricardo CP, Renaut J, Teixeira RT. Phellem Cell-Wall Components Are Discriminants of Cork Quality in Quercus suber. FRONTIERS IN PLANT SCIENCE 2019; 10:944. [PMID: 31417580 PMCID: PMC6682605 DOI: 10.3389/fpls.2019.00944] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 07/08/2019] [Indexed: 05/30/2023]
Abstract
Cork is a renewable, non-wood high valued forest product, with relevant ecological and economic impact in the Mediterranean-type ecosystems. Currently, cork is ranked according to its commercial quality. The most valuable planks are chosen for cork stoppers production. Cork planks with adequate thickness and porosity are classified as stoppable quality cork (SQC). The chemical composition of cork is known, but the regulation of metabolic pathways responsible of cork production and composition, hence of cork quality, is largely unknown. Here, we tested the hypothesis that post-genomic events may be responsible for the development of SQC and N-SQC (non-stoppable quality cork). Here, we show that combined proteomics and targeted metabolomics (namely soluble and cell wall bound phenolics) analyzed on recently formed phellem allows discriminate cork planks of different quality. Phellem cells of SQC and N-SQC displayed different reducing capacity, with consequential impact on both enzymatic pathways (e.g., glycolysis) and other cellular functions, including cell wall assembly and suberization. Glycolysis and respiration related proteins were abundant in both cork quality groups, whereas the level of several proteins associated to mitochondrial metabolism was higher in N-SQC. The soluble and cell wall-bound phenolics in recently formed phellem clearly discriminated SQC from N-SCQ. In our study, SQC was characterized by a high incorporation of aromatic components of the phenylpropanoid pathway in the cell wall, together with a lower content of hydrolysable tannins. Here, we propose that the level of hydrolysable tannins may represent a valuable diagnostic tool for screening recently formed phellem, and used as a proxy for the quality grade of cork plank produced by each tree.
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Affiliation(s)
- Carla Pinheiro
- Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Lisbon, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Stefanie Wienkoop
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - João Feio de Almeida
- UCIBIO – REQUIMTE, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Cecilia Brunetti
- National Research Council of Italy, Trees and Timber Institute, Florence, Italy
- Department of Agri-Food Production and Environmental Sciences, University of Florence, Florence, Italy
| | - Olfa Zarrouk
- Instituto de Tecnologia Química e Biológica, Universidade NOVA de Lisboa, Lisbon, Portugal
| | | | - Antonella Gori
- Department of Agri-Food Production and Environmental Sciences, University of Florence, Florence, Italy
| | - Massimiliano Tattini
- Institute for Sustainable Plant Protection, National Research Council of Italy, Florence, Italy
| | - Cândido Pinto Ricardo
- Instituto de Tecnologia Química e Biológica, Universidade NOVA de Lisboa, Lisbon, Portugal
| | - Jenny Renaut
- Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
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16
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Inácio V, Martins MT, Graça J, Morais-Cecílio L. Cork Oak Young and Traumatic Periderms Show PCD Typical Chromatin Patterns but Different Chromatin-Modifying Genes Expression. FRONTIERS IN PLANT SCIENCE 2018; 9:1194. [PMID: 30210513 PMCID: PMC6120546 DOI: 10.3389/fpls.2018.01194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 07/25/2018] [Indexed: 05/20/2023]
Abstract
Plants are subjected to adverse conditions being outer protective tissues fundamental to their survival. Tree stems are enveloped by a periderm made of cork cells, resulting from the activity of the meristem phellogen. DNA methylation and histone modifications have important roles in the regulation of plant cell differentiation. However, studies on its involvement in cork differentiation are scarce despite periderm importance. Cork oak periderm development was used as a model to study the formation and differentiation of secondary protective tissues, and their behavior after traumatic wounding (traumatic periderm). Nuclei structural changes, dynamics of DNA methylation, and posttranslational histone modifications were assessed in young and traumatic periderms, after cork harvesting. Lenticular phellogen producing atypical non-suberized cells that disaggregate and form pores was also studied, due to high impact for cork industrial uses. Immunolocalization of active and repressive marks, transcription analysis of the corresponding genes, and correlations between gene expression and cork porosity were investigated. During young periderm development, a reduction in nuclei area along with high levels of DNA methylation occurred throughout epidermis disruption. As cork cells became more differentiated, whole nuclei progressive chromatin condensation with accumulation in the nuclear periphery and increasing DNA methylation was observed. Lenticular cells nuclei were highly fragmented with faint 5-mC labeling. Phellogen nuclei were less methylated than in cork cells, and in lenticular phellogen were even lower. No significant differences were detected in H3K4me3 and H3K18ac signals between cork cells layers, although an increase in H3K4me3 signals was found from the phellogen to cork cells. Distinct gene expression patterns in young and traumatic periderms suggest that cork differentiation might be under specific silencing regulatory pathways. Significant correlations were found between QsMET1, QsMET2, and QsSUVH4 gene expression and cork porosity. This work evidences that DNA methylation and histone modifications play a role in cork differentiation and epidermis induced tension-stress. It also provides the first insights into chromatin dynamics during cork and lenticular cells differentiation pointing to a distinct type of remodeling associated with cell death.
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Affiliation(s)
- Vera Inácio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
- *Correspondence: Vera Inácio,
| | - Madalena T. Martins
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - José Graça
- Forest Research Center (CEF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
| | - Leonor Morais-Cecílio
- Linking Landscape, Environment, Agriculture and Food (LEAF), Institute of Agronomy, University of Lisbon, Lisbon, Portugal
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