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Jayakodi M, Golicz AA, Kreplak J, Fechete LI, Angra D, Bednář P, Bornhofen E, Zhang H, Boussageon R, Kaur S, Cheung K, Čížková J, Gundlach H, Hallab A, Imbert B, Keeble-Gagnère G, Koblížková A, Kobrlová L, Krejčí P, Mouritzen TW, Neumann P, Nadzieja M, Nielsen LK, Novák P, Orabi J, Padmarasu S, Robertson-Shersby-Harvie T, Robledillo LÁ, Schiemann A, Tanskanen J, Törönen P, Warsame AO, Wittenberg AHJ, Himmelbach A, Aubert G, Courty PE, Doležel J, Holm LU, Janss LL, Khazaei H, Macas J, Mascher M, Smýkal P, Snowdon RJ, Stein N, Stoddard FL, Stougaard J, Tayeh N, Torres AM, Usadel B, Schubert I, O'Sullivan DM, Schulman AH, Andersen SU. The giant diploid faba genome unlocks variation in a global protein crop. Nature 2023; 615:652-659. [PMID: 36890232 PMCID: PMC10033403 DOI: 10.1038/s41586-023-05791-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/03/2023] [Indexed: 03/10/2023]
Abstract
Increasing the proportion of locally produced plant protein in currently meat-rich diets could substantially reduce greenhouse gas emissions and loss of biodiversity1. However, plant protein production is hampered by the lack of a cool-season legume equivalent to soybean in agronomic value2. Faba bean (Vicia faba L.) has a high yield potential and is well suited for cultivation in temperate regions, but genomic resources are scarce. Here, we report a high-quality chromosome-scale assembly of the faba bean genome and show that it has expanded to a massive 13 Gb in size through an imbalance between the rates of amplification and elimination of retrotransposons and satellite repeats. Genes and recombination events are evenly dispersed across chromosomes and the gene space is remarkably compact considering the genome size, although with substantial copy number variation driven by tandem duplication. Demonstrating practical application of the genome sequence, we develop a targeted genotyping assay and use high-resolution genome-wide association analysis to dissect the genetic basis of seed size and hilum colour. The resources presented constitute a genomics-based breeding platform for faba bean, enabling breeders and geneticists to accelerate the improvement of sustainable protein production across the Mediterranean, subtropical and northern temperate agroecological zones.
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Affiliation(s)
- Murukarthick Jayakodi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Agnieszka A Golicz
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Jonathan Kreplak
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Lavinia I Fechete
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Deepti Angra
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Petr Bednář
- Department of Analytical Chemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Elesandro Bornhofen
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus C, Denmark
| | - Hailin Zhang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Raphaël Boussageon
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Kwok Cheung
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Heidrun Gundlach
- Plant Genome and Systems Biology (PGSB), Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
| | - Asis Hallab
- IBG-4 Bioinformatics Forschungszentrum Jülich, Jülich, Germany
- Bingen Technical University of Applied Sciences, Bingen, Germany
| | - Baptiste Imbert
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | | | - Andrea Koblížková
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Lucie Kobrlová
- Department of Botany, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Petra Krejčí
- Department of Analytical Chemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Troels W Mouritzen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Pavel Neumann
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Marcin Nadzieja
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | | | - Petr Novák
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | | | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | - Laura Ávila Robledillo
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | | | | | - Petri Törönen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ahmed O Warsame
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | | | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Grégoire Aubert
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Emmanuel Courty
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Liisa U Holm
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Luc L Janss
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus C, Denmark
| | - Hamid Khazaei
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | - Jiří Macas
- Biology Centre, Czech Academy of Sciences, Institute of Plant Molecular Biology, České Budějovice, Czech Republic
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Petr Smýkal
- Department of Botany, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
- Center of Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Frederick L Stoddard
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland, Córdoba, Spain
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Nadim Tayeh
- Agroécologie, INRAE, Institut Agro, University Bourgogne, University Bourgogne Franche-Comté, Dijon, France
| | - Ana M Torres
- Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA), Área de Mejora y Biotecnología, Centro Alameda del Obispo, Córdoba, Spain
| | - Björn Usadel
- IBG-4 Bioinformatics Forschungszentrum Jülich, Jülich, Germany
- Institute for Biological Data Science, CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ingo Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | | | - Alan H Schulman
- Natural Resources Institute Finland (Luke), Helsinki, Finland.
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
- Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland, Córdoba, Spain.
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Hafner A, Mackenzie S. Re-analysis of publicly available methylomes using signal detection yields new information. Sci Rep 2023; 13:3307. [PMID: 36849495 PMCID: PMC9971211 DOI: 10.1038/s41598-023-30422-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/22/2023] [Indexed: 03/01/2023] Open
Abstract
Cytosine methylation is an epigenetic mark that participates in regulation of gene expression and chromatin stability in plants. Advancements in whole genome sequencing technologies have enabled investigation of methylome dynamics under different conditions. However, the computational methods for analyzing bisulfite sequence data have not been unified. Contention remains in the correlation of differentially methylated positions with the investigated treatment and exclusion of noise, inherent to these stochastic datasets. The prevalent approaches apply Fisher's exact test, logistic, or beta regression, followed by an arbitrary cut-off for differences in methylation levels. A different strategy, the MethylIT pipeline, utilizes signal detection to determine cut-off based on a fitted generalized gamma probability distribution of methylation divergence. Re-analysis of publicly available BS-seq data from two epigenetic studies in Arabidopsis and applying MethylIT revealed additional, previously unreported results. Methylome repatterning in response to phosphate starvation was confirmed to be tissue-specific and included phosphate assimilation genes in addition to sulfate metabolism genes not implicated in the original study. During seed germination plants undergo major methylome reprogramming and use of MethylIT allowed us to identify stage-specific gene networks. We surmise from these comparative studies that robust methylome experiments must account for data stochasticity to achieve meaningful functional analyses.
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Affiliation(s)
- Alenka Hafner
- grid.29857.310000 0001 2097 4281Department of Biology, The Pennsylvania State University, 362 Frear N Bldg, University Park, PA 16802 USA ,grid.29857.310000 0001 2097 4281Intercollege Graduate Degree Program in Plant Biology, The Pennsylvania State University, University Park, PA USA
| | - Sally Mackenzie
- Department of Biology, The Pennsylvania State University, 362 Frear N Bldg, University Park, PA, 16802, USA. .,Department of Plant Science, The Pennsylvania State University, University Park, PA, USA.
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53
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Zhong V, Archibald BN, Brophy JAN. Transcriptional and post-transcriptional controls for tuning gene expression in plants. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102315. [PMID: 36462457 DOI: 10.1016/j.pbi.2022.102315] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 10/22/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
Plant biotechnologists seek to modify plants through genetic reprogramming, but our ability to precisely control gene expression in plants is still limited. Here, we review transcription and translation in the model plants Arabidopsis thaliana and Nicotiana benthamiana with an eye toward control points that may be used to predictably modify gene expression. We highlight differences in gene expression requirements between these plants and other species, and discuss the ways in which our understanding of gene expression has been used to engineer plants. This review is intended to serve as a resource for plant scientists looking to achieve precise control over gene expression.
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Affiliation(s)
- Vivian Zhong
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Bella N Archibald
- Department of Bioengineering, Stanford University, Stanford, CA, USA
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Lee J, Shin SY, Lee SK, Park K, Gill H, Hyun Y, Jeong C, Jeon JS, Shin C, Choi Y. Contribution of RdDM to the ecotype-specific differential methylation on conserved as well as highly variable regions between Arabidopsis ecotypes. BMC Genomics 2023; 24:36. [PMID: 36658480 PMCID: PMC9854041 DOI: 10.1186/s12864-023-09128-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 01/11/2023] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Several studies showed genome-wide DNA methylation during Arabidopsis embryogenesis and germination. Although it has been known that the change of DNA methylation mainly occurs at CHH context mediated by small RNA-directed DNA methylation pathway during seed ripening and germination, the causality of the methylation difference exhibited in natural Arabidopsis ecotypes has not been thoroughly studied. RESULTS In this study we compared DNA methylation difference using comparative pairwise multi-omics dynamics in Columbia-0 (Col) and Cape Verde Island (Cvi) ecotypes. Arabidopsis genome was divided into two regions, common regions in both ecotypes and Col-specific regions, depending on the reads mapping of whole genome bisulfite sequencing libraries from both ecotypes. Ecotype comparison was conducted within common regions and the levels of DNA methylation on common regions and Col-specific regions were also compared. we confirmed transcriptome were relatively dynamic in stage-wise whereas the DNA methylome and small RNAome were more ecotype-dependent. While the global CG methylation remains steady during maturation and germination, we found genic CG methylation differs the most between the two accessions. We also found that ecotype-specific differentially methylated regions (eDMR) are positively correlated with ecotype-specifically expressed 24-nt small RNA clusters. In addition, we discovered that Col-specific regions enriched with transposable elements (TEs) and structural variants that tend to become hypermethylated, and TEs in Col-specific regions were longer in size, more pericentromeric, and more hypermethylated than those in the common regions. Through the analysis of RdDM machinery mutants, we confirmed methylation on Col-specific region as well as on eDMRs in common region are contributed by RdDM pathway. Lastly, we demonstrated that highly variable sequences between ecotypes (HOT regions) were also affected by RdDM-mediated regulation. CONCLUSIONS Through ecotype comparison, we revealed differences and similarities of their transcriptome, methylome and small RNAome both in global and local regions. We validated the contribution of RdDM causing differential methylation of common regions. Hypermethylated ecotype-specific regions contributed by RNA-directed DNA methylation pathway largely depend on the presence of TEs and copy-gain structural variations. These ecotype-specific regions are frequently associated with HOT regions, providing evolutionary insights into the epigenome dynamics within a species.
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Affiliation(s)
- Jaehoon Lee
- grid.31501.360000 0004 0470 5905Department of Biological Sciences, Seoul National University, Seoul, 08826 South Korea ,grid.31501.360000 0004 0470 5905Research Center for Plant Plasticity, Seoul National University, Seoul, 08826 Republic of Korea
| | - Sang-Yoon Shin
- grid.31501.360000 0004 0470 5905Research Center for Plant Plasticity, Seoul National University, Seoul, 08826 Republic of Korea ,grid.31501.360000 0004 0470 5905Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826 Republic of Korea
| | - Sang-Kyu Lee
- grid.289247.20000 0001 2171 7818Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea ,grid.256681.e0000 0001 0661 1492Current address: Division of Life Science, Gyeongsang National University, Jinju, 52828 South Korea
| | - Kyunghyuk Park
- grid.31501.360000 0004 0470 5905Department of Biological Sciences, Seoul National University, Seoul, 08826 South Korea
| | - Haechan Gill
- grid.31501.360000 0004 0470 5905Department of Biological Sciences, Seoul National University, Seoul, 08826 South Korea
| | - Youbong Hyun
- grid.31501.360000 0004 0470 5905Department of Biological Sciences, Seoul National University, Seoul, 08826 South Korea ,grid.31501.360000 0004 0470 5905Research Center for Plant Plasticity, Seoul National University, Seoul, 08826 Republic of Korea
| | - Choongwon Jeong
- grid.31501.360000 0004 0470 5905Department of Biological Sciences, Seoul National University, Seoul, 08826 South Korea
| | - Jong-Seong Jeon
- grid.289247.20000 0001 2171 7818Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Chanseok Shin
- grid.31501.360000 0004 0470 5905Research Center for Plant Plasticity, Seoul National University, Seoul, 08826 Republic of Korea ,grid.31501.360000 0004 0470 5905Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, 08826 Republic of Korea ,grid.31501.360000 0004 0470 5905Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea ,grid.31501.360000 0004 0470 5905Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 Republic of Korea ,grid.31501.360000 0004 0470 5905Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 South Korea
| | - Yeonhee Choi
- grid.31501.360000 0004 0470 5905Department of Biological Sciences, Seoul National University, Seoul, 08826 South Korea ,grid.31501.360000 0004 0470 5905Research Center for Plant Plasticity, Seoul National University, Seoul, 08826 Republic of Korea
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Gupta K, Garg R. Unravelling Differential DNA Methylation Patterns in Genotype Dependent Manner under Salinity Stress Response in Chickpea. Int J Mol Sci 2023; 24:ijms24031863. [PMID: 36768187 PMCID: PMC9915442 DOI: 10.3390/ijms24031863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 01/19/2023] Open
Abstract
DNA methylation is one of the epigenetic mechanisms that govern gene regulation in response to abiotic stress in plants. Here, we analyzed the role of epigenetic variations by exploring global DNA methylation and integrating it with differential gene expression in response to salinity stress in tolerant and sensitive chickpea genotypes. Genome-wide DNA methylation profiles showed higher CG methylation in the gene body regions and higher CHH methylation in the TE body regions. The analysis of differentially methylated regions (DMRs) suggested more hyper-methylation in response to stress in the tolerant genotype compared to the sensitive genotype. We observed higher enrichment of CG DMRs in genes and CHH DMRs in transposable elements (TEs). A positive correlation of gene expression with CG gene body methylation was observed. The enrichment analysis of DMR-associated differentially expressed genes revealed they are involved in biological processes, such as lateral root development, transmembrane transporter activity, GTPase activity, and regulation of gene expression. Further, a high correlation of CG methylation with CHG and CHH methylation under salinity stress was revealed, suggesting crosstalk among the methylation contexts. Further, we observed small RNA-mediated CHH hypermethylation in TEs. Overall, the interplay between DNA methylation, small RNAs, and gene expression provides new insights into the regulatory mechanism underlying salinity stress response in chickpeas.
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56
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Hao Y, Su X, Li W, Li L, Zhang Y, Mumtaz MA, Shu H, Cheng S, Zhu G, Wang Z. The creation of autotetraploid provides insights into critical features of DNA methylome changes after genome doubling in water spinach ( Ipomoea aquatica Forsk). FRONTIERS IN PLANT SCIENCE 2023; 14:1155531. [PMID: 37123819 PMCID: PMC10140364 DOI: 10.3389/fpls.2023.1155531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Water spinach (Ipomoea aquatica Forsk) is an essential green leafy vegetable in Asia. In this study, we induced autotetraploid water spinach by colchicine. Furthermore, DNA methylation and transcriptome of tetraploid and diploid were compared using Whole Genome Bisulfite Sequencing (WGBS) and RNA-sequencing techniques. Autotetraploid water spinach was created for the first time. Compared with the diploid parent, autotetraploid water spinach had wider leaves, thicker petioles and stems, thicker and shorter adventitious roots, longer stomas, and larger parenchyma cells. The whole genome methylation level of the autotetraploid was slightly higher than that of the diploid. Compared with the diploid, 12281 Differentially Methylated Regions (DMRs)were found in the autotetraploid, including 2356 hypermethylated and 1310 hypomethylated genes, mainly enriched in 'Arginine and Proline metabolism', 'beta - Alanine metabolism', 'Plant homone signal translation', 'Ribome', and 'Plant - pathgen interaction' pathways. Correlation analysis of transcriptome and DNA methylation data showed that 121 differentially expressed genes undergone differential methylation, related to four pathways 'Other types of O-glycan biosynthesis', 'Terpenoid backbone biosynthesis', 'Biosynthesis of secondary metabolites', and 'Metabolic paths'. This work obtained important autotetraploid resources of water spinach and revealed the genomic DNA methylation changes after genome doubling, being helpful for further studying the molecular mechanism of variations caused by polyploids of the Ipomoea genus.
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Affiliation(s)
- Yuanyuan Hao
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Xiao Su
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Wen Li
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Lin Li
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Yu Zhang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Muhammad Ali Mumtaz
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Huangying Shu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Shanhan Cheng
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Guopeng Zhu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
| | - Zhiwei Wang
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Sanya Nanfan Research Institute, Hainan University, Sanya, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Horticulture, Hainan University, Haikou, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
- *Correspondence: Zhiwei Wang,
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Van Antro M, Prelovsek S, Ivanovic S, Gawehns F, Wagemaker NCAM, Mysara M, Horemans N, Vergeer P, Verhoeven KJF. DNA methylation in clonal duckweed (Lemna minor L.) lineages reflects current and historical environmental exposures. Mol Ecol 2023; 32:428-443. [PMID: 36324253 PMCID: PMC10100429 DOI: 10.1111/mec.16757] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 09/16/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
Abstract
Environmentally induced DNA methylation variants may mediate gene expression responses to environmental changes. If such induced variants are transgenerationally stable, there is potential for expression responses to persist over multiple generations. Our current knowledge in plants, however, is almost exclusively based on studies conducted in sexually reproducing species where the majority of DNA methylation changes are subject to resetting in germlines, limiting the potential for transgenerational epigenetics stress memory. Asexual reproduction circumvents germlines, and may therefore be more conducive to long-term inheritance of epigenetic marks. Taking advantage of the rapid clonal reproduction of the common duckweed Lemna minor, we hypothesize that long-term, transgenerational stress memory from exposure to high temperature can be detected in DNA methylation profiles. Using a reduced representation bisulphite sequencing approach (epiGBS), we show that temperature stress induces DNA hypermethylation at many CG and CHG cytosine contexts but not CHH. Additionally, differential methylation in CHG context that was observed was still detected in a subset of cytosines, even after 3-12 generations of culturing in a common environment. This demonstrates a memory effect of stress reflected in the methylome and that persists over multiple clonal generations. Structural annotation revealed that this memory effect in CHG methylation was enriched in transposable elements. The observed epigenetic stress memory is probably caused by stable transgenerational persistence of temperature-induced DNA methylation variants across clonal generations. To the extent that such epigenetic memory has functional consequences for gene expression and phenotypes, this result suggests potential for long-term modulation of stress responses in asexual plants.
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Affiliation(s)
- Morgane Van Antro
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Stella Prelovsek
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Slavica Ivanovic
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Fleur Gawehns
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | | | - Mohamed Mysara
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Nele Horemans
- Biosphere Impact Studies, Belgian Nuclear Research Centre (SCK CEN), Mol, Belgium
| | - Philippine Vergeer
- Plant Ecology and Physiology, Radboud University, Nijmegen, The Netherlands.,Wageningen University and Research (WUR), Plant Ecology and Nature Conservation Group, Wageningen, The Netherlands
| | - Koen J F Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
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58
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Cao Q, Huang L, Li J, Qu P, Tao P, Crabbe MJC, Zhang T, Qiao Q. Integrated transcriptome and methylome analyses reveal the molecular regulation of drought stress in wild strawberry (Fragaria nilgerrensis). BMC PLANT BIOLOGY 2022; 22:613. [PMID: 36575384 PMCID: PMC9795625 DOI: 10.1186/s12870-022-04006-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Fragaria nilgerrensis, which is a diploid wild strawberry with excellent drought-resistance, would provide useful candidate genes for improving drought resistance of cultivated strawberry. So far, its molecular regulatory networks involved in drought stress are unclear. We therefore investigated the drought response regulatory networks of F. nilgerrensis based on the integrated analysis of DNA methylation, transcriptome and physiological traits during four time points under drought stress. RESULTS: The most differentially expressed genes and the physiological changes were found at 8 days (T8) compared with 0 day (T0, control). Methylome analysis revealed slight dynamic changes in genome-wide mC levels under drought conditions, while the most hypomethylated and hypermethylated regions were identified at T4 and T8. Association analysis of the methylome and transcriptome revealed that unexpressed genes exhibited expected hypermethylation levels in mCHG and mCHH contexts, and highly expressed genes exhibited corresponding hypomethylation levels in the gene body, but mCG contexts showed the opposite trend. Then, 835 differentially methylated and expressed genes were identified and grouped into four clustering patterns to characterize their functions. The genes with either negative or positive correlation between methylation and gene expression were mainly associated with kinases, Reactive Oxygen Species (ROS) synthesis, scavenging, and the abscisic acid (ABA) signal pathway. Consistently, weighted gene co-expression network analysis (WGCNA) revealed Hub genes including NCED, CYP707A2, PP2Cs and others that play important roles in the ABA signaling pathway. CONCLUSION F. nilgerrensis drought is dominated by ABA-dependent pathways, possibly accompanied by ABA-independent crosstalk. DNA methylation may affect gene expression, but their correlation was more subtle and multiple types of association exist. Maintaining the balance between ROS regeneration and scavenging is an important factor in drought resistance in F. nilgerrensis. These results deepen our understanding of drought resistance and its application in breeding in strawberry plants.
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Affiliation(s)
- Qiang Cao
- School of Agriculture, Yunnan University, 650091, Kunming, China
| | - Lin Huang
- School of Agriculture, Yunnan University, 650091, Kunming, China
| | - Jiamin Li
- School of Agriculture, Yunnan University, 650091, Kunming, China
| | - Peng Qu
- School of Agriculture, Yunnan University, 650091, Kunming, China
| | - Pang Tao
- Horticultural Research Institute, Yunnan Academy of Agricultural Sciences, 650205, Kunming, China
| | - M James C Crabbe
- Wolfson College, Oxford University, Oxford, OX26UD, UK
- Institute of Biomedical and Environmental Science and Technology, School of Life Sciences, University of Bedfordshire, Park Square, LU1 3JU, Luton, UK
- School of Life Science, Shanxi University, 030006, Taiyuan, Shanxi, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, 650500, Kunming, China.
| | - Qin Qiao
- College of Horticulture and Landscape, Yunnan Agricultural University, 650201, Kunming, China.
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Liu N, Wu B, Pandey MK, Huang L, Luo H, Chen Y, Zhou X, Chen W, Huai D, Yu B, Chen H, Guo J, Lei Y, Liao B, Varshney RK, Jiang H. Gene expression and DNA methylation altering lead to the high oil content in wild allotetraploid peanut ( A. monticola). FRONTIERS IN PLANT SCIENCE 2022; 13:1065267. [PMID: 36589096 PMCID: PMC9802669 DOI: 10.3389/fpls.2022.1065267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION The wild allotetraploid peanut Arachis monticola contains a higher oil content than the cultivated allotetraploid Arachis hypogaea. Besides the fact that increasing oil content is the most important peanut breeding objective, a proper understanding of its molecular mechanism controlling oil accumulation is still lacking. METHODS We investigated this aspect by performing comparative transcriptomics from developing seeds between three wild and five cultivated peanut varieties. RESULTS The analyses not only showed species-specific grouping transcriptional profiles but also detected two gene clusters with divergent expression patterns between two species enriched in lipid metabolism. Further analysis revealed that expression alteration of lipid metabolic genes with co-expressed transcription factors in wild peanut led to enhanced activity of oil biogenesis and retarded the rate of lipid degradation. In addition, bisulfite sequencing was conducted to characterize the variation of DNA methylation between wild allotetraploid (245, WH 10025) and cultivated allotetraploid (Z16, Zhh 7720) genotypes. CG and CHG context methylation was found to antagonistically correlate with gene expression during seed development. Differentially methylated region analysis and transgenic assay further illustrated that variations of DNA methylation between wild and cultivated peanuts could affect the oil content via altering the expression of peroxisomal acyl transporter protein (Araip.H6S1B). DISCUSSION From the results, we deduced that DNA methylation may negatively regulate lipid metabolic genes and transcription factors to subtly affect oil accumulation divergence between wild and cultivated peanuts. Our work provided the first glimpse on the regulatory mechanism of gene expression altering for oil accumulation in wild peanut and gene resources for future breeding applications.
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Affiliation(s)
- Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Bei Wu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Manish K. Pandey
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuning Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Dongxin Huai
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Bolun Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Hao Chen
- Institute of Crop Sciences, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jianbin Guo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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Xiang R, Ahmad B, Liang C, Shi X, Yang L, Du G, Wang L. Systematic genome-wide and expression analysis of RNA-directed DNA methylation pathway genes in grapes predicts their involvement in multiple biological processes. FRONTIERS IN PLANT SCIENCE 2022; 13:1089392. [PMID: 36570893 PMCID: PMC9780290 DOI: 10.3389/fpls.2022.1089392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
RNA-directed DNA methylation (RdDM) is an important epigenetic pathway in plants and mediates transcriptional silencing by siRNAs. Different gene families have role in the regulation of the RdDM pathway and there is a lack of information about these gene families in the grapes (Vitis vinifera L.). Here, we mentioned the genome-wide identification, bioinformatics analysis, evolutionary history, and expression profiling of VvRdDM pathway genes against various stresses, hormonal treatments as well as in different organs. Sixty VvRdDM genes belonging to fourteen different families were identified. All the genes were unevenly distributed and chromosome 4 contained the highest number of genes (7). Most of the genes showed similar exon-intron and motif distribution patterns within the same subfamilies. Out of 14 families, only members of 4 families underwent duplication events during the evolutionary process and 50% of members of the AGO family are the result of duplication events. Based on Ka/Ks ratio all duplicated gene pairs have a negative mode of selection. VvRdDM pathway genes showed differential spatiotemporal expression patterns against different hormone and stress treatments. Further, with multiple transcriptome analysis, some VvRdDM genes showed a broad spectrum of high expression in different organs at various stages, and VvRdDM genes also displayed different expression in seeded and seedless cultivars during different phases of seed development. This proposed that VvRdDM genes may play multiple roles in grape growth and development, especially in seed development. qRT-PCR analysis of selected genes further verified the critical roles of RdDM genes in multiple biological processes, especially in seed development/ovule abortion i.e., VvIDN2a, VvDRD1a, VvRDR1a, and VvRDR6. Our study provides detailed information about VvRdDM genes in perspective of gene structure and evolution, as well as expression pattern against different stress, hormones and in different plants parts. It provides new candidate gene resources for further functional characterization and molecular breeding of grapes.
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Affiliation(s)
- Rui Xiang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Bilal Ahmad
- College of Horticulture, Hebei Agricultural University, Baoding, China
- Department of Horticulture, Muhammad Nawaz Sharif (MNS)-University of Agriculture Multan, Multan, Pakistan
| | - Chen Liang
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xiaoxin Shi
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Lili Yang
- Shijiazhuang Fruit Research Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Guoqiang Du
- College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Li Wang
- College of Horticulture, Hebei Agricultural University, Baoding, China
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He L, Liang X, Wang Q, Yang C, Li Y, Liao L, Zhu Z, Wang Y. Genome-wide DNA methylation reveals potential epigenetic mechanism of age-dependent viral susceptibility in grass carp. Immun Ageing 2022; 19:28. [PMID: 35655223 PMCID: PMC9161582 DOI: 10.1186/s12979-022-00285-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/14/2022] [Indexed: 11/10/2022]
Abstract
Background Grass carp are an important farmed fish in China that are infected by many pathogens, especially grass carp reovirus (GCRV). Notably, grass carp showed age-dependent susceptibility to GCRV; that is, grass carp not older than one year were sensitive to GCRV, while those over three years old were resistant to this virus. However, the underlying mechanism remains unclear. Herein, whole genome-wide DNA methylation and gene expression variations between susceptible five-month-old (FMO) and resistant three-year-old (TYO) grass carp were investigated aiming to uncover potential epigenetic mechanisms. Results Colorimetric quantification revealed that the global methylation level in TYO fish was higher than that in FMO fish. Whole-genome bisulfite sequencing (WGBS) of the two groups revealed 6214 differentially methylated regions (DMRs) and 4052 differentially methylated genes (DMGs), with most DMRs and DMGs showing hypermethylation patterns in TYO fish. Correlation analysis revealed that DNA hypomethylation in promoter regions and DNA hypermethylation in gene body regions were associated with gene expression. Enrichment analysis revealed that promoter hypo-DMGs in TYO fish were significantly enriched in typical immune response pathways, whereas gene body hyper-DMGs in TYO fish were significantly enriched in terms related to RNA transcription, biosynthesis, and energy production. RNA-seq analysis of the corresponding samples indicated that most of the genes in the above terms were upregulated in TYO fish. Moreover, gene function analysis revealed that the two genes involved in energy metabolism displayed antiviral effects. Conclusions Collectively, these results revealed genome-wide variations in DNA methylation between grass carp of different ages. DNA methylation and gene expression variations in genes involved in immune response, biosynthesis, and energy production may contribute to age-dependent susceptibility to GCRV in grass carp. Our results provide important information for disease-resistant breeding programs for grass carp and may also benefit research on age-dependent diseases in humans. Supplementary Information The online version contains supplementary material available at 10.1186/s12979-022-00285-w.
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Wang Q, Xiong F, Wu G, Liu W, Chen J, Wang B, Chen Y. Gene body methylation in cancer: molecular mechanisms and clinical applications. Clin Epigenetics 2022; 14:154. [PMID: 36443876 PMCID: PMC9706891 DOI: 10.1186/s13148-022-01382-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
DNA methylation is an important epigenetic mechanism that regulates gene expression. To date, most DNA methylation studies have focussed on CpG islands in the gene promoter region, and the mechanism of methylation and the regulation of gene expression after methylation have been clearly elucidated. However, genome-wide methylation studies have shown that DNA methylation is widespread not only in promoters but also in gene bodies. Gene body methylation is widely involved in the expression regulation of many genes and is closely related to the occurrence and progression of malignant tumours. This review focusses on the formation of gene body methylation patterns, its regulation of transcription, and its relationship with tumours, providing clues to explore the mechanism of gene body methylation in regulating gene transcription and its significance and application in the field of oncology.
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Affiliation(s)
- Qi Wang
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Fei Xiong
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Guanhua Wu
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Wenzheng Liu
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Junsheng Chen
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Bing Wang
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
| | - Yongjun Chen
- grid.33199.310000 0004 0368 7223Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430074 Hubei Province China
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Canton M, Forestan C, Marconi G, Carrera E, Bonghi C, Varotto S. Evidence of chromatin and transcriptional dynamics for cold development in peach flower bud. THE NEW PHYTOLOGIST 2022; 236:974-988. [PMID: 35860865 PMCID: PMC9804738 DOI: 10.1111/nph.18393] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
In temperate zones, fruit trees regulate their annual growth cycle to seasonal environmental changes. During the cold season, growth is limited by both environmental and genetic factors. After the exposure to low temperature and fulfillment of chilling requirements, mild temperatures promote the growth and flowering. However, an insufficient chilling exposure may lead to nonuniform blooming, with a negative impact on fruit set. To gain insights into flower development in the fruit tree buds, peach is an interesting model, the flower and vegetative bud being distinct organs. To understand how flower bud development is regulated, we integrated cytological observations and epigenetic and chromatin genome-wide data with transcriptional changes to identify the main regulatory factors involved in flower development during chilling accumulation. We demonstrated that growth cessation does not occur in peach flower buds during chilling accumulation, but that there are changes in transcript abundance of key genes of hormone metabolism and flower bud development, distribution of histone modifications (H3K4me3 and H3K27me3) and DNA methylation. Altogether, our findings indicate that during the cold season the flower bud is in a nondormant state and that the chilling experience allows flower differentiation to be completed.
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Affiliation(s)
- Monica Canton
- Department of Agronomy Food Natural Resources, Animals and Environment (DAFNAE) AgripolisUniversity of Padova35020LegnaroPDItaly
| | - Cristian Forestan
- Department of Agricultural and Food Sciences (DISTAL)University of Bologna40127BolognaBOItaly
| | - Gianpiero Marconi
- Department Agricultural, Food and Environmental SciencesUniversity of Perugia06121PerugiaItaly
| | - Esther Carrera
- Instituto de Biologıa Molecular y Celular de Plantas (IBMCP)Universidad Politecnica de Valencia‐Consejo Superior de Investigaciones Cientıficas (CSIC)ValenciaSpain
| | - Claudio Bonghi
- Department of Agronomy Food Natural Resources, Animals and Environment (DAFNAE) AgripolisUniversity of Padova35020LegnaroPDItaly
| | - Serena Varotto
- Department of Agronomy Food Natural Resources, Animals and Environment (DAFNAE) AgripolisUniversity of Padova35020LegnaroPDItaly
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Varotto S, Krugman T, Aiese Cigliano R, Kashkush K, Kondić-Špika A, Aravanopoulos FA, Pradillo M, Consiglio F, Aversano R, Pecinka A, Miladinović D. Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3987-4003. [PMID: 35678824 PMCID: PMC9729329 DOI: 10.1007/s00122-022-04122-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/04/2022] [Indexed: 05/05/2023]
Abstract
Crop wild relatives (CWRs) are recognized as the best potential source of traits for crop improvement. However, successful crop improvement using CWR relies on identifying variation in genes controlling desired traits in plant germplasms and subsequently incorporating them into cultivars. Epigenetic diversity may provide an additional layer of variation within CWR and can contribute novel epialleles for key traits for crop improvement. There is emerging evidence that epigenetic variants of functional and/or agronomic importance exist in CWR gene pools. This provides a rationale for the conservation of epigenotypes of interest, thus contributing to agrobiodiversity preservation through conservation and (epi)genetic monitoring. Concepts and techniques of classical and modern breeding should consider integrating recent progress in epigenetics, initially by identifying their association with phenotypic variations and then by assessing their heritability and stability in subsequent generations. New tools available for epigenomic analysis offer the opportunity to capture epigenetic variation and integrate it into advanced (epi)breeding programmes. Advances in -omics have provided new insights into the sources and inheritance of epigenetic variation and enabled the efficient introduction of epi-traits from CWR into crops using epigenetic molecular markers, such as epiQTLs.
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Affiliation(s)
- Serena Varotto
- Department of Agronomy Animal Food Natural Resources and Environment, University of Padova, Viale dell'Università, 16 35020, Legnaro, Italy.
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Abba Khoushy Ave 199, 3498838, Haifa, Israel
| | | | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beersheba, 84105, Israel
| | - Ankica Kondić-Špika
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000, Novi Sad, Serbia
| | - Fillipos A Aravanopoulos
- Faculty of Agriculture, Forest Science & Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, GR54006, Greece
| | - Monica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040, Madrid, Spain
| | - Federica Consiglio
- Institute of Biosciences and Bioresources, National Research Council (CNR), Via Università 133, 80055, Portici, Italy
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy
| | - Ales Pecinka
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Acad Sci, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000, Novi Sad, Serbia
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Xiao G, Zhou J, Huo Z, Wu T, Li Y, Li Y, Wang Y, Wang M. The Shift in Synonymous Codon Usage Reveals Similar Genomic Variation during Domestication of Asian and African Rice. Int J Mol Sci 2022; 23:12860. [PMID: 36361651 PMCID: PMC9656316 DOI: 10.3390/ijms232112860] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 10/29/2023] Open
Abstract
The domestication of wild rice occurred together with genomic variation, including the synonymous nucleotide substitutions that result in synonymous codon usage bias (SCUB). SCUB mirrors the evolutionary specialization of plants, but its characteristics during domestication were not yet addressed. Here, we found cytosine- and guanidine-ending (NNC and NNG) synonymous codons (SCs) were more pronounced than adenosine- and thymine-ending SCs (NNA and NNT) in both wild and cultivated species of Asian and African rice. The ratios of NNC/G to NNA/T codons gradually decreased following the rise in the number of introns, and the preference for NNA/T codons became more obvious in genes with more introns in cultivated rice when compared with those in wild rice. SCUB frequencies were heterogeneous across the exons, with a higher preference for NNA/T in internal exons than in terminal exons. The preference for NNA/T in internal but not terminal exons was more predominant in cultivated rice than in wild rice, with the difference between wild and cultivated rice becoming more remarkable with the rise in exon numbers. The difference in the ratios of codon combinations representing DNA methylation-mediated conversion from cytosine to thymine between wild and cultivated rice coincided with their difference in SCUB frequencies, suggesting that SCUB reveals the possible association between genetic and epigenetic variation during the domestication of rice. Similar patterns of SCUB shift in Asian and African rice indicate that genomic variation occurs in the same non-random manner. SCUB representing non-neutral synonymous mutations can provide insight into the mechanism of genomic variation in domestication and can be used for the genetic dissection of agricultural traits in rice and other crops.
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Affiliation(s)
- Guilian Xiao
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Junzhi Zhou
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Zhiheng Huo
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Tong Wu
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Yingchun Li
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Yajing Li
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
| | - Yanxia Wang
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang 050041, China
| | - Mengcheng Wang
- The Key Laboratory of Plant Development and Environment Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China
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Patitaki E, Schivre G, Zioutopoulou A, Perrella G, Bourbousse C, Barneche F, Kaiserli E. Light, chromatin, action: nuclear events regulating light signaling in Arabidopsis. THE NEW PHYTOLOGIST 2022; 236:333-349. [PMID: 35949052 PMCID: PMC9826491 DOI: 10.1111/nph.18424] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/26/2022] [Indexed: 05/31/2023]
Abstract
The plant nucleus provides a major hub for environmental signal integration at the chromatin level. Multiple light signaling pathways operate and exchange information by regulating a large repertoire of gene targets that shape plant responses to a changing environment. In addition to the established role of transcription factors in triggering photoregulated changes in gene expression, there are eminent reports on the significance of chromatin regulators and nuclear scaffold dynamics in promoting light-induced plant responses. Here, we report and discuss recent advances in chromatin-regulatory mechanisms modulating plant architecture and development in response to light, including the molecular and physiological roles of key modifications such as DNA, RNA and histone methylation, and/or acetylation. The significance of the formation of biomolecular condensates of key light signaling components is discussed and potential applications to agricultural practices overviewed.
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Affiliation(s)
- Eirini Patitaki
- School of Molecular Biosciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Geoffrey Schivre
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERMUniversité PSLParis75005France
- Université Paris‐SaclayOrsay91400France
| | - Anna Zioutopoulou
- School of Molecular Biosciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Giorgio Perrella
- Department of BiosciencesUniversity of MilanVia Giovanni Celoria, 2620133MilanItaly
| | - Clara Bourbousse
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERMUniversité PSLParis75005France
| | - Fredy Barneche
- Institut de Biologie de l'École Normale Supérieure (IBENS), École Normale Supérieure, CNRS, INSERMUniversité PSLParis75005France
| | - Eirini Kaiserli
- School of Molecular Biosciences, College of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
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Choudhary V, Shekhawat D, Choudhary A, Jaiswal V. Development of EST-based methylation specific PCR (MSP) markers in Crocus sativus. Mol Biol Rep 2022; 49:11695-11703. [PMID: 36181582 DOI: 10.1007/s11033-022-07967-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/21/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Saffron (Crocus sativus) is high valued spice crop, but due to its sterile nature, the crop is propagated exclusively through corms. Thus, the genetic base of this crop is very narrow, however, frequency of phenotypic variability is observed; and suggested the potential role of epigenetics in saffron crop growth and development. METHODS AND RESULTS To facilitate epigenetic studies in saffron, we developed 1525 methylation-specific PCR (MSP) markers using MethPrimer. For this purpose, we used 6767 EST sequences of saffron available on the NCBI database. We also mine CpG islands (2555) and found that 32.7% of EST sequences had CpG islands. Out of 1525 MSP markers developed during the present study, 725 covered the CpG islands and 800 were without CpG islands. PCR amplification was found successful for 82% of MSP markers. A preliminary analysis suggested that 53.7% of genomic sites were methylated and more prominent (60% methylations) in non-CpG island regions, although, more comprehensive studies are required to validate it further. CONCLUSIONS The epigenetic resource developed during the present study will strengthen the epigenetic studies like epiQTL mapping, epiGWAS to explore the molecular mechanisms and genomic/epigenomic regions associated with phenotype; and further may be utilized for saffron improvement programs through epibreeding.
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Affiliation(s)
- Vishek Choudhary
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Deepika Shekhawat
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Anita Choudhary
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Vandana Jaiswal
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India.
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Junaid A, Singh NK, Gaikwad K. Evolutionary fates of gene-body methylation and its divergent association with gene expression in pigeonpea. THE PLANT GENOME 2022; 15:e20207. [PMID: 35790083 DOI: 10.1002/tpg2.20207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/07/2021] [Indexed: 06/15/2023]
Abstract
Pigeonpea (Cajanus cajan L. Huth) is an agronomically important legume cultivated worldwide. In this study, we extensively analyzed gene-body methylation (GbM) patterns in pigeonpea. We found a bimodal distribution of CG and CHG methylation patterns. GbM features- slow evolution rate and increased length remained conserved. Genes with moderate CG body methylation showed highest expression where as highly-methylated genes showed lowest expression. Transposable element (TE)-related genes were methylated in multiple contexts and hence classified as C-methylated genes. A low expression among C-methylated genes was associated with transposons insertion in gene-body and upstream regulatory regions. The CG methylation patterns were found to be conserved in orthologs compared with non-CG methylation. By comparing methylation patterns between differentially methylated regions (DMRs) of the three genotypes, we found that variably methylated marks are less likely to target evolutionary conserved sequences. Finally, our analysis showed enrichment of nitrogen-related genes in GbM orthologs of legumes, which could be promising candidates for generating epialleles for crop improvement.
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Affiliation(s)
- Alim Junaid
- National Institute of Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Nagendra Kumar Singh
- National Institute of Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Kishor Gaikwad
- National Institute of Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
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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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70
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Ma W, Cui S, Lu Z, Yan X, Cai L, Lu Y, Cai K, Zhou H, Ma R, Zhou S, Wang X. YTH Domain Proteins Play an Essential Role in Rice Growth and Stress Response. PLANTS 2022; 11:plants11172206. [PMID: 36079588 PMCID: PMC9460353 DOI: 10.3390/plants11172206] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022]
Abstract
As the most prevalent epi-transcriptional modification, m6A modifications play essential roles in regulating RNA fate. The molecular functions of YTH521-B homology (YTH) domain proteins, the most known READER proteins of m6A modifications, have been well-studied in animals. Although plants contain more YTH domain proteins than other eukaryotes, little is known about their biological importance. In dicot species Arabidopsis thaliana, the YTHDFA clade members ECT2/3/4 and CPSF30-L are well-studied and important for cell proliferation, plant organogenesis, and nitrate transport. More emphasis is needed on the biological functions of plant YTH proteins, especially monocot YTHs. Here we presented a detailed phylogenetic relationship of eukaryotic YTH proteins and clustered plant YTHDFC clade into three subclades. To determine the importance of monocot YTH proteins, YTH knockout mutants and RNAi-induced knockdown plants were constructed and used for phenotyping, transcriptomic analysis, and stress treatments. Knocking out or knocking down OsYTHs led to the downregulation of multicellular organismal regulation genes and resulted in growth defects. In addition, loss-of-function ythdfa mutants led to better salinity tolerance whereas ythdfc mutants were more sensitive to abiotic stress. Overall, our study establishes the functional relevance of rice YTH genes in plant growth regulation and stress response.
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Affiliation(s)
- Weiwei Ma
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Song Cui
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhenfei Lu
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Xiaofeng Yan
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Long Cai
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Yongfa Lu
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Kefeng Cai
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Huacheng Zhou
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Rongrong Ma
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
| | - Shirong Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (S.Z.); (X.W.)
| | - Xiaole Wang
- Institute of Crop Sciences, Ningbo Academy of Agricultural Sciences, Ningbo 315000, China
- Correspondence: (S.Z.); (X.W.)
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71
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Bennett M, Piya S, Baum TJ, Hewezi T. miR778 mediates gene expression, histone modification, and DNA methylation during cyst nematode parasitism. PLANT PHYSIOLOGY 2022; 189:2432-2453. [PMID: 35579365 PMCID: PMC9342967 DOI: 10.1093/plphys/kiac228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/27/2022] [Indexed: 05/20/2023]
Abstract
Despite the known critical regulatory functions of microRNAs, histone modifications, and DNA methylation in reprograming plant epigenomes in response to pathogen infection, the molecular mechanisms underlying the tight coordination of these components remain poorly understood. Here, we show how Arabidopsis (Arabidopsis thaliana) miR778 coordinately modulates the root transcriptome, histone methylation, and DNA methylation via post-transcriptional regulation of the H3K9 methyltransferases SU(var)3-9 homolog 5 (SUVH5) and SUVH6 upon infection by the beet cyst nematode Heterodera schachtii. miR778 post-transcriptionally silences SUVH5 and SUVH6 upon nematode infection. Manipulation of the expression of miR778 and its two target genes significantly altered plant susceptibility to H. schachtii. RNA-seq analysis revealed a key role of SUVH5 and SUVH6 in reprograming the transcriptome of Arabidopsis roots upon H. schachtii infection. In addition, chromatin immunoprecipitation (ChIP)-seq analysis established SUVH5 and SUVH6 as the main enzymes mediating H3K9me2 deposition in Arabidopsis roots in response to nematode infection. ChIP-seq analysis also showed that these methyltransferases possess distinct DNA binding preferences in that they are targeting transposable elements under noninfected conditions and protein-coding genes in infected plants. Further analyses indicated that H3K9me2 deposition directed by SUVH5 and SUVH6 contributes to gene expression changes both in roots and in nematode feeding sites and preferentially associates with CG DNA methylation. Together, our results uncovered multi-layered epigenetic regulatory mechanisms coordinated by miR778 during Arabidopsis-H. schachtii interactions.
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Affiliation(s)
- Morgan Bennett
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
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72
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Immune priming in plants: from the onset to transgenerational maintenance. Essays Biochem 2022; 66:635-646. [PMID: 35822618 PMCID: PMC9528079 DOI: 10.1042/ebc20210082] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/17/2022] [Accepted: 06/27/2022] [Indexed: 12/24/2022]
Abstract
Enhancing plant resistance against pests and diseases by priming plant immunity is an attractive concept for crop protection because it provides long-lasting broad-spectrum protection against pests and diseases. This review provides a selected overview of the latest advances in research on the molecular, biochemical and epigenetic drivers of plant immune priming. We review recent findings about the perception and signalling mechanisms controlling the onset of priming by the plant stress metabolite β-aminobutyric acid. In addition, we review the evidence for epigenetic regulation of long-term maintenance of priming and discuss how stress-induced reductions in DNA hypomethylation at transposable elements can prime defence genes. Finally, we examine how priming can be exploited in crop protection and articulate the opportunities and challenges of translating research results from the Arabidopsis model system to crops.
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73
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Villagómez-Aranda AL, Feregrino-Pérez AA, García-Ortega LF, González-Chavira MM, Torres-Pacheco I, Guevara-González RG. Activating stress memory: eustressors as potential tools for plant breeding. PLANT CELL REPORTS 2022; 41:1481-1498. [PMID: 35305133 PMCID: PMC8933762 DOI: 10.1007/s00299-022-02858-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/26/2022] [Indexed: 05/08/2023]
Abstract
Plants are continuously exposed to stress conditions, such that they have developed sophisticated and elegant survival strategies, which are reflected in their phenotypic plasticity, priming capacity, and memory acquisition. Epigenetic mechanisms play a critical role in modulating gene expression and stress responses, allowing malleability, reversibility, stability, and heritability of favourable phenotypes to enhance plant performance. Considering the urgency to improve our agricultural system because of going impacting climate change, potential and sustainable strategies rely on the controlled use of eustressors, enhancing desired characteristics and yield and shaping stress tolerance in crops. However, for plant breeding purposes is necessary to focus on the use of eustressors capable of establishing stable epigenetic marks to generate a transgenerational memory to stimulate a priming state in plants to face the changing environment.
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Affiliation(s)
- A L Villagómez-Aranda
- Biosystems Engineering Group. Engineering Faculty, Amazcala Campus, Autonomous University of Querétaro, Highway Chichimequillas s/n Km 1, Amazcala, El Marques, Querétaro, Mexico
| | - A A Feregrino-Pérez
- Biosystems Engineering Group. Engineering Faculty, Amazcala Campus, Autonomous University of Querétaro, Highway Chichimequillas s/n Km 1, Amazcala, El Marques, Querétaro, Mexico
| | - L F García-Ortega
- Laboratory of Learning and Research in Biological Computing, Centre for Research and Advanced Studies, National Polytechnic Institute (CINVESTAV), Irapuato, Guanajuato, Mexico
| | - M M González-Chavira
- Molecular Markers Laboratory, Bajío Experimental Field, National Institute for Forestry, Agriculture and Livestock Research (INIFAP), Celaya-San Miguel de Allende, Celaya, Guanajuato, Mexico
| | - I Torres-Pacheco
- Biosystems Engineering Group. Engineering Faculty, Amazcala Campus, Autonomous University of Querétaro, Highway Chichimequillas s/n Km 1, Amazcala, El Marques, Querétaro, Mexico
| | - R G Guevara-González
- Biosystems Engineering Group. Engineering Faculty, Amazcala Campus, Autonomous University of Querétaro, Highway Chichimequillas s/n Km 1, Amazcala, El Marques, Querétaro, Mexico.
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Sarkies P. Encyclopaedia of eukaryotic DNA methylation: from patterns to mechanisms and functions. Biochem Soc Trans 2022; 50:1179-1190. [PMID: 35521905 PMCID: PMC9246332 DOI: 10.1042/bst20210725] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 12/14/2022]
Abstract
DNA methylation is an epigenetic modification with a very long evolutionary history. However, DNA methylation evolves surprisingly rapidly across eukaryotes. The genome-wide distribution of methylation diversifies rapidly in different lineages, and DNA methylation is lost altogether surprisingly frequently. The growing availability of genomic and epigenomic sequencing across organisms highlights this diversity but also illuminates potential factors that could explain why both the DNA methylation machinery and its genome-wide distribution evolve so rapidly. Key to this are new discoveries about the fitness costs associated with DNA methylation, and new theories about how the fundamental biochemical mechanisms of DNA methylation introduction and maintenance could explain how new genome-wide patterns of methylation evolve.
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Affiliation(s)
- Peter Sarkies
- Department of Biochemistry, University of Oxford, Oxford, U.K
- MRC London Institute of Molecular Biology, London, U.K
- Institute of Clinical Sciences, Imperial College London, London, U.K
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75
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Verma P, Singh A, Purru S, Bhat KV, Lakhanpaul S. Comparative DNA Methylome of Phytoplasma Associated Retrograde Metamorphosis in Sesame (Sesamum indicum L.). BIOLOGY 2022; 11:biology11070954. [PMID: 36101335 PMCID: PMC9311523 DOI: 10.3390/biology11070954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022]
Abstract
Phytoplasma-associated diseases such as phyllody and little leaf are critical threats to sesame cultivation worldwide. The mechanism of the dramatic conversion of flowers to leafy structures leading to yield losses and the drastic reduction in leaf size due to Phytoplasma infection remains yet to be identified. Cytosine methylation profiles of healthy and infected sesame plants studied using Whole Genome Bisulfite Sequencing (WGBS) and Quantitative analysis of DNA methylation with the real-time PCR (qAMP) technique revealed altered DNA methylation patterns upon infection. Phyllody was associated with global cytosine hypomethylation, though predominantly in the CHH (where H = A, T or C) context. Interestingly, comparable cytosine methylation levels were observed between healthy and little leaf-affected plant samples in CG, CHG and CHH contexts. Among the different genomic fractions, the highest number of differentially methylated Cytosines was found in the intergenic regions, followed by promoter, exonic and intronic regions in decreasing order. Further, most of the differentially methylated genes were hypomethylated and were mainly associated with development and defense-related processes. Loci for STOREKEEPER protein-like, a DNA-binding protein and PP2-B15, an F-Box protein, responsible for plugging sieve plates to maintain turgor pressure within the sieve tubes were found to be hypomethylated by WGBS, which was confirmed by methylation-dependent restriction digestion and qPCR. Likewise, serine/threonine-protein phosphatase-7 homolog, a positive regulator of cryptochrome signaling involved in hypocotyl and cotyledon growth and probable O-methyltransferase 3 locus were determined to be hypermethylated. Phytoplasma infection-associated global differential methylation as well as the defense and development-related loci reported here for the first time significantly elucidate the mechanism of phytoplasma-associated disease development.
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Affiliation(s)
- Pratima Verma
- Department of Botany, University of Delhi, New Delhi 110007, India;
| | - Amrita Singh
- Department of Botany, Gargi College, University of Delhi, New Delhi 110049, India;
| | - Supriya Purru
- ICAR-NAARM, Rajender Nagar, Hyderabad 500030, India;
| | | | - Suman Lakhanpaul
- Department of Botany, University of Delhi, New Delhi 110007, India;
- Correspondence: ; Tel.: +91-9868375756
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Pereira G, Pereira J, Santos RB, Figueiredo A. Uncovering the role of DNA methyltransferases in grapevine - Plasmopara viticola interaction: From genome-wide characterization to global methylation patterns. Gene 2022; 837:146693. [PMID: 35738444 DOI: 10.1016/j.gene.2022.146693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 05/10/2022] [Accepted: 06/17/2022] [Indexed: 11/04/2022]
Abstract
Epigenetic regulation has recently gained prominence in the field of plant-pathogen interactions, providing a deeper understanding of the molecular mechanisms associated with plant infection. In grapevine interaction with pathogens, epigenetic regulation still remains a black box. In this work, we characterized grapevine DNA methyltransferase gene family and identified nine DNA methyltransferases genes across eight grapevine chromosomes coding for 17 proteins. We also assessed the modulation of global cytosine methylation and gene expression levels of these genes with the aim of establishing a connection between DNA methylation and grapevine resistance towards downy mildew. Our results revealed that, in the incompatible interaction, an early hypomethylation, coupled with downregulation of DNMT and CMT genes occurs very early after pathogen inoculation. Additionally, the compatible interaction is characterized by a hypermethylation at 6hpi. A temporal delay is evident between the shifts in DNA methyltransferases gene expression in both compatible and incompatible interactions which in turn may be reflected in the global methylation percentage. Overall, we present the first evidence of an epigenetic regulation role in grapevine defense against P. viticola.
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Affiliation(s)
- Gonçalo Pereira
- Grapevine Pathogen Systems Lab, BioISI - Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisboa, Portugal
| | - João Pereira
- Grapevine Pathogen Systems Lab, BioISI - Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisboa, Portugal
| | - Rita B Santos
- Grapevine Pathogen Systems Lab, BioISI - Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisboa, Portugal; Plant Biology Department, Faculty of Sciences, BioISI, University of Lisbon, Lisboa, Portugal.
| | - Andreia Figueiredo
- Grapevine Pathogen Systems Lab, BioISI - Biosystems & Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, Lisboa, Portugal; Plant Biology Department, Faculty of Sciences, BioISI, University of Lisbon, Lisboa, Portugal
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77
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Flavonoid Biosynthesis Genes in Triticum aestivum L.: Methylation Patterns in Cis-Regulatory Regions of the Duplicated CHI and F3H Genes. Biomolecules 2022; 12:biom12050689. [PMID: 35625617 PMCID: PMC9138379 DOI: 10.3390/biom12050689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Flavonoids are a diverse group of secondary plant metabolites that play an important role in the regulation of plant development and protection against stressors. The biosynthesis of flavonoids occurs through the activity of several enzymes, including chalcone isomerase (CHI) and flavanone 3-hydroxylase (F3H). A functional divergence between some copies of the structural TaCHI and TaF3H genes was previously shown in the allohexaploid bread wheat Triticum aestivum L. (BBAADD genome). We hypothesized that the specific nature of TaCHI and TaF3H expression may be induced by the methylation of the promoter. It was found that the predicted position of CpG islands in the promoter regions of the analyzed genes and the actual location of methylation sites did not match. We found for the first time that differences in the methylation status could affect the expression of TaCHI copies, but not the expression of TaF3Hs. At the same time, we revealed significant differences in the structure of the promoters of only the TaF3H genes, while the TaCHI promoters were highly homologous. We assume that the promoter structure in TaF3Hs primarily affects the change in the nature of gene expression. The data obtained are important for understanding the mechanisms that regulate the synthesis of flavonoids in allopolyploid wheat and show that differences in the structure of promoters have a key effect on gene expression.
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Nunn A, Rodríguez‐Arévalo I, Tandukar Z, Frels K, Contreras‐Garrido A, Carbonell‐Bejerano P, Zhang P, Ramos Cruz D, Jandrasits K, Lanz C, Brusa A, Mirouze M, Dorn K, Galbraith DW, Jarvis BA, Sedbrook JC, Wyse DL, Otto C, Langenberger D, Stadler PF, Weigel D, Marks MD, Anderson JA, Becker C, Chopra R. Chromosome-level Thlaspi arvense genome provides new tools for translational research and for a newly domesticated cash cover crop of the cooler climates. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:944-963. [PMID: 34990041 PMCID: PMC9055812 DOI: 10.1111/pbi.13775] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/28/2021] [Accepted: 12/23/2021] [Indexed: 05/20/2023]
Abstract
Thlaspi arvense (field pennycress) is being domesticated as a winter annual oilseed crop capable of improving ecosystems and intensifying agricultural productivity without increasing land use. It is a selfing diploid with a short life cycle and is amenable to genetic manipulations, making it an accessible field-based model species for genetics and epigenetics. The availability of a high-quality reference genome is vital for understanding pennycress physiology and for clarifying its evolutionary history within the Brassicaceae. Here, we present a chromosome-level genome assembly of var. MN106-Ref with improved gene annotation and use it to investigate gene structure differences between two accessions (MN108 and Spring32-10) that are highly amenable to genetic transformation. We describe non-coding RNAs, pseudogenes and transposable elements, and highlight tissue-specific expression and methylation patterns. Resequencing of forty wild accessions provided insights into genome-wide genetic variation, and QTL regions were identified for a seedling colour phenotype. Altogether, these data will serve as a tool for pennycress improvement in general and for translational research across the Brassicaceae.
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Affiliation(s)
- Adam Nunn
- ecSeq Bioinformatics GmbHLeipzigGermany
- Department of Computer ScienceLeipzig UniversityLeipzigGermany
| | - Isaac Rodríguez‐Arévalo
- GeneticsFaculty of BiologyLudwig Maximilians UniversityMartinsriedGermany
- Gregor Mendel Institute of Molecular Plant Biology GmbHAustrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC)ViennaAustria
| | - Zenith Tandukar
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | - Katherine Frels
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNEUSA
| | | | | | - Panpan Zhang
- Institut de Recherche pour le DéveloppementUMR232 DIADEMontpellierFrance
- Laboratory of Plant Genome and DevelopmentUniversity of PerpignanPerpignanFrance
| | - Daniela Ramos Cruz
- GeneticsFaculty of BiologyLudwig Maximilians UniversityMartinsriedGermany
- Gregor Mendel Institute of Molecular Plant Biology GmbHAustrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC)ViennaAustria
| | - Katharina Jandrasits
- GeneticsFaculty of BiologyLudwig Maximilians UniversityMartinsriedGermany
- Gregor Mendel Institute of Molecular Plant Biology GmbHAustrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC)ViennaAustria
| | - Christa Lanz
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| | - Anthony Brusa
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | - Marie Mirouze
- Institut de Recherche pour le DéveloppementUMR232 DIADEMontpellierFrance
- Laboratory of Plant Genome and DevelopmentUniversity of PerpignanPerpignanFrance
| | - Kevin Dorn
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMNUSA
- USDA‐ARSSoil Management and Sugarbeet ResearchFort CollinsCOUSA
| | - David W Galbraith
- BIO5 InstituteArizona Cancer CenterDepartment of Biomedical EngineeringUniversity of ArizonaSchool of Plant SciencesTucsonAZUSA
| | - Brice A. Jarvis
- School of Biological SciencesIllinois State UniversityNormalILUSA
| | - John C. Sedbrook
- School of Biological SciencesIllinois State UniversityNormalILUSA
| | - Donald L. Wyse
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | | | | | - Peter F. Stadler
- Department of Computer ScienceLeipzig UniversityLeipzigGermany
- Max Planck Institute for Mathematics in the SciencesLeipzigGermany
| | - Detlef Weigel
- Department of Molecular BiologyMax Planck Institute for Developmental BiologyTübingenGermany
| | - M. David Marks
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMNUSA
| | - James A. Anderson
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
| | - Claude Becker
- GeneticsFaculty of BiologyLudwig Maximilians UniversityMartinsriedGermany
- Gregor Mendel Institute of Molecular Plant Biology GmbHAustrian Academy of Sciences (ÖAW), Vienna BioCenter (VBC)ViennaAustria
| | - Ratan Chopra
- Department of Agronomy and Plant GeneticsUniversity of MinnesotaSaint PaulMNUSA
- Department of Plant and Microbial BiologyUniversity of MinnesotaSaint PaulMNUSA
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Bianchetti R, Bellora N, de Haro LA, Zuccarelli R, Rosado D, Freschi L, Rossi M, Bermudez L. Phytochrome-Mediated Light Perception Affects Fruit Development and Ripening Through Epigenetic Mechanisms. FRONTIERS IN PLANT SCIENCE 2022; 13:870974. [PMID: 35574124 PMCID: PMC9096621 DOI: 10.3389/fpls.2022.870974] [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: 02/07/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Phytochrome (PHY)-mediated light and temperature perception has been increasingly implicated as important regulator of fruit development, ripening, and nutritional quality. Fruit ripening is also critically regulated by chromatin remodeling via DNA demethylation, though the molecular basis connecting epigenetic modifications in fruits and environmental cues remains largely unknown. Here, to unravel whether the PHY-dependent regulation of fruit development involves epigenetic mechanisms, an integrative analysis of the methylome, transcriptome and sRNAome of tomato fruits from phyA single and phyB1B2 double mutants was performed in immature green (IG) and breaker (BK) stages. The transcriptome analysis showed that PHY-mediated light perception regulates more genes in BK than in the early stages of fruit development (IG) and that PHYB1B2 has a more substantial impact than PHYA in the fruit transcriptome, in both analyzed stages. The global profile of methylated cytosines revealed that both PHYA and PHYB1B2 affect the global methylome, but PHYB1B2 has a greater impact on ripening-associated methylation reprogramming across gene-rich genomic regions in tomato fruits. Remarkably, promoters of master ripening-associated transcription factors (TF) (RIN, NOR, CNR, and AP2a) and key carotenoid biosynthetic genes (PSY1, PDS, ZISO, and ZDS) remained highly methylated in phyB1B2 from the IG to BK stage. The positional distribution and enrichment of TF binding sites were analyzed over the promoter region of the phyB1B2 DEGs, exposing an overrepresentation of binding sites for RIN as well as the PHY-downstream effectors PIFs and HY5/HYH. Moreover, phyA and phyB1B2 mutants showed a positive correlation between the methylation level of sRNA cluster-targeted genome regions in gene bodies and mRNA levels. The experimental evidence indicates that PHYB1B2 signal transduction is mediated by a gene expression network involving chromatin organization factors (DNA methylases/demethylases, histone-modifying enzymes, and remodeling factors) and transcriptional regulators leading to altered mRNA profile of ripening-associated genes. This new level of understanding provides insights into the orchestration of epigenetic mechanisms in response to environmental cues affecting agronomical traits.
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Affiliation(s)
- Ricardo Bianchetti
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Nicolas Bellora
- Institute of Nuclear Technologies for Health (Intecnus), National Scientific and Technical Research Council (CONICET), Bariloche, Argentina
| | - Luis A. de Haro
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Rafael Zuccarelli
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Daniele Rosado
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Magdalena Rossi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Luisa Bermudez
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), CICVyA, INTA-CONICET, Castelar, Argentina
- Cátedra de Genética, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina
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80
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Genetic and Epigenetic Signatures Associated with the Divergence of Aquilegia Species. Genes (Basel) 2022; 13:genes13050793. [PMID: 35627179 PMCID: PMC9141525 DOI: 10.3390/genes13050793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/21/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022] Open
Abstract
Widely grown in the Northern Hemisphere, the genus Aquilegia (columbine) is a model system in adaptive radiation research. While morphological variations between species have been associated with environmental factors, such as pollinators, how genetic and epigenetic factors are involved in the rapid divergence in this genus remains under investigated. In this study, we surveyed the genomes and DNA methylomes of ten Aquilegia species, representative of the Asian, European and North American lineages. Our analyses of the phylogeny and population structure revealed high genetic and DNA methylomic divergence across these three lineages. By multi-level genome-wide scanning, we identified candidate genes exhibiting lineage-specific genetic or epigenetic variation patterns that were signatures of inter-specific divergence. We demonstrated that these species-specific genetic variations and epigenetic variabilities are partially independent and are both functionally related to various biological processes vital to adaptation, including stress tolerance, cell reproduction and DNA repair. Our study provides an exploratory overview of how genetic and epigenetic signatures are associated with the diversification of the Aquilegia species.
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81
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Jing M, Zhang H, Wei M, Tang Y, Xia Y, Chen Y, Shen Z, Chen C. Reactive Oxygen Species Partly Mediate DNA Methylation in Responses to Different Heavy Metals in Pokeweed. FRONTIERS IN PLANT SCIENCE 2022; 13:845108. [PMID: 35463456 PMCID: PMC9021841 DOI: 10.3389/fpls.2022.845108] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
DNA methylation is a rapid response strategy promoting plant survival under heavy metal (HM) stress. However, the roles of DNA methylation underlying plant adaptation to HM stress remain largely unknown. Here, we used pokeweed, a hyperaccumulator of manganese (Mn) and cadmium (Cd), to explore responses of plant to HM stress at phenotypic, transcriptional and DNA methylation levels. Mn- and Cd-specific response patterns were detected in pokeweed. The growth of pokeweed was both inhibited with exposure to excess Mn/Cd, but pokeweed distinguished Mn and Cd with different subcellular distributions, ROS scavenging systems, transcriptional patterns including genes involved in DNA methylation, and differentially methylated loci (DML). The number of DML between Mn/Cd treated and untreated samples increased with increased Mn/Cd concentrations. Meanwhile, pretreatment with NADPH oxidase inhibitors prior to HM exposure markedly reduced HM-induced reactive oxygen species (ROS), which caused reductions in expressions of DNA methylase and demethylase in pretreated samples. The increased levels of HM-induced demethylation were suppressed with alleviated ROS stress, and a series of HM-related methylated loci were also ROS-related. Taken together, our study demonstrates that different HMs affect different DNA methylation sites in a dose-dependent manner and changes in DNA methylation under Mn/Cd stress are partly mediated by HM-induced ROS.
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Affiliation(s)
- Minyu Jing
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Hanchao Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mingyue Wei
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yongwei Tang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yan Xia
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
| | - Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China
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82
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Williams BP, Bechen LL, Pohlmann DA, Gehring M. Somatic DNA demethylation generates tissue-specific methylation states and impacts flowering time. THE PLANT CELL 2022; 34:1189-1206. [PMID: 34954804 PMCID: PMC8972289 DOI: 10.1093/plcell/koab319] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/21/2021] [Indexed: 05/29/2023]
Abstract
Cytosine methylation is a reversible epigenetic modification of DNA. In plants, removal of cytosine methylation is accomplished by the four members of the DEMETER (DME) family of 5-methylcytosine DNA glycosylases, named DME, DEMETER-LIKE2 (DML2), DML3, and REPRESSOR OF SILENCING1 (ROS1) in Arabidopsis thaliana. Demethylation by DME is critical for seed development, preventing experiments to determine the function of the entire gene family in somatic tissues by mutant analysis. Here, we bypassed the reproductive defects of dme mutants to create somatic quadruple homozygous mutants of the entire DME family. dme; ros1; dml2; and dml3 (drdd) leaves exhibit hypermethylated regions compared with wild-type leaves and rdd triple mutants, indicating functional redundancy among all four demethylases. Targets of demethylation include regions co-targeted by RNA-directed DNA methylation and, surprisingly, CG gene body methylation, indicating dynamic methylation at these less-understood sites. Additionally, many tissue-specific methylation differences are absent in drdd, suggesting a role for active demethylation in generating divergent epigenetic states across wild-type tissues. Furthermore, drdd plants display an early flowering phenotype, which involves 5'-hypermethylation and transcriptional down-regulation of FLOWERING LOCUS C. Active DNA demethylation is therefore required for proper methylation across somatic tissues and defines the epigenetic landscape of intergenic and coding regions.
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Affiliation(s)
- Ben P Williams
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Lindsey L Bechen
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Deborah A Pohlmann
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mary Gehring
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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83
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Yadav NS, Titov V, Ayemere I, Byeon B, Ilnytskyy Y, Kovalchuk I. Multigenerational Exposure to Heat Stress Induces Phenotypic Resilience, and Genetic and Epigenetic Variations in Arabidopsis thaliana Offspring. FRONTIERS IN PLANT SCIENCE 2022; 13:728167. [PMID: 35419019 PMCID: PMC8996174 DOI: 10.3389/fpls.2022.728167] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Plants are sedentary organisms that constantly sense changes in their environment and react to various environmental cues. On a short-time scale, plants respond through alterations in their physiology, and on a long-time scale, plants alter their development and pass on the memory of stress to the progeny. The latter is controlled genetically and epigenetically and allows the progeny to be primed for future stress encounters, thus increasing the likelihood of survival. The current study intended to explore the effects of multigenerational heat stress in Arabidopsis thaliana. Twenty-five generations of Arabidopsis thaliana were propagated in the presence of heat stress. The multigenerational stressed lineage F25H exhibited a higher tolerance to heat stress and elevated frequency of homologous recombination, as compared to the parallel control progeny F25C. A comparison of genomic sequences revealed that the F25H lineage had a three-fold higher number of mutations [single nucleotide polymorphisms (SNPs) and insertions and deletions (INDELs)] as compared control lineages, suggesting that heat stress induced genetic variations in the heat-stressed progeny. The F25H stressed progeny showed a 7-fold higher number of non-synonymous mutations than the F25C line. Methylome analysis revealed that the F25H stressed progeny showed a lower global methylation level in the CHH context than the control progeny. The F25H and F25C lineages were different from the parental control lineage F2C by 66,491 and 80,464 differentially methylated positions (DMPs), respectively. F25H stressed progeny displayed higher frequency of methylation changes in the gene body and lower in the body of transposable elements (TEs). Gene Ontology analysis revealed that CG-DMRs were enriched in processes such as response to abiotic and biotic stimulus, cell organizations and biogenesis, and DNA or RNA metabolism. Hierarchical clustering of these epimutations separated the heat stressed and control parental progenies into distinct groups which revealed the non-random nature of epimutations. We observed an overall higher number of epigenetic variations than genetic variations in all comparison groups, indicating that epigenetic variations are more prevalent than genetic variations. The largest difference in epigenetic and genetic variations was observed between control plants comparison (F25C vs. F2C), which clearly indicated that the spontaneous nature of epigenetic variations and heat-inducible nature of genetic variations. Overall, our study showed that progenies derived from multigenerational heat stress displayed a notable adaption in context of phenotypic, genotypic and epigenotypic resilience.
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84
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Lin X, Zhou M, Yao J, Li QQ, Zhang YY. Phenotypic and Methylome Responses to Salt Stress in Arabidopsis thaliana Natural Accessions. FRONTIERS IN PLANT SCIENCE 2022; 13:841154. [PMID: 35310665 PMCID: PMC8931716 DOI: 10.3389/fpls.2022.841154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Salt stress threatens plant growth, development and crop yields, and has become a critical global environmental issue. Increasing evidence has suggested that the epigenetic mechanism such as DNA methylation can mediate plant response to salt stress through transcriptional regulation and transposable element (TE) silencing. However, studies exploring genome-wide methylation dynamics under salt stress remain limited, in particular, for studies on multiple genotypes. Here, we adopted four natural accessions of the model species Arabidopsis thaliana and investigated the phenotypic and genome-wide methylation responses to salt stress through whole-genome bisulfite sequencing (WGBS). We found that salt stress significantly changed plant phenotypes, including plant height, rosette diameter, fruit number, and aboveground biomass, and the change in biomass tended to depend on accessions. Methylation analysis revealed that genome-wide methylation patterns depended primarily on accessions, and salt stress caused significant methylation changes in ∼ 0.1% cytosines over the genomes. About 33.5% of these salt-induced differential methylated cytosines (DMCs) were located to transposable elements (TEs). These salt-induced DMCs were mainly hypermethylated and accession-specific. TEs annotated to have DMCs (DMC-TEs) across accessions were found mostly belonged to the superfamily of Gypsy, a type II transposon, indicating a convergent DMC dynamic on TEs across different genetic backgrounds. Moreover, 8.0% of salt-induced DMCs were located in gene bodies and their proximal regulatory regions. These DMCs were also accession-specific, and genes annotated to have DMCs (DMC-genes) appeared to be more accession-specific than DMC-TEs. Intriguingly, both accession-specific DMC-genes and DMC-genes shared by multiple accessions were enriched in similar functions, including methylation, gene silencing, chemical homeostasis, polysaccharide catabolic process, and pathways relating to shifts between vegetative growth and reproduction. These results indicate that, across different genetic backgrounds, methylation changes may have convergent functions in post-transcriptional, physiological, and phenotypic modulation under salt stress. These convergent methylation dynamics across accession may be autonomous from genetic variation or due to convergent genetic changes, which requires further exploration. Our study provides a more comprehensive picture of genome-wide methylation dynamics under salt stress, and highlights the importance of exploring stress response mechanisms from diverse genetic backgrounds.
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Affiliation(s)
- Xiaohe Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Ming Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Jing Yao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qingshun Q. Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, United States
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
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85
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Chen C, Wang M, Zhu J, Tang Y, Zhang H, Zhao Q, Jing M, Chen Y, Xu X, Jiang J, Shen Z. Long-term effect of epigenetic modification in plant-microbe interactions: modification of DNA methylation induced by plant growth-promoting bacteria mediates promotion process. MICROBIOME 2022; 10:36. [PMID: 35209943 PMCID: PMC8876431 DOI: 10.1186/s40168-022-01236-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 01/23/2022] [Indexed: 05/15/2023]
Abstract
BACKGROUND Soil microbiomes are considered a cornerstone of the next green revolution, and plant growth-promoting bacteria (PGPB) are critical for microbiome engineering. However, taking plant-beneficial microorganisms from discovery to agricultural application remains challenging, as the mechanisms underlying the interactions between beneficial strains and plants in native soils are still largely unknown. Increasing numbers of studies have indicated that strains introduced to manipulate microbiomes are usually eliminated in soils, while others have reported that application of PGPB as inocula significantly improves plant growth. This contradiction suggests the need for a deeper understanding of the mechanisms underlying microbe-induced growth promotion. RESULTS We showed PGPB-induced long-term plant growth promotion after elimination of the PGPB inoculum in soils and explored the three-way interactions among the exogenous inoculum, indigenous microbiome, and plant, which were key elements of the plant growth-promoting process. We found the rhizosphere microbiome assembly was mainly driven by plant development and root recruitments greatly attenuated the influence of inocula on the rhizosphere microbiome. Neither changes in the rhizosphere microbiome nor colonization of inocula in roots was necessary for plant growth promotion. In roots, modification of DNA methylation in response to inoculation affects gene expression related to PGPB-induced growth promotion, and disruptions of the inoculation-induced DNA methylation patterns greatly weakened the plant growth promotion. Together, our results showed PGPB-induced DNA methylation modifications in roots mediated the promotion process and these modifications remained functional after elimination of the inoculum from the microbiome. CONCLUSION This study suggests a new mechanism in which PGPB affect DNA methylation in roots to promote plant growth, which provides important insights into microbiome-plant interactions and offers new strategies for plant microbiome engineering beyond the perspective of maintaining inoculum persistence in soils. Video abstract.
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Affiliation(s)
- Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Miao Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Jingzhi Zhu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Yongwei Tang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Hanchao Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Qiming Zhao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Minyu Jing
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xihui Xu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China.
| | - Jiandong Jiang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China.
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, People's Republic of China.
- Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
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86
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Liu D, Mu Q, Li X, Xu S, Li Y, Gu T. The callus formation capacity of strawberry leaf explant is modulated by DNA methylation. HORTICULTURE RESEARCH 2022; 9:uhab073. [PMID: 35043170 PMCID: PMC8947209 DOI: 10.1093/hr/uhab073] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/16/2021] [Accepted: 11/04/2021] [Indexed: 05/30/2023]
Abstract
Shoot regeneration from leaf tissue requires de-differentiation of cells from a highly differentiated state into an active dividing state, but how this physiological transition occurs and is regulated especially at epigenetic level remains obscure. Here we have characterized the DNA methylome represented by 5-methylcytosine (5mC) in leaf and the callus tissue derived from the leaf explant of woodland strawberry Fragaria vesca. We detected an overall increase of DNA methylation and distinct 5mC enrichment patterns in the CG, CHG and CHH sequence contexts in genetic and transposable elements. Our analyses revealed an intricate relation between DNA methylation and gene expression levels in leaf or leaf-derived callus. However, when considering the genes involved in callus formation and shoot regeneration, e.g. FvePLT3/7, FveWIND3, FveWIND4, FveLOG4 and FveIAA14, their dynamic transcription levels were associated with the differentially methylated regions located in the promoters or gene bodies, indicating a regulatory role of DNA methylation in the transcriptional regulation of pluripotency acquisition in strawberry. Furthermore, application of a DNA methyltransferase inhibitor 5'-azacytidine (5'-Aza) hampered both callus formation and shoot regeneration from the leaf explant. We further showed that 5'-Aza down-regulated the genes involved in cell wall integrity, such as expansin, pectin lyase and pectin methylesterase genes, suggesting an essential role of cell wall metabolism during callus formation. This study reveals the contribution of DNA methylation in callus formation capacity and will provide a basis for developing a strategy to improve shoot regeneration for basic and applied research applications.
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Affiliation(s)
- Decai Liu
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qin Mu
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xianyang Li
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Sheng Xu
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269, USA
| | - Tingting Gu
- State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
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87
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Brown KE, Kelly JK. Genome-wide association mapping of transcriptome variation in Mimulus guttatus indicates differing patterns of selection on cis- versus trans-acting mutations. Genetics 2022; 220:iyab189. [PMID: 34791192 PMCID: PMC8733635 DOI: 10.1093/genetics/iyab189] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/28/2021] [Indexed: 11/14/2022] Open
Abstract
We measured the floral bud transcriptome of 151 fully sequenced lines of Mimulus guttatus from one natural population. Thousands of single nucleotide polymorphisms (SNPs) are implicated as transcription regulators, but there is a striking difference in the allele frequency spectrum of cis-acting and trans-acting mutations. Cis-SNPs have intermediate frequencies (consistent with balancing selection) while trans-SNPs exhibit a rare-alleles model (consistent with purifying selection). This pattern only becomes clear when transcript variation is normalized on a gene-to-gene basis. If a global normalization is applied, as is typically in RNAseq experiments, asymmetric transcript distributions combined with "rarity disequilibrium" produce a superabundance of false positives for trans-acting SNPs. To explore the cause of purifying selection on trans-acting mutations, we identified gene expression modules as sets of coexpressed genes. The extent to which trans-acting mutations influence modules is a strong predictor of allele frequency. Mutations altering expression of genes with high "connectedness" (those that are highly predictive of the representative module expression value) have the lowest allele frequency. The expression modules can also predict whole-plant traits such as flower size. We find that a substantial portion of the genetic (co)variance among traits can be described as an emergent property of genetic effects on expression modules.
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Affiliation(s)
- Keely E Brown
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
| | - John K Kelly
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA
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88
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Lee H. Analysis of Bisulfite Sequencing Data Using Bismark and DMRcaller to Identify Differentially Methylated Regions. Methods Mol Biol 2022; 2443:451-463. [PMID: 35037220 DOI: 10.1007/978-1-0716-2067-0_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The mechanism of the addition of a methyl group to cytosine has been identified as one of several heritable epigenetic mechanisms. In plants, DNA methylation is involved in mediating response to stress, plant development, polyploidy, and domestication through regulation of gene expression. The correlation of epigenetic variation to phenotypic traits expands our understanding toward plant evolution, and provides new source for targeted manipulation in crop improvement. To address the increasing interest to map methylation landscape in plant species, this chapter describes methods to analyze bisulfite sequencing data and identify epigenetic variation between samples. We also detailed guidelines to highlight possible optimizations, as well as ways to tailor parameters according to data and biological variability.
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Affiliation(s)
- HueyTyng Lee
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany.
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89
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Hannan Parker A, Wilkinson SW, Ton J. Epigenetics: a catalyst of plant immunity against pathogens. THE NEW PHYTOLOGIST 2022; 233:66-83. [PMID: 34455592 DOI: 10.1111/nph.17699] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/20/2021] [Indexed: 05/11/2023]
Abstract
The plant immune system protects against pests and diseases. The recognition of stress-related molecular patterns triggers localised immune responses, which are often followed by longer-lasting systemic priming and/or up-regulation of defences. In some cases, this induced resistance (IR) can be transmitted to following generations. Such transgenerational IR is gradually reversed in the absence of stress at a rate that is proportional to the severity of disease experienced in previous generations. This review outlines the mechanisms by which epigenetic responses to pathogen infection shape the plant immune system across expanding time scales. We review the cis- and trans-acting mechanisms by which stress-inducible epigenetic changes at transposable elements (TEs) regulate genome-wide defence gene expression and draw particular attention to one regulatory model that is supported by recent evidence about the function of AGO1 and H2A.Z in transcriptional control of defence genes. Additionally, we explore how stress-induced mobilisation of epigenetically controlled TEs acts as a catalyst of Darwinian evolution by generating (epi)genetic diversity at environmentally responsive genes. This raises questions about the long-term evolutionary consequences of stress-induced diversification of the plant immune system in relation to the long-held dichotomy between Darwinian and Lamarckian evolution.
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Affiliation(s)
- Adam Hannan Parker
- Department of Animal and Plant Sciences, Institute for Sustainable Food, Western Bank, University of Sheffield, Sheffield, S10 2TN, UK
| | - Samuel W Wilkinson
- Department of Animal and Plant Sciences, Institute for Sustainable Food, Western Bank, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jurriaan Ton
- Department of Animal and Plant Sciences, Institute for Sustainable Food, Western Bank, University of Sheffield, Sheffield, S10 2TN, UK
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90
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Katsuya-Gaviria K, Paris G, Dendooven T, Bandyra KJ. Bacterial RNA chaperones and chaperone-like riboregulators: behind the scenes of RNA-mediated regulation of cellular metabolism. RNA Biol 2021; 19:419-436. [PMID: 35438047 PMCID: PMC9037510 DOI: 10.1080/15476286.2022.2048565] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/26/2022] [Indexed: 11/02/2022] Open
Abstract
In all domains of life, RNA chaperones safeguard and guide the fate of the cellular RNA pool. RNA chaperones comprise structurally diverse proteins that ensure proper folding, stability, and ribonuclease resistance of RNA, and they support regulatory activities mediated by RNA. RNA chaperones constitute a topologically diverse group of proteins that often present an unstructured region and bind RNA with limited nucleotide sequence preferences. In bacteria, three main proteins - Hfq, ProQ, and CsrA - have been shown to regulate numerous complex processes, including bacterial growth, stress response and virulence. Hfq and ProQ have well-studied activities as global chaperones with pleiotropic impact, while CsrA has a chaperone-like role with more defined riboregulatory function. Here, we describe relevant novel insights into their common features, including RNA binding properties, unstructured domains, and interplay with other proteins important to RNA metabolism.
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Affiliation(s)
- Kai Katsuya-Gaviria
- Department of Biochemistry, University of Cambridge, Tennis Court Road, CambridgeCB2 1GA, UK
| | - Giulia Paris
- Department of Biochemistry, University of Cambridge, Tennis Court Road, CambridgeCB2 1GA, UK
| | - Tom Dendooven
- Department of Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Katarzyna J. Bandyra
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, 02-089Warsaw, Poland
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91
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Kirov I, Polkhovskaya E, Dudnikov M, Merkulov P, Vlasova A, Karlov G, Soloviev A. Searching for a Needle in a Haystack: Cas9-Targeted Nanopore Sequencing and DNA Methylation Profiling of Full-Length Glutenin Genes in a Big Cereal Genome. PLANTS (BASEL, SWITZERLAND) 2021; 11:5. [PMID: 35009008 PMCID: PMC8746966 DOI: 10.3390/plants11010005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 12/29/2022]
Abstract
Sequencing and epigenetic profiling of target genes in plants are important tasks with various applications ranging from marker design for plant breeding to the study of gene expression regulation. This is particularly interesting for plants with big genome size for which whole-genome sequencing can be time-consuming and costly. In this study, we asked whether recently proposed Cas9-targeted nanopore sequencing (nCATS) is efficient for target gene sequencing for plant species with big genome size. We applied nCATS to sequence the full-length glutenin genes (Glu-1Ax, Glu-1Bx and Glu-1By) and their promoters in hexaploid triticale (X Triticosecale, AABBRR, genome size is 24 Gb). We showed that while the target gene enrichment per se was quite high for the three glutenin genes (up to 645×), the sequencing depth that was achieved from two MinION flowcells was relatively low (5-17×). However, this sequencing depth was sufficient for various tasks including detection of InDels and single-nucleotide variations (SNPs), read phasing and methylation profiling. Using nCATS, we uncovered SNP and InDel variation of full-length glutenin genes providing useful information for marker design and deciphering of variation of individual Glu-1By alleles. Moreover, we demonstrated that glutenin genes possess a 'gene-body' methylation epigenetic profile with hypermethylated CDS part and hypomethylated promoter region. The obtained information raised an interesting question on the role of gene-body methylation in glutenin gene expression regulation. Taken together, our work disclosures the potential of the nCATS approach for sequencing of target genes in plants with big genome size.
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Affiliation(s)
- Ilya Kirov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (E.P.); (M.D.); (P.M.); (A.V.); (G.K.); (A.S.)
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
| | - Ekaterina Polkhovskaya
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (E.P.); (M.D.); (P.M.); (A.V.); (G.K.); (A.S.)
| | - Maxim Dudnikov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (E.P.); (M.D.); (P.M.); (A.V.); (G.K.); (A.S.)
- Kurchatov Genomics Center of ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia
| | - Pavel Merkulov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (E.P.); (M.D.); (P.M.); (A.V.); (G.K.); (A.S.)
| | - Anastasia Vlasova
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (E.P.); (M.D.); (P.M.); (A.V.); (G.K.); (A.S.)
| | - Gennady Karlov
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (E.P.); (M.D.); (P.M.); (A.V.); (G.K.); (A.S.)
| | - Alexander Soloviev
- Laboratory of Marker-Assisted and Genomic Selection of Plants, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Str. 42, 127550 Moscow, Russia; (E.P.); (M.D.); (P.M.); (A.V.); (G.K.); (A.S.)
- N.V. Tsitsin Main Botanical Garden of the Russian Academy of Sciences, Botanicheskaya Str. 4, 127276 Moscow, Russia
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92
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Zhang Z, Liu J, Sun Y, Wang S, Xing X, Feng X, Pérez-Pérez JM, Li Y. Genome-wide high-resolution mapping of DNA methylation reveals epigenetic variation in the offspring of sexual and asexual propagation in Robinia pseudoacacia. PLANT CELL REPORTS 2021; 40:2435-2447. [PMID: 34524479 DOI: 10.1007/s00299-021-02787-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 09/07/2021] [Indexed: 06/13/2023]
Abstract
We detected the genome-wide pattern of DNA methylation and its association with gene expression in sexual and asexual progenies of mature Robinia pseudoacacia trees. DNA methylation plays an important role in plant reproduction and development. Although some studies on sexual reproduction have been carried out in model plants, little is known about the dynamic changes in DNA methylation and their effect on gene expression in sexual and asexual progeny of woody plants. Here, through whole-genome bisulfite sequencing, we revealed DNA methylation patterns in the sexual and asexual progenies of mature Robinia pseudoacacia to understand the regulation of gene expression by DNA methylation in juvenile seedlings. An average of 53% CG, 34% CHG and 5% CHH contexts was methylated in the leaves of mature and juvenile individuals. The CHH methylation level of asexually propagated seedlings was significantly lower than that of seed-derived seedlings and mature trees. The intergenic regions had the highest methylation level. Analysis of differentially methylated regions (DMRs) showed that most of them were hypermethylated and located in the gene upstream and introns. A total of 24, 108 and 162 differentially expressed genes containing DMRs were identified in root sprouts (RSs), root cuttings (RCs) and seed-derived seedlings (SSs), respectively, and a large proportion of them showed hypermethylation. In addition, DMRs were enriched within GO subcategories including catalytic activity, metabolic process and cellular process. The results reveal widespread DNA methylation changes between mature plants and their progenies through sexual/asexual reproduction, which provides novel insights into DNA methylation reprogramming and the regulation of gene expression in woody plants.
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Affiliation(s)
- Zijie Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Jie Liu
- National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Yuhan Sun
- National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, People's Republic of China
| | - Shaoming Wang
- State-Owned Quanbaoshan Forestry Station in Luoning County of He'nan Province, Luoyang, 471717, People's Republic of China
| | - Xiuxia Xing
- Agricultural Service Center of Wangfan Hui Town in Luoning County of He'nan Province, Luoyang, 471700, People's Republic of China
| | - Xiaojing Feng
- State-Owned Lvcun Forestry Station in Luoning County of He'nan Province, Luoyang, 471700, People's Republic of China
| | | | - Yun Li
- National Engineering Laboratory for Tree Breeding, College of Biological Science and Technology, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, 100083, People's Republic of China.
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93
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Bansal J, Gupta K, Rajkumar MS, Garg R, Jain M. Draft genome and transcriptome analyses of halophyte rice Oryza coarctata provide resources for salinity and submergence stress response factors. PHYSIOLOGIA PLANTARUM 2021; 173:1309-1322. [PMID: 33215706 DOI: 10.1111/ppl.13284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/05/2020] [Accepted: 11/17/2020] [Indexed: 05/24/2023]
Abstract
Oryza coarctata is a wild relative of rice that has adapted to diverse ecological environments, including high salinity and submergence. Thus, it can provide an important resource for discovering candidate genes/factors involved in tolerance to these stresses. Here, we report a draft genome assembly of 573 Mb comprised of 8877 scaffolds with N50 length of 205 kb. We predicted a total of 50,562 protein-coding genes, of which a significant fraction was found to be involved in secondary metabolite biosynthesis and hormone signal transduction pathways. Several salinity and submergence stress-responsive protein-coding and long noncoding RNAs involved in diverse biological processes were identified using RNA-sequencing data. Based on small RNA sequencing, we identified 168 unique miRNAs and 3219 target transcripts (coding and noncoding) involved in several biological processes, including abiotic stress responses. Further, whole genome bisulphite sequencing data analysis revealed at least 19%-48% methylcytosines in different sequence contexts and the influence of methylation status on gene expression. The genome assembly along with other datasets have been made publicly available at http://ccbb.jnu.ac.in/ory-coar. Altogether, we provide a comprehensive genomic resource for understanding the regulation of salinity and submergence stress responses and identification of candidate genes/factors involved for functional genomics studies.
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Affiliation(s)
- Juhi Bansal
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Khushboo Gupta
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Noida, India
| | - Mohan Singh Rajkumar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Noida, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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94
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Vigneau J, Borg M. The epigenetic origin of life history transitions in plants and algae. PLANT REPRODUCTION 2021; 34:267-285. [PMID: 34236522 PMCID: PMC8566409 DOI: 10.1007/s00497-021-00422-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 05/17/2023]
Abstract
Plants and algae have a complex life history that transitions between distinct life forms called the sporophyte and the gametophyte. This phenomenon-called the alternation of generations-has fascinated botanists and phycologists for over 170 years. Despite the mesmerizing array of life histories described in plants and algae, we are only now beginning to learn about the molecular mechanisms controlling them and how they evolved. Epigenetic silencing plays an essential role in regulating gene expression during multicellular development in eukaryotes, raising questions about its impact on the life history strategy of plants and algae. Here, we trace the origin and function of epigenetic mechanisms across the plant kingdom, from unicellular green algae through to angiosperms, and attempt to reconstruct the evolutionary steps that influenced life history transitions during plant evolution. Central to this evolutionary scenario is the adaption of epigenetic silencing from a mechanism of genome defense to the repression and control of alternating generations. We extend our discussion beyond the green lineage and highlight the peculiar case of the brown algae. Unlike their unicellular diatom relatives, brown algae lack epigenetic silencing pathways common to animals and plants yet display complex life histories, hinting at the emergence of novel life history controls during stramenopile evolution.
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Affiliation(s)
- Jérômine Vigneau
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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95
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Zeng WY, Tan YR, Long SF, Sun ZD, Lai ZG, Yang SZ, Chen HZ, Qing XY. Methylome and transcriptome analyses of soybean response to bean pyralid larvae. BMC Genomics 2021; 22:836. [PMID: 34794392 PMCID: PMC8603512 DOI: 10.1186/s12864-021-08140-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/27/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Bean pyralid is one of the major leaf-feeding insects that affect soybean crops. DNA methylation can control the networks of gene expressions, and it plays an important role in responses to biotic stress. However, at present the genome-wide DNA methylation profile of the soybean resistance to bean pyralid has not been reported so far. RESULTS Using whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq), we analyzed the highly resistant material (Gantai-2-2, HRK) and highly susceptible material (Wan82-178, HSK), under bean pyralid larvae feeding 0 h and 48 h, to clarify the molecular mechanism of the soybean resistance and explore its insect-resistant genes. We identified 2194, 6872, 39,704 and 40,018 differentially methylated regions (DMRs), as well as 497, 1594, 9596 and 9554 differentially methylated genes (DMGs) in the HRK0/HRK48, HSK0/HSK48, HSK0/HRK0 and HSK48/HRK48 comparisons, respectively. Through the analysis of global methylation and transcription, 265 differentially expressed genes (DEGs) were negatively correlated with DMGs, there were 34, 49, 141 and 116 negatively correlated genes in the HRK0/HRK48, HSK0/HSK48, HSK0/HRK0 and HSK48/HRK48, respectively. The MapMan cluster analysis showed that 114 negatively correlated genes were clustered in 24 pathways, such as protein biosynthesis and modification; primary metabolism; secondary metabolism; cell cycle, cell structure and component; RNA biosynthesis and processing, and so on. Moreover, CRK40; CRK62; STK; MAPK9; L-type lectin-domain containing receptor kinase VIII.2; CesA; CSI1; fimbrin-1; KIN-14B; KIN-14 N; KIN-4A; cytochrome P450 81E8; BEE1; ERF; bHLH25; bHLH79; GATA26, were likely regulatory genes involved in the soybean responses to bean pyralid larvae. Finally, 5 DMRs were further validated that the genome-wide DNA data were reliable through PS-PCR and 5 DEGs were confirmed the relationship between DNA methylation and gene expression by qRT-PCR. The results showed an excellent agreement with deep sequencing. CONCLUSIONS Genome-wide DNA methylation profile of soybean response to bean pyralid was obtained for the first time. Several specific DMGs which participated in protein kinase, cell and organelle, flavonoid biosynthesis and transcription factor were further identified to be likely associated with soybean response to bean pyralid. Our data will provide better understanding of DNA methylation alteration and their potential role in soybean insect resistance.
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Affiliation(s)
- Wei-Ying Zeng
- Guangxi Academy of Agricultural Sciences, Nanning, 530007 Guangxi China
| | - Yu-Rong Tan
- Guangxi Academy of Agricultural Sciences, Nanning, 530007 Guangxi China
| | - Sheng-Feng Long
- Guangxi Academy of Agricultural Sciences, Nanning, 530007 Guangxi China
| | - Zu-Dong Sun
- Guangxi Academy of Agricultural Sciences, Nanning, 530007 Guangxi China
| | - Zhen-Guang Lai
- Guangxi Academy of Agricultural Sciences, Nanning, 530007 Guangxi China
| | - Shou-Zhen Yang
- Guangxi Academy of Agricultural Sciences, Nanning, 530007 Guangxi China
| | - Huai-Zhu Chen
- Guangxi Academy of Agricultural Sciences, Nanning, 530007 Guangxi China
| | - Xia-Yan Qing
- Guangxi Academy of Agricultural Sciences, Nanning, 530007 Guangxi China
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96
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Wang JH, Xu ZM, Qiu XB, Li LL, Yu SY, Li T, Tang YY, Pu X, Zhang JY, Zhang HL, Liang JJ, Tang YW, Li W, Long H, Deng GB. Genetic and molecular characterization of determinant of six-rowed spike of barley carrying vrs1.a4. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3225-3236. [PMID: 34132847 DOI: 10.1007/s00122-021-03887-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 06/08/2021] [Indexed: 06/12/2023]
Abstract
Decisive role of reduced vrs1 transcript abundance in six-rowed spike of barley carrying vrs1.a4 was genetically proved and its potential causes were preliminarily analyzed. Six-rowed spike 1 (vrs1) is the major determinant of the six-rowed spike phenotype of barley (Hordeum vulgare L.). Alleles of Vrs1 have been extensively investigated. Allele vrs1.a4 in six-rowed barley is unique in that it has the same coding sequence as Vrs1.b4 in two-rowed barley. The determinant of row-type in vrs1.a4 carriers has not been experimentally identified. Here, we identified Vrs1.b4 in two-rowed accessions and vrs1.a4 in six-rowed accessions from the Qinghai-Tibet Plateau at high frequency. Genetic analyses revealed a single nuclear gene accounting for row-type alteration in these accessions. Physical mapping identified a 0.08-cM (~ 554-kb) target interval on chromosome 2H, wherein Vrs1 was the most likely candidate gene. Further analysis of Vrs1 expression in offspring of the mapping populations or different Vrs1.b4 and vrs1.a4 lines confirmed that downregulated expression of vrs1.a4 causes six-rowed spike. Regulatory sequence analysis found a single 'TA' dinucleotide deletion in vrs1.a4 carriers within a 'TA' tandem-repeat-enriched region ~ 1 kb upstream of the coding region. DNA methylation levels did not correspond to the expression difference and therefore did not affect Vrs1 expression. More evidence is needed to verify the causal link between the 'TA' deletion and the downregulated Vrs1 expression and hence the six-rowed spike phenotype.
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Affiliation(s)
- Jin-Hui Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
- Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhen-Mei Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Xue-Bing Qiu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Li-Lan Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Shui-Yang Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Tao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Yan-Yan Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Xi Pu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Juan-Yu Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Hai-Li Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Jun-Jun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China
| | - Ya-Wei Tang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850000, Tibet, China
| | - Wei Li
- Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China.
| | - Guang-Bing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, China.
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97
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Wang Y, Dai A, Chen Y, Tang T. Gene Body Methylation Confers Transcription Robustness in Mangroves During Long-Term Stress Adaptation. FRONTIERS IN PLANT SCIENCE 2021; 12:733846. [PMID: 34630483 PMCID: PMC8493031 DOI: 10.3389/fpls.2021.733846] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/02/2021] [Indexed: 05/23/2023]
Abstract
Whether induced epigenetic changes contribute to long-term adaptation remains controversial. Recent studies indicate that environmentally cued changes in gene body methylation (gbM) can facilitate acclimatization. However, such changes are often associated with genetic variation and their contribution to long-term stress adaptation remains unclear. Using whole-genome bisulfite sequencing, we examined evolutionary gains and losses of gbM in mangroves that adapted to extreme intertidal environments. We treated mangrove seedlings with salt stress, and investigated expression changes in relation with stress-induced or evolutionarily-acquired gbM changes. Evolution and function of gbM was compared with that of genetic variation. Mangroves gained much more gbM than their terrestrial relatives, mainly through convergent evolution. Genes that convergently gained gbM during evolution are more likely to become methylated in response to salt stress in species where they are normally not marked. Stress-induced and evolutionarily convergent gains of gbM both correlate with reduction in expression variation, conferring genome-wide expression robustness under salt stress. Moreover, convergent gbM evolution is uncoupled with convergent sequence evolution. Our findings suggest that transgenerational inheritance of acquired gbM helps environmental canalization of gene expression, facilitating long-term stress adaptation of mangroves in the face of a severe reduction in genetic diversity.
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Affiliation(s)
- Yushuai Wang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Aimei Dai
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Yiping Chen
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tian Tang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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98
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Abstract
Plant intra-individual and inter-individual variation can be determined by the epigenome, a set of covalent modifications of DNA and chromatin that can alter genome structure and activity without changes to the genome sequence. The epigenome of plant cells is plastic, that is, it can change in response to internal or external cues, such as during development or due to environmental changes, to create a memory of such events. Ongoing advances in technologies to read and write epigenomic patterns with increasing resolution, scale and precision are enabling the extent of plant epigenome variation to be more extensively characterized and functionally interrogated. In this Review, we discuss epigenome dynamics and variation within plants during development and in response to environmental changes, including stress, as well as between plants. We review known or potential functions of such plasticity and emphasize the importance of investigating the causality of epigenomic changes. Finally, we discuss emerging technologies that may underpin future research into plant epigenome plasticity.
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Affiliation(s)
- James P B Lloyd
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
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99
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Smolikova G, Strygina K, Krylova E, Leonova T, Frolov A, Khlestkina E, Medvedev S. Transition from Seeds to Seedlings: Hormonal and Epigenetic Aspects. PLANTS (BASEL, SWITZERLAND) 2021; 10:1884. [PMID: 34579418 PMCID: PMC8467299 DOI: 10.3390/plants10091884] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/02/2021] [Accepted: 09/08/2021] [Indexed: 01/21/2023]
Abstract
Transition from seed to seedling is one of the critical developmental steps, dramatically affecting plant growth and viability. Before plants enter the vegetative phase of their ontogenesis, massive rearrangements of signaling pathways and switching of gene expression programs are required. This results in suppression of the genes controlling seed maturation and activation of those involved in regulation of vegetative growth. At the level of hormonal regulation, these events are controlled by the balance of abscisic acid and gibberellins, although ethylene, auxins, brassinosteroids, cytokinins, and jasmonates are also involved. The key players include the members of the LAFL network-the transcription factors LEAFY COTYLEDON1 and 2 (LEC 1 and 2), ABSCISIC ACID INSENSITIVE3 (ABI3), and FUSCA3 (FUS3), as well as DELAY OF GERMINATION1 (DOG1). They are the negative regulators of seed germination and need to be suppressed before seedling development can be initiated. This repressive signal is mediated by chromatin remodeling complexes-POLYCOMB REPRESSIVE COMPLEX 1 and 2 (PRC1 and PRC2), as well as PICKLE (PKL) and PICKLE-RELATED2 (PKR2) proteins. Finally, epigenetic methylation of cytosine residues in DNA, histone post-translational modifications, and post-transcriptional downregulation of seed maturation genes with miRNA are discussed. Here, we summarize recent updates in the study of hormonal and epigenetic switches involved in regulation of the transition from seed germination to the post-germination stage.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Ksenia Strygina
- Postgenomic Studies Laboratory, Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190121 St. Petersburg, Russia; (K.S.); (E.K.); (E.K.)
| | - Ekaterina Krylova
- Postgenomic Studies Laboratory, Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190121 St. Petersburg, Russia; (K.S.); (E.K.); (E.K.)
| | - Tatiana Leonova
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany; (T.L.); (A.F.)
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Andrej Frolov
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany; (T.L.); (A.F.)
- Department of Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Elena Khlestkina
- Postgenomic Studies Laboratory, Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources, 190121 St. Petersburg, Russia; (K.S.); (E.K.); (E.K.)
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University, 199034 St. Petersburg, Russia;
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Bennett M, Cleaves K, Hewezi T. Expression Patterns of DNA Methylation and Demethylation Genes during Plant Development and in Response to Phytohormones. Int J Mol Sci 2021; 22:ijms22189681. [PMID: 34575855 PMCID: PMC8470644 DOI: 10.3390/ijms22189681] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 01/02/2023] Open
Abstract
DNA methylation and demethylation precisely and effectively modulate gene expression during plant growth and development and in response to stress. However, expression profiles of genes involved in DNA methylation and demethylation during plant development and their responses to phytohormone treatments remain largely unknown. We characterized the spatiotemporal expression patterns of genes involved in de novo methylation, methyl maintenance, and active demethylation in roots, shoots, and reproductive organs using β-glucuronidase (GUS) reporter lines. Promoters of DNA demethylases were generally more highly active at the mature root tissues, whereas the promoters of genes involved in DNA methylation were more highly active at fast-growing root tissues. The promoter activity also implies that methylation status in shoot apex, leaf primordia, floral organs, and developing embryos is under tight equilibrium through the activity of genes involved in DNA methylation and demethylation. The promoter activity of DNA methylation and demethylation-related genes in response to various phytohormone treatments revealed that phytohormones can alter DNA methylation status in specific and redundant ways. Overall, our results illustrate that DNA methylation and demethylation pathways act synergistically and antagonistically in various tissues and in response to phytohormone treatments and point to the existence of hormone-linked methylome regulation mechanisms that may contribute to tissue differentiation and development.
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