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Oxidosqualene cyclases involved in the biosynthesis of triterpenoids in Quercus suber cork. Sci Rep 2020; 10:8011. [PMID: 32415159 PMCID: PMC7229149 DOI: 10.1038/s41598-020-64913-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 02/24/2020] [Indexed: 11/30/2022] Open
Abstract
Cork is a water-impermeable, suberin-based material harboring lignin, (hemi)cellulose, and extractable small molecules (primarily triterpenoids). Extractables strongly influence the properties of suberin-based materials. Though these previous findings suggest a key role for triterpenoids in cork material quality, directly testing this idea is hindered in part because it is not known which genes control cork triterpenoid biosynthesis. Here, we used gas chromatography and mass spectrometry to determine that the majority (>85%) of non-polar extractables from cork were pentacyclic triterpenoids, primarily betulinic acid, friedelin, and hydroxy-friedelin. In other plants, triterpenoids are generated by oxidosqualene cyclases (OSCs). Accordingly, we mined Quercus suber EST libraries for OSC fragments to use in a RACE PCR-based approach and cloned three full-length OSC transcripts from cork (QsOSC1-3). Heterologous expression in Saccharomyces cerevisiae revealed that QsOSC1-3 respectively encoded enzymes with lupeol synthase, mixed α- and β-amyrin synthase, and mixed β-amyrin and friedelin synthase activities. These activities together account for the backbone structures of the major cork triterpenoids. Finally, we analyzed the sequences of QsOSC1-3 and other plant OSCs to identify residues associated with specific OSC activities, then combined this with analyses of Q. suber transcriptomic and genomic data to evaluate potential redundancies in cork triterpenoid biosynthesis.
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Plomion C, Martin F. Oak genomics is proving its worth. THE NEW PHYTOLOGIST 2020; 226:943-946. [PMID: 32301515 DOI: 10.1111/nph.16560] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 05/10/2023]
Affiliation(s)
| | - Francis Martin
- INRAE, UMR IAM, Centre INRAE-Grand Est, Université de Lorraine, F-54280, Champenoux, France
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53
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Leroy T, Plomion C, Kremer A. Oak symbolism in the light of genomics. THE NEW PHYTOLOGIST 2020; 226:1012-1017. [PMID: 31183874 PMCID: PMC7166128 DOI: 10.1111/nph.15987] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 05/31/2019] [Indexed: 05/09/2023]
Abstract
Throughout the Northern Hemisphere, human societies, political systems, and religions have appropriated oaks in symbolic representations. In this review, we explore the possible associations between recent genetic and genomic findings and the symbolic representations of oaks. We first consider the ways in which evolutionary history during the Holocene has tightened links between humans and oaks in Europe, and how this may have led to symbolic representations. We then show how recent findings concerning the structure and evolution of the oak genome have provided additional knowledge about symbolic representations, such as longevity, cohesiveness, and robustness.
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Affiliation(s)
- Thibault Leroy
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095 Montpellier, France
- BIOGECO, INRA, Université de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Christophe Plomion
- BIOGECO, INRA, Université de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
| | - Antoine Kremer
- BIOGECO, INRA, Université de Bordeaux, 69 Route d'Arcachon, 33612 Cestas, France
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Hipp AL, Manos PS, Hahn M, Avishai M, Bodénès C, Cavender-Bares J, Crowl AA, Deng M, Denk T, Fitz-Gibbon S, Gailing O, González-Elizondo MS, González-Rodríguez A, Grimm GW, Jiang XL, Kremer A, Lesur I, McVay JD, Plomion C, Rodríguez-Correa H, Schulze ED, Simeone MC, Sork VL, Valencia-Avalos S. Genomic landscape of the global oak phylogeny. THE NEW PHYTOLOGIST 2020; 226:1198-1212. [PMID: 31609470 DOI: 10.1111/nph.16162] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 06/05/2019] [Indexed: 05/10/2023]
Abstract
The tree of life is highly reticulate, with the history of population divergence emerging from populations of gene phylogenies that reflect histories of introgression, lineage sorting and divergence. In this study, we investigate global patterns of oak diversity and test the hypothesis that there are regions of the oak genome that are broadly informative about phylogeny. We utilize fossil data and restriction-site associated DNA sequencing (RAD-seq) for 632 individuals representing nearly 250 Quercus species to infer a time-calibrated phylogeny of the world's oaks. We use a reversible-jump Markov chain Monte Carlo method to reconstruct shifts in lineage diversification rates, accounting for among-clade sampling biases. We then map the > 20 000 RAD-seq loci back to an annotated oak genome and investigate genomic distribution of introgression and phylogenetic support across the phylogeny. Oak lineages have diversified among geographic regions, followed by ecological divergence within regions, in the Americas and Eurasia. Roughly 60% of oak diversity traces back to four clades that experienced increases in net diversification, probably in response to climatic transitions or ecological opportunity. The strong support for the phylogeny contrasts with high genomic heterogeneity in phylogenetic signal and introgression. Oaks are phylogenomic mosaics, and their diversity may in fact depend on the gene flow that shapes the oak genome.
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Affiliation(s)
- Andrew L Hipp
- The Morton Arboretum, Lisle, IL, 60532-1293, USA
- The Field Museum, Chicago, IL, 60605, USA
| | | | - Marlene Hahn
- The Morton Arboretum, Lisle, IL, 60532-1293, USA
| | - Michael Avishai
- Previously of, The Hebrew University of Jerusalem, Botanical Garden, Zalman Shne'ur St. 1, Jerusalem, Israel
| | | | | | | | - Min Deng
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Thomas Denk
- Swedish Museum of Natural History, Stockholm, 10405, Sweden
| | | | - Oliver Gailing
- Büsgen-Institute, Georg-August-University Göttingen, Göttingen, D-37077, Germany
| | | | - Antonio González-Rodríguez
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, 58190, México
| | | | - Xiao-Long Jiang
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai, 201602, China
| | | | | | | | | | - Hernando Rodríguez-Correa
- Escuela Nacional de Estudios Superiores Unidad Morelia, Universidad Nacional Autónoma de México, Morelia, 58190, México
| | - Ernst-Detlef Schulze
- Max Planck Institute for Biogeochemistry, Hans-Knoell-Str. 10, Jena, 07745, Germany
| | | | - Victoria L Sork
- University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Susana Valencia-Avalos
- Herbario de la Facultad de Ciencias, Departamento de Biología Comparada, Universidad Nacional Autónoma de México, Circuito Exterior, s.n., Ciudad Universitaria, Coyoacán, México City, CP 04510, México
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55
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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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Soltani N, Best T, Grace D, Nelms C, Shumaker K, Romero-Severson J, Moses D, Schuster S, Staton M, Carlson J, Gwinn K. Transcriptome profiles of Quercus rubra responding to increased O 3 stress. BMC Genomics 2020; 21:160. [PMID: 32059640 PMCID: PMC7023784 DOI: 10.1186/s12864-020-6549-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 01/31/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Climate plays an essential role in forest health, and climate change may increase forest productivity losses due to abiotic and biotic stress. Increased temperature leads to the increased formation of ozone (O3). Ozone is formed by the interaction of sunlight, molecular oxygen and by the reactions of chemicals commonly found in industrial and automobile emissions such as nitrogen oxides and volatile organic compounds. Although it is well known that productivity of Northern red oak (Quercus rubra) (NRO), an ecologically and economically important species in the forests of eastern North America, is reduced by exposure to O3, limited information is available on its responses to exogenous stimuli at the level of gene expression. RESULTS RNA sequencing yielded more than 323 million high-quality raw sequence reads. De novo assembly generated 52,662 unigenes, of which more than 42,000 sequences could be annotated through homology-based searches. A total of 4140 differential expressed genes (DEGs) were detected in response to O3 stress, as compared to their respective controls. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of the O3-response DEGs revealed perturbation of several biological pathways including energy, lipid, amino acid, carbohydrate and terpenoid metabolism as well as plant-pathogen interaction. CONCLUSION This study provides the first reference transcriptome for NRO and initial insights into the genomic responses of NRO to O3. Gene expression profiling reveals altered primary and secondary metabolism of NRO seedlings, including known defense responses such as terpenoid biosynthesis.
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Affiliation(s)
- Nourolah Soltani
- The Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Teo Best
- The Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA
| | - Dantria Grace
- Department of Biological & Environmental Sciences, University of West Alabama, Livingston, AL, 35470, USA
| | - Christen Nelms
- Department of Biological & Environmental Sciences, University of West Alabama, Livingston, AL, 35470, USA
| | - Ketia Shumaker
- Department of Biological & Environmental Sciences, University of West Alabama, Livingston, AL, 35470, USA
| | | | - Daniela Moses
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Nanyang Technological University, Nanyang Avenue, 637551, Singapore
| | - Stephan Schuster
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Nanyang Technological University, Nanyang Avenue, 637551, Singapore
| | - Margaret Staton
- The Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA.
| | - John Carlson
- The Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA, 16802, USA.
| | - Kimberly Gwinn
- The Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, 37996, USA.
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57
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López de Heredia U, Mora-Márquez F, Goicoechea PG, Guillardín-Calvo L, Simeone MC, Soto Á. ddRAD Sequencing-Based Identification of Genomic Boundaries and Permeability in Quercus ilex and Q. suber Hybrids. FRONTIERS IN PLANT SCIENCE 2020; 11:564414. [PMID: 33013984 PMCID: PMC7498617 DOI: 10.3389/fpls.2020.564414] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/13/2020] [Indexed: 05/03/2023]
Abstract
Hybridization and its relevance is a hot topic in ecology and evolutionary biology. Interspecific gene flow may play a key role in species adaptation to environmental change, as well as in the survival of endangered populations. Despite the fact that hybridization is quite common in plants, many hybridizing species, such as Quercus spp., maintain their integrity, while precise determination of genomic boundaries between species remains elusive. Novel high throughput sequencing techniques have opened up new perspectives in the comparative analysis of genomes and in the study of historical and current interspecific gene flow. In this work, we applied ddRADseq technique and developed an ad hoc bioinformatics pipeline for the study of ongoing hybridization between two relevant Mediterranean oaks, Q. ilex and Q. suber. We adopted a local scale approach, analyzing adult hybrids (sensu lato) identified in a mixed stand and their open-pollinated progenies. We have identified up to 9,435 markers across the genome and have estimated individual introgression levels in adults and seedlings. Estimated contribution of Q. suber to the genome is higher, on average, in hybrid progenies than in hybrid adults, suggesting preferential backcrossing with this parental species, maybe followed by selection during juvenile stages against individuals with higher Q. suber genomic contribution. Most discriminating markers seem to be scattered throughout the genome, suggesting that a large number of small genomic regions underlie boundaries between these species. A noticeable proportion of the markers (26%) showed allelic frequencies in adult hybrids very similar to one of the parental species, and very different from the other; a finding that seems relevant for understanding the hybridization process and the occurrence of adaptive introgression. Candidate marker databases developed in this study constitute a valuable resource to design large scale re-sequencing experiments in Mediterranean sclerophyllous oak species and could provide insight in species boundaries and on adaptive introgression between Q. suber and Q. ilex.
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Affiliation(s)
- Unai López de Heredia
- G.I. Genética, Fisiología e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | - Fernando Mora-Márquez
- G.I. Genética, Fisiología e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Laura Guillardín-Calvo
- G.I. Genética, Fisiología e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
| | - Marco C. Simeone
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università degli Studi della Tuscia, Viterbo, Italy
| | - Álvaro Soto
- G.I. Genética, Fisiología e Historia Forestal, Dpto. Sistemas y Recursos Naturales, ETSI Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Spain
- *Correspondence: Álvaro Soto,
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58
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Müller M, Gailing O. Abiotic genetic adaptation in the Fagaceae. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21:783-795. [PMID: 31081234 DOI: 10.1111/plb.13008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/09/2019] [Indexed: 06/09/2023]
Abstract
Fagaceae can be found in tropical and temperate regions and contain species of major ecological and economic importance. In times of global climate change, tree populations need to adapt to rapidly changing environmental conditions. The predicted warmer and drier conditions will potentially result in locally maladapted populations. There is evidence that major genera of the Fagaceae are already negatively affected by climate change-related factors such as drought and associated biotic stressors. Therefore, knowledge of the mechanisms underlying adaptation is of great interest. In this review, we summarise current literature related to genetic adaptation to abiotic environmental conditions. We begin with an overview of genetic diversity in Fagaceae species and then summarise current knowledge related to drought stress tolerance, bud burst timing and frost tolerance in the Fagaceae. Finally, we discuss the role of hybridisation, epigenetics and phenotypic plasticity in adaptation.
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Affiliation(s)
- M Müller
- Faculty for Forest Sciences and Forest Ecology, Forest Genetics and Forest Tree Breeding, University of Goettingen, Göttingen, Germany
| | - O Gailing
- Faculty for Forest Sciences and Forest Ecology, Forest Genetics and Forest Tree Breeding, University of Goettingen, Göttingen, Germany
- Center for Integrated Breeding Research (CiBreed), University of Goettingen, Göttingen, Germany
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59
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Xing Y, Liu Y, Zhang Q, Nie X, Sun Y, Zhang Z, Li H, Fang K, Wang G, Huang H, Bisseling T, Cao Q, Qin L. Hybrid de novo genome assembly of Chinese chestnut (Castanea mollissima). Gigascience 2019; 8:giz112. [PMID: 31513707 PMCID: PMC6741814 DOI: 10.1093/gigascience/giz112] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 04/01/2019] [Accepted: 08/19/2019] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The Chinese chestnut (Castanea mollissima) is widely cultivated in China for nut production. This plant also plays an important ecological role in afforestation and ecosystem services. To facilitate and expand the use of C. mollissima for breeding and its genetic improvement, we report here the whole-genome sequence of C. mollissima. FINDINGS We produced a high-quality assembly of the C. mollissima genome using Pacific Biosciences single-molecule sequencing. The final draft genome is ∼785.53 Mb long, with a contig N50 size of 944 kb, and we further annotated 36,479 protein-coding genes in the genome. Phylogenetic analysis showed that C. mollissima diverged from Quercus robur, a member of the Fagaceae family, ∼13.62 million years ago. CONCLUSIONS The high-quality whole-genome assembly of C. mollissima will be a valuable resource for further genetic improvement and breeding for disease resistance and nut quality.
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Affiliation(s)
- Yu Xing
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China
- College of Plant Science and Technology, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China
| | - Yang Liu
- College of Plant Science and Technology, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China
| | - Qing Zhang
- College of Plant Science and Technology, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China
| | - Xinghua Nie
- College of Plant Science and Technology, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China
| | - Yamin Sun
- Research Center for Functional Genomics and Biochip, 23 Hongda St., Tianjin 300457, China
| | - Zhiyong Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China
- College of Plant Science and Technology, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China
| | - Huchen Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Kefeng Fang
- College of Landscape Architecture, Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China
| | - Guangpeng Wang
- Changli Institute of Pomology, Hebei Academy of Agriculture and Forestry Sciences, 39 E Jieyangdajie, Changli 066600, China
| | - Hongwen Huang
- South China Botanical Garden, Chinese Academy of Sciences, 723 Xingke Rd., Guangzhou 510650, China
| | - Ton Bisseling
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands
| | - Qingqin Cao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China
- College of Plant Science and Technology, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China
| | - Ling Qin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China
- College of Plant Science and Technology, Beijing Key Laboratory for Agricultural Application and New Technique, Beijing University of Agriculture, 7 Beinong Rd., Beijing 102206, China
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60
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Rey MD, Castillejo MÁ, Sánchez-Lucas R, Guerrero-Sanchez VM, López-Hidalgo C, Romero-Rodríguez C, Valero-Galván J, Sghaier-Hammami B, Simova-Stoilova L, Echevarría-Zomeño S, Jorge I, Gómez-Gálvez I, Papa ME, Carvalho K, Rodríguez de Francisco LE, Maldonado-Alconada AM, Valledor L, Jorrín-Novo JV. Proteomics, Holm Oak ( Quercus ilex L.) and Other Recalcitrant and Orphan Forest Tree Species: How do They See Each Other? Int J Mol Sci 2019; 20:ijms20030692. [PMID: 30736277 PMCID: PMC6386906 DOI: 10.3390/ijms20030692] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 01/28/2019] [Accepted: 01/30/2019] [Indexed: 02/07/2023] Open
Abstract
Proteomics has had a big impact on plant biology, considered as a valuable tool for several forest species, such as Quercus, Pines, Poplars, and Eucalyptus. This review assesses the potential and limitations of the proteomics approaches and is focused on Quercus ilex as a model species and other forest tree species. Proteomics has been used with Q. ilex since 2003 with the main aim of examining natural variability, developmental processes, and responses to biotic and abiotic stresses as in other species of the genus Quercus or Pinus. As with the progress in techniques in proteomics in other plant species, the research in Q. ilex moved from 2-DE based strategy to the latest gel-free shotgun workflows. Experimental design, protein extraction, mass spectrometric analysis, confidence levels of qualitative and quantitative proteomics data, and their interpretation are a true challenge with relation to forest tree species due to their extreme orphan and recalcitrant (non-orthodox) nature. Implementing a systems biology approach, it is time to validate proteomics data using complementary techniques and integrate it with the -omics and classical approaches. The full potential of the protein field in plant research is quite far from being entirely exploited. However, despite the methodological limitations present in proteomics, there is no doubt that this discipline has contributed to deeper knowledge of plant biology and, currently, is increasingly employed for translational purposes.
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Affiliation(s)
- María-Dolores Rey
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - María Ángeles Castillejo
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Rosa Sánchez-Lucas
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Victor M Guerrero-Sanchez
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Cristina López-Hidalgo
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Cristina Romero-Rodríguez
- Departamento de Fitoquímica, Dirección de Investigación de la Facultad de Ciencias Químicas de la Universidad Nacional de Asunción, Asunción 1001-1925, Paraguay.
| | - José Valero-Galván
- Department of Chemical and Biological Science, Biomedicine Science Institute, Autonomous University of Ciudad Juárez, Anillo Envolvente del Pronaf y Estocolmo s/n, Ciudad Juarez 32310, Mexico.
| | - Besma Sghaier-Hammami
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Lyudmila Simova-Stoilova
- Plant Molecular Biology Department, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl 21, 1113 Sofia, Bulgaria.
| | - Sira Echevarría-Zomeño
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Inmaculada Jorge
- Department of Vascular Biology and Inflammation (BVI), Spanish National Centre for Cardiovascular Research, Melchor Fernández Almagro 3, 28029 Madrid, Spain.
| | - Isabel Gómez-Gálvez
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - María Eugenia Papa
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Kamilla Carvalho
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | | | - Ana María Maldonado-Alconada
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
| | - Luis Valledor
- Department of Organisms and Systems Biology and University Institute of Biotechnology (IUBA), University of Oviedo, Santiago Gascón Building, 2nd Floor (Office 2.9), 33006 Oviedo, Spain.
| | - Jesús V Jorrín-Novo
- Department of Biochemistry and Molecular Biology, Agrifood Campus of International Excellence, University of Cordoba, Carretera Nacional IV, km 396, 14014 Córdoba, Spain.
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Recent Advances in MS-Based Plant Proteomics: Proteomics Data Validation Through Integration with Other Classic and -Omics Approaches. PROGRESS IN BOTANY 2019. [DOI: 10.1007/124_2019_32] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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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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