1
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Sutherland CA, Prigozhin DM, Monroe JG, Krasileva KV. High allelic diversity in Arabidopsis NLRs is associated with distinct genomic features. EMBO Rep 2024; 25:2306-2322. [PMID: 38528170 PMCID: PMC11093987 DOI: 10.1038/s44319-024-00122-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/27/2024] Open
Abstract
Plants rely on Nucleotide-binding, Leucine-rich repeat Receptors (NLRs) for pathogen recognition. Highly variable NLRs (hvNLRs) show remarkable intraspecies diversity, while their low-variability paralogs (non-hvNLRs) are conserved between ecotypes. At a population level, hvNLRs provide new pathogen-recognition specificities, but the association between allelic diversity and genomic and epigenomic features has not been established. Our investigation of NLRs in Arabidopsis Col-0 has revealed that hvNLRs show higher expression, less gene body cytosine methylation, and closer proximity to transposable elements than non-hvNLRs. hvNLRs show elevated synonymous and nonsynonymous nucleotide diversity and are in chromatin states associated with an increased probability of mutation. Diversifying selection maintains variability at a subset of codons of hvNLRs, while purifying selection maintains conservation at non-hvNLRs. How these features are established and maintained, and whether they contribute to the observed diversity of hvNLRs is key to understanding the evolution of plant innate immune receptors.
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Affiliation(s)
- Chandler A Sutherland
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA
| | - Daniil M Prigozhin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - J Grey Monroe
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Ksenia V Krasileva
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, 94720, USA.
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2
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Herrick J. DNA Damage, Genome Stability, and Adaptation: A Question of Chance or Necessity? Genes (Basel) 2024; 15:520. [PMID: 38674454 PMCID: PMC11049855 DOI: 10.3390/genes15040520] [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] [Received: 03/17/2024] [Revised: 04/14/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
DNA damage causes the mutations that are the principal source of genetic variation. DNA damage detection and repair mechanisms therefore play a determining role in generating the genetic diversity on which natural selection acts. Speciation, it is commonly assumed, occurs at a rate set by the level of standing allelic diversity in a population. The process of speciation is driven by a combination of two evolutionary forces: genetic drift and ecological selection. Genetic drift takes place under the conditions of relaxed selection, and results in a balance between the rates of mutation and the rates of genetic substitution. These two processes, drift and selection, are necessarily mediated by a variety of mechanisms guaranteeing genome stability in any given species. One of the outstanding questions in evolutionary biology concerns the origin of the widely varying phylogenetic distribution of biodiversity across the Tree of Life and how the forces of drift and selection contribute to shaping that distribution. The following examines some of the molecular mechanisms underlying genome stability and the adaptive radiations that are associated with biodiversity and the widely varying species richness and evenness in the different eukaryotic lineages.
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Affiliation(s)
- John Herrick
- Independent Researcher at 3, Rue des Jeûneurs, 75002 Paris, France
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3
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Horvath R, Minadakis N, Bourgeois Y, Roulin AC. The evolution of transposable elements in Brachypodium distachyon is governed by purifying selection, while neutral and adaptive processes play a minor role. eLife 2024; 12:RP93284. [PMID: 38606833 PMCID: PMC11014726 DOI: 10.7554/elife.93284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2024] Open
Abstract
Understanding how plants adapt to changing environments and the potential contribution of transposable elements (TEs) to this process is a key question in evolutionary genomics. While TEs have recently been put forward as active players in the context of adaptation, few studies have thoroughly investigated their precise role in plant evolution. Here, we used the wild Mediterranean grass Brachypodium distachyon as a model species to identify and quantify the forces acting on TEs during the adaptation of this species to various conditions, across its entire geographic range. Using sequencing data from more than 320 natural B. distachyon accessions and a suite of population genomics approaches, we reveal that putatively adaptive TE polymorphisms are rare in wild B. distachyon populations. After accounting for changes in past TE activity, we show that only a small proportion of TE polymorphisms evolved neutrally (<10%), while the vast majority of them are under moderate purifying selection regardless of their distance to genes. TE polymorphisms should not be ignored when conducting evolutionary studies, as they can be linked to adaptation. However, our study clearly shows that while they have a large potential to cause phenotypic variation in B. distachyon, they are not favored during evolution and adaptation over other types of mutations (such as point mutations) in this species.
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Affiliation(s)
- Robert Horvath
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
| | - Nikolaos Minadakis
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
| | - Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRDMontpellierFrance
- University of PortsmouthPortsmouthUnited Kingdom
| | - Anne C Roulin
- Department of Plant and Microbial Biology, University of ZurichZurichSwitzerland
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4
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Nabi Z, Manzoor S, Nabi SU, Wani TA, Gulzar H, Farooq M, Arya VM, Baloch FS, Vlădulescu C, Popescu SM, Mansoor S. Pattern-Triggered Immunity and Effector-Triggered Immunity: crosstalk and cooperation of PRR and NLR-mediated plant defense pathways during host-pathogen interactions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:587-604. [PMID: 38737322 PMCID: PMC11087456 DOI: 10.1007/s12298-024-01452-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 05/14/2024]
Abstract
The elucidation of the molecular basis underlying plant-pathogen interactions is imperative for the development of sustainable resistance strategies against pathogens. Plants employ a dual-layered immunological detection and response system wherein cell surface-localized Pattern Recognition Receptors (PRRs) and intracellular Nucleotide-Binding Leucine-Rich Repeat Receptors (NLRs) play pivotal roles in initiating downstream signalling cascades in response to pathogen-derived chemicals. Pattern-Triggered Immunity (PTI) is associated with PRRs and is activated by the recognition of conserved molecular structures, known as Pathogen-Associated Molecular Patterns. When PTI proves ineffective due to pathogenic effectors, Effector-Triggered Immunity (ETI) frequently confers resistance. In ETI, host plants utilize NLRs to detect pathogen effectors directly or indirectly, prompting a rapid and more robust defense response. Additionally epigenetic mechanisms are participating in plant immune memory. Recently developed technologies like CRISPR/Cas9 helps in exposing novel prospects in plant pathogen interactions. In this review we explore the fascinating crosstalk and cooperation between PRRs and NLRs. We discuss epigenomic processes and CRISPR/Cas9 regulating immune response in plants and recent findings that shed light on the coordination of these defense layers. Furthermore, we also have discussed the intricate interactions between the salicylic acid and jasmonic acid signalling pathways in plants, offering insights into potential synergistic interactions that would be harnessed for the development of novel and sustainable resistance strategies against diverse group of pathogens.
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Affiliation(s)
- Zarka Nabi
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Subaya Manzoor
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Sajad Un Nabi
- ICAR-Central Institute of Temperate Horticulture, Srinagar, 191132 India
| | | | - Humira Gulzar
- Division of Plant Pathology, FOA-SKUAST-K, Wadura, 193201 India
| | - Mehreena Farooq
- Division of Plant Pathology, FOH-SKUAST-K, Shalimar, Srinagar, 190025 India
| | - Vivak M. Arya
- Division of Soil Science and Agriculture Chemistry, Sher-e-Kashmir University of Agricultural Sciences and Technology, Jammu, India
| | - Faheem Shehzad Baloch
- Department of Biotechnology, Faculty of Science, Mersin University, 33100 Yenişehir, Mersin Turkey
| | - Carmen Vlădulescu
- Department of Biology and Environmental Engineering, University of Craiova, A. I. Cuza 13, 200585 Craiova, Romania
| | - Simona Mariana Popescu
- Department of Biology and Environmental Engineering, University of Craiova, A. I. Cuza 13, 200585 Craiova, Romania
| | - Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, Jeju, 63243 Republic of Korea
- Subtropical/Tropical Organism Gene Bank, Jeju National University, Jeju, 63243 Republic of Korea
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5
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Kakoulidou I, Piecyk RS, Meyer RC, Kuhlmann M, Gutjahr C, Altmann T, Johannes F. Mapping parental DMRs predictive of local and distal methylome remodeling in epigenetic F1 hybrids. Life Sci Alliance 2024; 7:e202402599. [PMID: 38290756 PMCID: PMC10828516 DOI: 10.26508/lsa.202402599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/01/2024] Open
Abstract
F1 hybrids derived from a cross between two inbred parental lines often display widespread changes in DNA methylation and gene expression patterns relative to their parents. An emerging challenge is to understand how parental epigenomic differences contribute to these events. Here, we generated a large mapping panel of F1 epigenetic hybrids, whose parents are isogenic but variable in their DNA methylation patterns. Using a combination of multi-omic profiling and epigenetic mapping strategies we show that differentially methylated regions in parental pericentromeres act as major reorganizers of hybrid methylomes and transcriptomes, even in the absence of genetic variation. These parental differentially methylated regions are associated with hybrid methylation remodeling events at thousands of target regions throughout the genome, both locally (in cis) and distally (in trans). Many of these distally-induced methylation changes lead to nonadditive expression of nearby genes and associate with phenotypic heterosis. Our study highlights the pleiotropic potential of parental pericentromeres in the functional remodeling of hybrid genomes and phenotypes.
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Affiliation(s)
- Ioanna Kakoulidou
- https://ror.org/02kkvpp62 Plant Epigenomics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Robert S Piecyk
- https://ror.org/02kkvpp62 Plant Epigenomics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
| | - Rhonda C Meyer
- https://ror.org/02skbsp27 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Markus Kuhlmann
- https://ror.org/02skbsp27 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Caroline Gutjahr
- Plant Genetics, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Thomas Altmann
- https://ror.org/02skbsp27 Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Frank Johannes
- https://ror.org/02kkvpp62 Plant Epigenomics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Munich, Germany
- https://ror.org/02kkvpp62 Institute of Advanced Studies, Technical University of Munich, Munich, Germany
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6
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Jiang J, Xu YC, Zhang ZQ, Chen JF, Niu XM, Hou XH, Li XT, Wang L, Zhang YE, Ge S, Guo YL. Forces driving transposable element load variation during Arabidopsis range expansion. THE PLANT CELL 2024; 36:840-862. [PMID: 38036296 PMCID: PMC10980350 DOI: 10.1093/plcell/koad296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/25/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Genetic load refers to the accumulated and potentially life-threatening deleterious mutations in populations. Understanding the mechanisms underlying genetic load variation of transposable element (TE) insertion, a major large-effect mutation, during range expansion is an intriguing question in biology. Here, we used 1,115 global natural accessions of Arabidopsis (Arabidopsis thaliana) to study the driving forces of TE load variation during its range expansion. TE load increased with range expansion, especially in the recently established Yangtze River basin population. Effective population size, which explains 62.0% of the variance in TE load, high transposition rate, and selective sweeps contributed to TE accumulation in the expanded populations. We genetically mapped and identified multiple candidate causal genes and TEs, and revealed the genetic architecture of TE load variation. Overall, this study reveals the variation in TE genetic load during Arabidopsis expansion and highlights the causes of TE load variation from the perspectives of both population genetics and quantitative genetics.
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Affiliation(s)
- Juan Jiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Zhi-Qin Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Fu Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Min Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xing-Hui Hou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xin-Tong Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Wang
- Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yong E Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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7
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Cranz-Mileva S, Reilly E, Chalhoub N, Patel R, Atanassova T, Cao W, Ellison C, Zaratiegui M. Transposon Removal Reveals Their Adaptive Fitness Contribution. Genome Biol Evol 2024; 16:evae010. [PMID: 38245838 PMCID: PMC10836971 DOI: 10.1093/gbe/evae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 01/22/2024] Open
Abstract
Transposable elements are molecular parasites that persist in their host genome by generating new copies to outpace natural selection. Transposable elements exert a large influence on host genome evolution, in some cases providing adaptive changes. Here we measure the fitness effect of the transposable element insertions in the fission yeast Schizosaccharomyces pombe type strain by removing all insertions of its only native transposable element family, the long terminal repeat retrotransposon Tf2. We show that Tf2 elements provide a positive fitness contribution to its host. Tf2 ablation results in changes to the regulation of a mitochondrial gene and, consistently, the fitness effect are sensitive to growth conditions. We propose that Tf2 influences host fitness in a directed manner by dynamically rewiring the transcriptional response to metabolic stress.
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Affiliation(s)
- Susanne Cranz-Mileva
- Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Eve Reilly
- Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Noor Chalhoub
- Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Rohan Patel
- Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Tania Atanassova
- Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Weihuan Cao
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Christopher Ellison
- Department of Genetics, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Mikel Zaratiegui
- Department of Molecular Biology and Biochemistry, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
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8
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Hassan AH, Mokhtar MM, El Allali A. Transposable elements: multifunctional players in the plant genome. FRONTIERS IN PLANT SCIENCE 2024; 14:1330127. [PMID: 38239225 PMCID: PMC10794571 DOI: 10.3389/fpls.2023.1330127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/06/2023] [Indexed: 01/22/2024]
Abstract
Transposable elements (TEs) are indispensable components of eukaryotic genomes that play diverse roles in gene regulation, recombination, and environmental adaptation. Their ability to mobilize within the genome leads to gene expression and DNA structure changes. TEs serve as valuable markers for genetic and evolutionary studies and facilitate genetic mapping and phylogenetic analysis. They also provide insight into how organisms adapt to a changing environment by promoting gene rearrangements that lead to new gene combinations. These repetitive sequences significantly impact genome structure, function and evolution. This review takes a comprehensive look at TEs and their applications in biotechnology, particularly in the context of plant biology, where they are now considered "genomic gold" due to their extensive functionalities. The article addresses various aspects of TEs in plant development, including their structure, epigenetic regulation, evolutionary patterns, and their use in gene editing and plant molecular markers. The goal is to systematically understand TEs and shed light on their diverse roles in plant biology.
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Affiliation(s)
- Asmaa H. Hassan
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Agricultural Genetic Engineering Research Institute, Agriculture Research Center, Giza, Egypt
| | - Morad M. Mokhtar
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Agricultural Genetic Engineering Research Institute, Agriculture Research Center, Giza, Egypt
| | - Achraf El Allali
- Bioinformatics Laboratory, College of Computing, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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9
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Contreras-Garrido A, Galanti D, Movilli A, Becker C, Bossdorf O, Drost HG, Weigel D. Transposon dynamics in the emerging oilseed crop Thlaspi arvense. PLoS Genet 2024; 20:e1011141. [PMID: 38295109 PMCID: PMC10881000 DOI: 10.1371/journal.pgen.1011141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 02/21/2024] [Accepted: 01/17/2024] [Indexed: 02/02/2024] Open
Abstract
Genome evolution is partly driven by the mobility of transposable elements (TEs) which often leads to deleterious effects, but their activity can also facilitate genetic novelty and catalyze local adaptation. We explored how the intraspecific diversity of TE polymorphisms might contribute to the broad geographic success and adaptive capacity of the emerging oil crop Thlaspi arvense (field pennycress). We classified the TE inventory based on a high-quality genome assembly, estimated the age of retrotransposon TE families and comprehensively assessed their mobilization potential. A survey of 280 accessions from 12 regions across the Northern hemisphere allowed us to quantify over 90,000 TE insertion polymorphisms (TIPs). Their distribution mirrored the genetic differentiation as measured by single nucleotide polymorphisms (SNPs). The number and types of mobile TE families vary substantially across populations, but there are also shared patterns common to all accessions. Ty3/Athila elements are the main drivers of TE diversity in T. arvense populations, while a single Ty1/Alesia lineage might be particularly important for transcriptome divergence. The number of retrotransposon TIPs is associated with variation at genes related to epigenetic regulation, including an apparent knockout mutation in BROMODOMAIN AND ATPase DOMAIN-CONTAINING PROTEIN 1 (BRAT1), while DNA transposons are associated with variation at the HSP19 heat shock protein gene. We propose that the high rate of mobilization activity can be harnessed for targeted gene expression diversification, which may ultimately present a toolbox for the potential use of transposition in breeding and domestication of T. arvense.
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Affiliation(s)
| | - Dario Galanti
- Plant Evolutionary Ecology, University of Tübingen, Tübingen, Germany
| | - Andrea Movilli
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Claude Becker
- LMU Biocenter, Faculty of Biology, Ludwig Maximilians University Munich, Martinsried, Germany
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, University of Tübingen, Tübingen, Germany
| | - Hajk-Georg Drost
- Computational Biology Group, Max Planck Institute for Biology Tübingen,Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
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10
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Kirov I. Toward Transgene-Free Transposon-Mediated Biological Mutagenesis for Plant Breeding. Int J Mol Sci 2023; 24:17054. [PMID: 38069377 PMCID: PMC10706983 DOI: 10.3390/ijms242317054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
Genetic diversity is a key factor for plant breeding. The birth of novel genic and genomic variants is also crucial for plant adaptation in nature. Therefore, the genomes of almost all living organisms possess natural mutagenic mechanisms. Transposable elements (TEs) are a major mutagenic force driving genetic diversity in wild plants and modern crops. The relatively rare TE transposition activity during the thousand-year crop domestication process has led to the phenotypic diversity of many cultivated species. The utilization of TE mutagenesis by artificial and transient acceleration of their activity in a controlled mode is an attractive foundation for a novel type of mutagenesis called TE-mediated biological mutagenesis. Here, I focus on TEs as mutagenic sources for plant breeding and discuss existing and emerging transgene-free approaches for TE activation in plants. Furthermore, I also review the non-randomness of TE insertions in a plant genome and the molecular and epigenetic factors involved in shaping TE insertion preferences. Additionally, I discuss the molecular mechanisms that prevent TE transpositions in germline plant cells (e.g., meiocytes, pollen, egg and embryo cells, and shoot apical meristem), thereby reducing the chances of TE insertion inheritance. Knowledge of these mechanisms can expand the TE activation toolbox using novel gene targeting approaches. Finally, the challenges and future perspectives of plant populations with induced novel TE insertions (iTE plant collections) are discussed.
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Affiliation(s)
- Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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11
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Kreiner JM, Hnatovska S, Stinchcombe JR, Wright SI. Quantifying the role of genome size and repeat content in adaptive variation and the architecture of flowering time in Amaranthus tuberculatus. PLoS Genet 2023; 19:e1010865. [PMID: 38150485 PMCID: PMC10775983 DOI: 10.1371/journal.pgen.1010865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/09/2024] [Accepted: 12/11/2023] [Indexed: 12/29/2023] Open
Abstract
Genome size variation, largely driven by repeat content, is poorly understood within and among populations, limiting our understanding of its significance for adaptation. Here we characterize intraspecific variation in genome size and repeat content across 186 individuals of Amaranthus tuberculatus, a ubiquitous native weed that shows flowering time adaptation to climate across its range and in response to agriculture. Sequence-based genome size estimates vary by up to 20% across individuals, consistent with the considerable variability in the abundance of transposable elements, unknown repeats, and rDNAs across individuals. The additive effect of this variation has important phenotypic consequences-individuals with more repeats, and thus larger genomes, show slower flowering times and growth rates. However, compared to newly-characterized gene copy number and polygenic nucleotide changes underlying variation in flowering time, we show that genome size is a marginal contributor. Differences in flowering time are reflected by genome size variation across sexes and marginally, habitats, while polygenic variation and a gene copy number variant within the ATP synthesis pathway show consistently stronger environmental clines than genome size. Repeat content nonetheless shows non-neutral distributions across the genome, and across latitudinal and environmental gradients, demonstrating the numerous governing processes that in turn influence quantitative genetic variation for phenotypes key to plant adaptation.
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Affiliation(s)
- Julia M. Kreiner
- Department of Botany, Biodiversity Research Centre, University of British Columbia
- Department of Ecology & Evolutionary Biology, University of Toronto
| | - Solomiya Hnatovska
- Department of Ecology & Evolutionary Biology, University of Toronto
- Department of Molecular Genetics, University of Toronto
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12
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Hisanaga T, Romani F, Wu S, Kowar T, Wu Y, Lintermann R, Fridrich A, Cho CH, Chaumier T, Jamge B, Montgomery SA, Axelsson E, Akimcheva S, Dierschke T, Bowman JL, Fujiwara T, Hirooka S, Miyagishima SY, Dolan L, Tirichine L, Schubert D, Berger F. The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes. Curr Biol 2023; 33:4367-4380.e9. [PMID: 37738971 DOI: 10.1016/j.cub.2023.08.073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 06/19/2023] [Accepted: 08/24/2023] [Indexed: 09/24/2023]
Abstract
The mobility of transposable elements (TEs) contributes to evolution of genomes. Their uncontrolled activity causes genomic instability; therefore, expression of TEs is silenced by host genomes. TEs are marked with DNA and H3K9 methylation, which are associated with silencing in flowering plants, animals, and fungi. However, in distantly related groups of eukaryotes, TEs are marked by H3K27me3 deposited by the Polycomb repressive complex 2 (PRC2), an epigenetic mark associated with gene silencing in flowering plants and animals. The direct silencing of TEs by PRC2 has so far only been shown in one species of ciliates. To test if PRC2 silences TEs in a broader range of eukaryotes, we generated mutants with reduced PRC2 activity and analyzed the role of PRC2 in extant species along the lineage of Archaeplastida and in the diatom P. tricornutum. In this diatom and the red alga C. merolae, a greater proportion of TEs than genes were repressed by PRC2, whereas a greater proportion of genes than TEs were repressed by PRC2 in bryophytes. In flowering plants, TEs contained potential cis-elements recognized by transcription factors and associated with neighbor genes as transcriptional units repressed by PRC2. Thus, silencing of TEs by PRC2 is observed not only in Archaeplastida but also in diatoms and ciliates, suggesting that PRC2 deposited H3K27me3 to silence TEs in the last common ancestor of eukaryotes. We hypothesize that during the evolution of Archaeplastida, TE fragments marked with H3K27me3 were selected to shape transcriptional regulation, controlling networks of genes regulated by PRC2.
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Affiliation(s)
- Tetsuya Hisanaga
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Facundo Romani
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Shuangyang Wu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Teresa Kowar
- Epigenetics of Plants, Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Yue Wu
- Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
| | - Ruth Lintermann
- Epigenetics of Plants, Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany
| | - Arie Fridrich
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Chung Hyun Cho
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea
| | | | - Bhagyshree Jamge
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Sean A Montgomery
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030 Vienna, Austria
| | - Elin Axelsson
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Svetlana Akimcheva
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Tom Dierschke
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - John L Bowman
- School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia; ARC Centre of Excellence for Plant Success in Nature and Agriculture, Monash University, Clayton, Melbourne, VIC 3800, Australia
| | - Takayuki Fujiwara
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Shunsuke Hirooka
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, Graduate University for Advanced Studies, SOKENDAI, Mishima, Shizuoka 411-8540, Japan
| | - Liam Dolan
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France
| | - Daniel Schubert
- Epigenetics of Plants, Institute of Biology, Freie Universität Berlin, 14195 Berlin, Germany.
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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13
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Kang M, Wu H, Liu H, Liu W, Zhu M, Han Y, Liu W, Chen C, Song Y, Tan L, Yin K, Zhao Y, Yan Z, Lou S, Zan Y, Liu J. The pan-genome and local adaptation of Arabidopsis thaliana. Nat Commun 2023; 14:6259. [PMID: 37802986 PMCID: PMC10558531 DOI: 10.1038/s41467-023-42029-4] [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] [Received: 12/18/2022] [Accepted: 09/27/2023] [Indexed: 10/08/2023] Open
Abstract
Arabidopsis thaliana serves as a model species for investigating various aspects of plant biology. However, the contribution of genomic structural variations (SVs) and their associate genes to the local adaptation of this widely distribute species remains unclear. Here, we de novo assemble chromosome-level genomes of 32 A. thaliana ecotypes and determine that variable genes expand the gene pool in different ecotypes and thus assist local adaptation. We develop a graph-based pan-genome and identify 61,332 SVs that overlap with 18,883 genes, some of which are highly involved in ecological adaptation of this species. For instance, we observe a specific 332 bp insertion in the promoter region of the HPCA1 gene in the Tibet-0 ecotype that enhances gene expression, thereby promotes adaptation to alpine environments. These findings augment our understanding of the molecular mechanisms underlying the local adaptation of A. thaliana across diverse habitats.
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Affiliation(s)
- Minghui Kang
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Haolin Wu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Huanhuan Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Wenyu Liu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Mingjia Zhu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Yu Han
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Wei Liu
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chunlin Chen
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yan Song
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Luna Tan
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Kangqun Yin
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yusen Zhao
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Zhen Yan
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Shangling Lou
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Yanjun Zan
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266000, China.
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-ecosystem, College of Ecology, Lanzhou University, Lanzhou, 730000, China.
- Key Laboratory of Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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14
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Merkulov P, Gvaramiya S, Dudnikov M, Komakhin R, Omarov M, Kocheshkova A, Konstantinov Z, Soloviev A, Karlov G, Divashuk M, Kirov I. Cas9-targeted Nanopore sequencing rapidly elucidates the transposition preferences and DNA methylation profiles of mobile elements in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:2242-2261. [PMID: 37555565 DOI: 10.1111/jipb.13555] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/27/2023] [Accepted: 08/08/2023] [Indexed: 08/10/2023]
Abstract
Transposable element insertions (TEIs) are an important source of genomic innovation by contributing to plant adaptation, speciation, and the production of new varieties. The often large, complex plant genomes make identifying TEIs from short reads difficult and expensive. Moreover, rare somatic insertions that reflect mobilome dynamics are difficult to track using short reads. To address these challenges, we combined Cas9-targeted Nanopore sequencing (CANS) with the novel pipeline NanoCasTE to trace both genetically inherited and somatic TEIs in plants. We performed CANS of the EVADÉ (EVD) retrotransposon in wild-type Arabidopsis thaliana and rapidly obtained up to 40× sequence coverage. Analysis of hemizygous T-DNA insertion sites and genetically inherited insertions of the EVD transposon in the ddm1 (decrease in DNA methylation 1) genome uncovered the crucial role of DNA methylation in shaping EVD insertion preference. We also investigated somatic transposition events of the ONSEN transposon family, finding that genes that are downregulated during heat stress are preferentially targeted by ONSENs. Finally, we detected hypomethylation of novel somatic insertions for two ONSENs. CANS and NanoCasTE are effective tools for detecting TEIs and exploring mobilome organization in plants in response to stress and in different genetic backgrounds, as well as screening T-DNA insertion mutants and transgenic plants.
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Affiliation(s)
- Pavel Merkulov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Sofya Gvaramiya
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - Maxim Dudnikov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Roman Komakhin
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - Murad Omarov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - Alina Kocheshkova
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - Zakhar Konstantinov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - Alexander Soloviev
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
- All-Russia Center for Plant Quarantine, Ramenski, 140150, Russia
- N.V. Tsitsin Main Botanical Garden of the Russian Academy of Sciences, Moscow, 127276, Russia
| | - Gennady Karlov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - Mikhail Divashuk
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - Ilya Kirov
- All-Russia Research Institute of Agricultural Biotechnology, Moscow, 127550, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
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15
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Baduel P, Sasaki E. The genetic basis of epigenetic variation and its consequences for adaptation. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102409. [PMID: 37451221 DOI: 10.1016/j.pbi.2023.102409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/28/2023] [Accepted: 06/01/2023] [Indexed: 07/18/2023]
Abstract
Recent population genomic studies in plants have shed new light on natural epigenetic variation by identifying key genetic determinants, "trans modifiers," that influence epigenetic states genome-wide and their interplay with environmental factors. Here, we review this progress by focusing on the epigenetic control of transposition and life-cycle transitions to highlight the ecological consequences of this genetic architecture and its evolutionary significance. This knowledge provides new opportunities to address long-standing questions about the establishment of environment-associated epigenetic variation and its relevance in adaptation.
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Affiliation(s)
- Pierre Baduel
- Institut de Biologie de l'École Normale Supérieure (IBENS), ENS, PSL University, CNRS, 46 rue d'Ulm, Paris 75005, France
| | - Eriko Sasaki
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka Nishi-ku, Fukuoka 819-0395, Japan.
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16
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Pulido M, Casacuberta JM. Transposable element evolution in plant genome ecosystems. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102418. [PMID: 37459733 DOI: 10.1016/j.pbi.2023.102418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/22/2023] [Accepted: 06/20/2023] [Indexed: 09/18/2023]
Abstract
The relationship of transposable elements (TEs) with their host genomes has usually been seen as an arms race between TEs and their host genomes. Consequently, TEs are supposed to amplify by bursts of transposition, when the TE escapes host surveillance, followed by long periods of TE quiescence and efficient host control. Recent data obtained from an increasing number of assembled plant genomes and resequencing population datasets show that TE dynamics is more complex and varies among TE families and their host genomes. This variation ranges from large genomes that accommodate large TE populations to genomes that are very active in TE elimination, and from inconspicuous elements with very low activity to elements with high transposition and elimination rates. The dynamics of each TE family results from a long history of interaction with the host in a genome populated by many other TE families, very much like an evolving ecosystem.
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Affiliation(s)
- Marc Pulido
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain
| | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus UAB, Cerdanyola del Vallès, 08193 Barcelona, Spain.
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17
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Duhamel M, Hood ME, Rodríguez de la Vega RC, Giraud T. Dynamics of transposable element accumulation in the non-recombining regions of mating-type chromosomes in anther-smut fungi. Nat Commun 2023; 14:5692. [PMID: 37709766 PMCID: PMC10502011 DOI: 10.1038/s41467-023-41413-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
In the absence of recombination, the number of transposable elements (TEs) increases due to less efficient selection, but the dynamics of such TE accumulations are not well characterized. Leveraging a dataset of 21 independent events of recombination cessation of different ages in mating-type chromosomes of Microbotryum fungi, we show that TEs rapidly accumulated in regions lacking recombination, but that TE content reached a plateau at ca. 50% of occupied base pairs by 1.5 million years following recombination suppression. The same TE superfamilies have expanded in independently evolved non-recombining regions, in particular rolling-circle replication elements (Helitrons). Long-terminal repeat (LTR) retrotransposons of the Copia and Ty3 superfamilies also expanded, through transposition bursts (distinguished from gene conversion based on LTR divergence), with both non-recombining regions and autosomes affected, suggesting that non-recombining regions constitute TE reservoirs. This study improves our knowledge of genome evolution by showing that TEs can accumulate through bursts, following non-linear decelerating dynamics.
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Affiliation(s)
- Marine Duhamel
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France.
- Evolution der Pflanzen und Pilze, Ruhr-Universität Bochum, Universitätsstraße 150, 44780, Bochum, Germany.
| | - Michael E Hood
- Department of Biology, Amherst College, 01002-5000, Amherst, MA, USA
| | - Ricardo C Rodríguez de la Vega
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France
| | - Tatiana Giraud
- Ecologie Systématique Evolution, IDEEV, CNRS, Université Paris-Saclay, AgroParisTech, Bâtiment 680, 12 route RD128, 91190, Gif-sur-Yvette, France
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18
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Rehman S, Ahmad Z, Ramakrishnan M, Kalendar R, Zhuge Q. Regulation of plant epigenetic memory in response to cold and heat stress: towards climate resilient agriculture. Funct Integr Genomics 2023; 23:298. [PMID: 37700098 DOI: 10.1007/s10142-023-01219-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 09/14/2023]
Abstract
Plants have evolved to adapt and grow in hot and cold climatic conditions. Some also adapt to daily and seasonal temperature changes. Epigenetic modifications play an important role in regulating plant tolerance under such conditions. DNA methylation and post-translational modifications of histone proteins influence gene expression during plant developmental stages and under stress conditions, including cold and heat stress. While short-term modifications are common, some modifications may persist and result in stress memory that can be inherited by subsequent generations. Understanding the mechanisms of epigenomes responding to stress and the factors that trigger stress memory is crucial for developing climate-resilient agriculture, but such an integrated view is currently limited. This review focuses on the plant epigenetic stress memory during cold and heat stress. It also discusses the potential of machine learning to modify stress memory through epigenetics to develop climate-resilient crops.
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Affiliation(s)
- Shamsur Rehman
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, China
| | - Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, China
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, Viikinkaari 1, FI-00014 University of Helsinki, Helsinki, Finland.
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan.
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China.
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19
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Lozano-Arce D, García T, Gonzalez-Garcia LN, Guyot R, Chacón-Sánchez MI, Duitama J. Selection signatures and population dynamics of transposable elements in lima bean. Commun Biol 2023; 6:803. [PMID: 37532823 PMCID: PMC10397206 DOI: 10.1038/s42003-023-05144-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 07/13/2023] [Indexed: 08/04/2023] Open
Abstract
The domestication process in lima bean (Phaseolus lunatus L.) involves two independent events, within the Mesoamerican and Andean gene pools. This makes lima bean an excellent model to understand convergent evolution. The mechanisms of adaptation followed by Mesoamerican and Andean landraces are largely unknown. Genes related to these adaptations can be selected by identification of selective sweeps within gene pools. Previous genetic analyses in lima bean have relied on Single Nucleotide Polymorphism (SNP) loci, and have ignored transposable elements (TEs). Here we show the analysis of whole-genome sequencing data from 61 lima bean accessions to characterize a genomic variation database including TEs and SNPs, to associate selective sweeps with variable TEs and to predict candidate domestication genes. A small percentage of genes under selection are shared among gene pools, suggesting that domestication followed different genetic avenues in both gene pools. About 75% of TEs are located close to genes, which shows their potential to affect gene functions. The genetic structure inferred from variable TEs is consistent with that obtained from SNP markers, suggesting that TE dynamics can be related to the demographic history of wild and domesticated lima bean and its adaptive processes, in particular selection processes during domestication.
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Affiliation(s)
- Daniela Lozano-Arce
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Tatiana García
- Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Laura Natalia Gonzalez-Garcia
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, CIRAD, 34394, Montpellier, France
| | - Romain Guyot
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, CIRAD, 34394, Montpellier, France
| | - Maria Isabel Chacón-Sánchez
- Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
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20
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Auge G, Hankofer V, Groth M, Antoniou-Kourounioti R, Ratikainen I, Lampei C. Plant environmental memory: implications, mechanisms and opportunities for plant scientists and beyond. AOB PLANTS 2023; 15:plad032. [PMID: 37415723 PMCID: PMC10321398 DOI: 10.1093/aobpla/plad032] [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: 11/14/2022] [Accepted: 06/01/2023] [Indexed: 07/08/2023]
Abstract
Plants are extremely plastic organisms. They continuously receive and integrate environmental information and adjust their growth and development to favour fitness and survival. When this integration of information affects subsequent life stages or the development of subsequent generations, it can be considered an environmental memory. Thus, plant memory is a relevant mechanism by which plants respond adaptively to different environments. If the cost of maintaining the response is offset by its benefits, it may influence evolutionary trajectories. As such, plant memory has a sophisticated underlying molecular mechanism with multiple components and layers. Nonetheless, when mathematical modelling is combined with knowledge of ecological, physiological, and developmental effects as well as molecular mechanisms as a tool for understanding plant memory, the combined potential becomes unfathomable for the management of plant communities in natural and agricultural ecosystems. In this review, we summarize recent advances in the understanding of plant memory, discuss the ecological requirements for its evolution, outline the multilayered molecular network and mechanisms required for accurate and fail-proof plant responses to variable environments, point out the direct involvement of the plant metabolism and discuss the tremendous potential of various types of models to further our understanding of the plant's environmental memory. Throughout, we emphasize the use of plant memory as a tool to unlock the secrets of the natural world.
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Affiliation(s)
| | - Valentin Hankofer
- Institute of Biochemical Plant Pathology, Helmholtz Munich, Ingolstädter Landstraße 1, 85764 Oberschleißheim, Neuherberg, Germany
| | - Martin Groth
- Institute of Functional Epigenetics, Helmholtz Munich, Ingolstädter Landstraße 1, 85764 Oberschleißheim, Neuherberg, Germany
| | - Rea Antoniou-Kourounioti
- School of Molecular Biosciences, University of Glasgow, Sir James Black Building, University Ave, Glasgow G12 8QQ, UK
| | - Irja Ratikainen
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Realfagbygget, NO-7491 Trondheim, Norway
| | - Christian Lampei
- Department of Biology (FB17), Plant Ecology and Geobotany Group, University of Marburg, Karl-von-Frisch-Straße 8, 35032 Marburg, Germany
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21
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Yoosefzadeh Najafabadi M, Hesami M, Rajcan I. Unveiling the Mysteries of Non-Mendelian Heredity in Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:1956. [PMID: 37653871 PMCID: PMC10221147 DOI: 10.3390/plants12101956] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 07/30/2023]
Abstract
Mendelian heredity is the cornerstone of plant breeding and has been used to develop new varieties of plants since the 19th century. However, there are several breeding cases, such as cytoplasmic inheritance, methylation, epigenetics, hybrid vigor, and loss of heterozygosity (LOH), where Mendelian heredity is not applicable, known as non-Mendelian heredity. This type of inheritance can be influenced by several factors besides the genetic architecture of the plant and its breeding potential. Therefore, exploring various non-Mendelian heredity mechanisms, their prevalence in plants, and the implications for plant breeding is of paramount importance to accelerate the pace of crop improvement. In this review, we examine the current understanding of non-Mendelian heredity in plants, including the mechanisms, inheritance patterns, and applications in plant breeding, provide an overview of the various forms of non-Mendelian inheritance (including epigenetic inheritance, cytoplasmic inheritance, hybrid vigor, and LOH), explore insight into the implications of non-Mendelian heredity in plant breeding, and the potential it holds for future research.
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Affiliation(s)
| | | | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada; (M.Y.N.); (M.H.)
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22
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Brestovitsky A, Iwasaki M, Cho J, Adulyanukosol N, Paszkowski J, Catoni M. Specific suppression of long terminal repeat retrotransposon mobilization in plants. PLANT PHYSIOLOGY 2023; 191:2245-2255. [PMID: 36583226 PMCID: PMC10069891 DOI: 10.1093/plphys/kiac605] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/16/2022] [Accepted: 11/18/2022] [Indexed: 05/19/2023]
Abstract
The tissue culture passage necessary for the generation of transgenic plants induces genome instability. This instability predominantly involves the uncontrolled mobilization of LTR retrotransposons (LTR-TEs), which are the most abundant class of mobile genetic elements in plant genomes. Here, we demonstrate that in conditions inductive for high LTR-TE mobilization, like abiotic stress in Arabidopsis (Arabidopsis thaliana) and callus culture in rice (Oryza sativa), application of the reverse transcriptase (RT) inhibitor known as Tenofovir substantially affects LTR-TE RT activity without interfering with plant development. We observed that Tenofovir reduces extrachromosomal DNA accumulation and prevents new genomic integrations of the active LTR-TE ONSEN in heat-stressed Arabidopsis seedlings, and transposons of O. sativa 17 and 19 (Tos17 and Tos19) in rice calli. In addition, Tenofovir allows the recovery of plants free from new LTR-TE insertions. We propose the use of Tenofovir as a tool for studies of LTR-TE transposition and for limiting genetic instabilities of plants derived from tissue culture.
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Affiliation(s)
- Anna Brestovitsky
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
| | - Mayumi Iwasaki
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
- Department of Plant Biology, University of Geneva, Geneva CH-1211, Switzerland
| | - Jungnam Cho
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | | | - Jerzy Paszkowski
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
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23
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Yushkova E, Moskalev A. Transposable elements and their role in aging. Ageing Res Rev 2023; 86:101881. [PMID: 36773759 DOI: 10.1016/j.arr.2023.101881] [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: 11/17/2022] [Revised: 01/16/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
Transposable elements (TEs) are an important part of eukaryotic genomes. The role of somatic transposition in aging, carcinogenesis, and other age-related diseases has been determined. This review discusses the fundamental properties of TEs and their complex interactions with cellular processes, which are crucial for understanding the diverse effects of their activity on the genetics and epigenetics of the organism. The interactions of TEs with recombination, replication, repair, and chromosomal regulation; the ability of TEs to maintain a balance between their own activity and repression, the involvement of TEs in the creation of new or alternative genes, the expression of coding/non-coding RNA, and the role in DNA damage and modification of regulatory networks are reviewed. The contribution of the derepressed TEs to age-dependent effects in individual cells/tissues in different organisms was assessed. Conflicting information about TE activity under stress as well as theories of aging mechanisms related to TEs is discussed. On the one hand, transposition activity in response to stressors can lead to organisms acquiring adaptive innovations of great importance for evolution at the population level. On the other hand, the TE expression can cause decreased longevity and stress tolerance at the individual level. The specific features of TE effects on aging processes in germline and soma and the ways of their regulation in cells are highlighted. Recent results considering somatic mutations in normal human and animal tissues are indicated, with the emphasis on their possible functional consequences. In the context of aging, the correlation between somatic TE activation and age-related changes in the number of proteins required for heterochromatin maintenance and longevity regulation was analyzed. One of the original features of this review is a discussion of not only effects based on the TEs insertions and the associated consequences for the germline cell dynamics and somatic genome, but also the differences between transposon- and retrotransposon-mediated structural genome changes and possible phenotypic characteristics associated with aging and various age-related pathologies. Based on the analysis of published data, a hypothesis about the influence of the species-specific features of number, composition, and distribution of TEs on aging dynamics of different animal genomes was formulated.
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Affiliation(s)
- Elena Yushkova
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Center, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russian Federation
| | - Alexey Moskalev
- Laboratory of Geroprotective and Radioprotective Technologies, Institute of Biology, Komi Science Center, Ural Branch, Russian Academy of Sciences, 28 Kommunisticheskaya st., 167982 Syktyvkar, Russian Federation; Laboratory of Genetics and Epigenetics of Aging, Russian Clinical Research Center for Gerontology, Pirogov Russian National Research Medical University, Moscow 129226, Russian Federation; Longaevus Technologies, London, UK.
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24
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Monroe JG. Potential and limits of (mal)adaptive mutation rate plasticity in plants. THE NEW PHYTOLOGIST 2023; 237:2020-2026. [PMID: 36444532 DOI: 10.1111/nph.18640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Genetic mutations provide the heritable material for plant adaptation to their environments. At the same time, the environment can affect the mutation rate across plant genomes. However, the extent to which environmental plasticity in mutation rates can facilitate or hinder adaptation remains a longstanding and unresolved question. Emerging discoveries of mechanisms affecting mutation rate variability provide opportunities to consider this question in a new light. Links between chromatin states, transposable elements, and DNA repair suggest cases of adaptive mutation rate plasticity could occur. Yet, numerous evolutionary and biological forces are expected to limit the impact of any such mutation rate plasticity on adaptive evolution. Persistent uncertainty about the significance of mutation rate plasticity on adaptation motivates new experimental and theoretical research relevant to understanding plant responses in changing environments.
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Affiliation(s)
- J Grey Monroe
- Department of Plant Sciences, University of California, Davis, Davis, CA, 95616, USA
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25
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Berger F, Muegge K, Richards EJ. Seminars in cell and development biology on histone variants remodelers of H2A variants associated with heterochromatin. Semin Cell Dev Biol 2023; 135:93-101. [PMID: 35249811 PMCID: PMC9440159 DOI: 10.1016/j.semcdb.2022.02.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 01/04/2023]
Abstract
Variants of the histone H2A occupy distinct locations in the genome. There is relatively little known about the mechanisms responsible for deposition of specific H2A variants. Notable exceptions are chromatin remodelers that control the dynamics of H2A.Z at promoters. Here we review the steps that identified the role of a specific class of chromatin remodelers, including LSH and DDM1 that deposit the variants macroH2A in mammals and H2A.W in plants, respectively. The function of these remodelers in heterochromatin is discussed together with their multiple roles in genome stability.
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Affiliation(s)
- Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
| | - Kathrin Muegge
- Epigenetics Section, Frederick National Laboratory for Cancer Research in the Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA.
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26
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Gallusci P, Agius DR, Moschou PN, Dobránszki J, Kaiserli E, Martinelli F. Deep inside the epigenetic memories of stressed plants. TRENDS IN PLANT SCIENCE 2023; 28:142-153. [PMID: 36404175 DOI: 10.1016/j.tplants.2022.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Recent evidence sheds light on the peculiar type of plant intelligence. Plants have developed complex molecular networks that allow them to remember, choose, and make decisions depending on the stress stimulus, although they lack a nervous system. Being sessile, plants can exploit these networks to optimize their resources cost-effectively and maximize their fitness in response to multiple environmental stresses. Even more interesting is the capability to transmit this experience to the next generation(s) through epigenetic modifications that add to the classical genetic inheritance. In this opinion article, we present concepts and perspectives regarding the capabilities of plants to sense, perceive, remember, re-elaborate, respond, and to some extent transmit to their progeny information to adapt more efficiently to climate change.
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Affiliation(s)
- Philippe Gallusci
- Ecophysiologie et Génomique Fonctionnelle de la Vigne (EGFV), University of Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, Villenave d'Ornon, France
| | - Dolores R Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta; Ġ.F. Abela Junior College, Ġuzè Debono Square, Msida, Malta
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden; Department of Biology, University of Crete, Heraklion, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Judit Dobránszki
- Centre for Agricultural Genomics and Biotechnology, University of Debrecen, Debrecen, Hungary
| | - Eirini Kaiserli
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
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27
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Gui S, Martinez-Rivas FJ, Wen W, Meng M, Yan J, Usadel B, Fernie AR. Going broad and deep: sequencing-driven insights into plant physiology, evolution, and crop domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:446-459. [PMID: 36534120 DOI: 10.1111/tpj.16070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
Deep sequencing is a term that has become embedded in the plant genomic literature in recent years and with good reason. A torrent of (largely) high-quality genomic and transcriptomic data has been collected and most of this has been publicly released. Indeed, almost 1000 plant genomes have been reported (www.plabipd.de) and the 2000 Plant Transcriptomes Project has long been completed. The EarthBioGenome project will dwarf even these milestones. That said, massive progress in understanding plant physiology, evolution, and crop domestication has been made by sequencing broadly (across a species) as well as deeply (within a single individual). We will outline the current state of the art in genome and transcriptome sequencing before we briefly review the most visible of these broad approaches, namely genome-wide association and transcriptome-wide association studies, as well as the compilation of pangenomes. This will include both (i) the most commonly used methods reliant on single nucleotide polymorphisms and short InDels and (ii) more recent examples which consider structural variants. We will subsequently present case studies exemplifying how their application has brought insight into either plant physiology or evolution and crop domestication. Finally, we will provide conclusions and an outlook as to the perspective for the extension of such approaches to different species, tissues, and biological processes.
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Affiliation(s)
- Songtao Gui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | | | - Weiwei Wen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Minghui Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Björn Usadel
- IBG-4 Bioinformatics, Forschungszentrum Jülich, Wilhelm Johnen Str, BioSc, 52428, Jülich, Germany
- Institute for Biological Data Science, CEPLAS, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476, Germany
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28
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Genome-wide analysis of heat stress-stimulated transposon mobility in the human fungal pathogen Cryptococcus deneoformans. Proc Natl Acad Sci U S A 2023; 120:e2209831120. [PMID: 36669112 PMCID: PMC9942834 DOI: 10.1073/pnas.2209831120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
We recently reported transposon mutagenesis as a significant driver of spontaneous mutations in the human fungal pathogen Cryptococcus deneoformans during murine infection. Mutations caused by transposable element (TE) insertion into reporter genes were dramatically elevated at high temperatures (37° vs. 30°) in vitro, suggesting that heat stress stimulates TE mobility in the Cryptococcus genome. To explore the genome-wide impact of TE mobilization, we generated transposon accumulation lines by in vitro passage of C. deneoformans strain XL280α for multiple generations at both 30° and at the host-relevant temperature of 37°. Utilizing whole-genome sequencing, we identified native TE copies and mapped multiple de novo TE insertions in these lines. Movements of the T1 DNA transposon occurred at both temperatures with a strong bias for insertion between gene-coding regions. By contrast, the Tcn12 retrotransposon integrated primarily within genes and movement occurred exclusively at 37°. In addition, we observed a dramatic amplification in copy number of the Cnl1 (Cryptococcus neoformans LINE-1) retrotransposon in subtelomeric regions under heat-stress conditions. Comparing TE mutations to other sequence variations detected in passaged lines, the increase in genomic changes at elevated temperatures was primarily due to mobilization of the retroelements Tcn12 and Cnl1. Finally, we found multiple TE movements (T1, Tcn12, and Cnl1) in the genomes of single C. deneoformans isolates recovered from infected mice, providing evidence that mobile elements are likely to facilitate microevolution and rapid adaptation during infection.
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29
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Yaish MW, Sunkar R, Liu J, Varotto S. Editorial: Epigenetic modifications associated with abiotic and biotic stresses in plants: An implication for understanding plant evolution, volume II. FRONTIERS IN PLANT SCIENCE 2023; 13:1117063. [PMID: 36684734 PMCID: PMC9859721 DOI: 10.3389/fpls.2022.1117063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Mahmoud W. Yaish
- Department of Biology, College of Sciences, Sultan Qaboos University, Muscat, Oman
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
| | - Junzhong Liu
- School of Life Sciences, Yunnan University, Kunming, China
| | - Serena Varotto
- Department of Agronomy Animal Food Natural Resources and Environment, University of Padua, Legnaro, Italy
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30
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Wang Y, Liu Y, Qu S, Liang W, Sun L, Ci D, Ren Z, Fan LM, Qian W. Nitrogen starvation induces genome-wide activation of transposable elements in Arabidopsis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2374-2384. [PMID: 36178606 DOI: 10.1111/jipb.13376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Nitrogen (N) availability is a major limiting factor for plant growth and agricultural productivity. Although the gene regulation network in response to N starvation has been extensively studied, it remains unknown whether N starvation has an impact on the activity of transposable elements (TEs). Here, we report that TEs can be transcriptionally activated in Arabidopsis under N starvation conditions. Through genetic screening of idm1-14 suppressors, we cloned GLU1, which encodes a glutamate synthase that catalyzes the synthesis of glutamate in the primary N assimilation pathway. We found that glutamate synthase 1 (GLU1) and its functional homologs GLU2 and glutamate transport 1 (GLT1) are redundantly required for TE silencing, suggesting that N metabolism can regulate TE activity. Transcriptome and methylome analyses revealed that N starvation results in genome-wide TE activation without inducing obvious alteration of DNA methylation. Genetic analysis indicated that N starvation-induced TE activation is also independent of other well-established epigenetic mechanisms, including histone methylation and heterochromatin decondensation. Our results provide new insights into the regulation of TE activity under stressful environments in planta.
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Affiliation(s)
- Yue Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Yi Liu
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Shaofeng Qu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Wenjie Liang
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Linhua Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Dong Ci
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, China
| | - Zhitong Ren
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Liu-Min Fan
- School of Life Sciences, Peking University, Beijing, 100871, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, China
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31
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De Kort H, Legrand S, Honnay O, Buckley J. Transposable elements maintain genome-wide heterozygosity in inbred populations. Nat Commun 2022; 13:7022. [PMID: 36396660 PMCID: PMC9672359 DOI: 10.1038/s41467-022-34795-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022] Open
Abstract
Elevated levels of inbreeding increase the risk of inbreeding depression and extinction, yet many inbred species are widespread, suggesting that inbreeding has little impact on evolutionary potential. Here, we explore the potential for transposable elements (TEs) to maintain genetic variation in functional genomic regions under extreme inbreeding. Capitalizing on the mixed mating system of Arabidopsis lyrata, we assess genome-wide heterozygosity and signatures of selection at single nucleotide polymorphisms near transposable elements across an inbreeding gradient. Under intense inbreeding, we find systematically elevated heterozygosity downstream of several TE superfamilies, associated with signatures of balancing selection. In addition, we demonstrate increased heterozygosity in stress-responsive genes that consistently occur downstream of TEs. We finally reveal that TE superfamilies are associated with specific signatures of selection that are reproducible across independent evolutionary lineages of A. lyrata. Together, our study provides an important hypothesis for the success of self-fertilizing species.
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Affiliation(s)
- Hanne De Kort
- grid.5596.f0000 0001 0668 7884Plant Conservation and Population Biology, University of Leuven, Kasteelpark Arenberg 31-2435, BE-3001 Leuven, Belgium
| | - Sylvain Legrand
- grid.503422.20000 0001 2242 6780Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000 Lille, France
| | - Olivier Honnay
- grid.5596.f0000 0001 0668 7884Plant Conservation and Population Biology, University of Leuven, Kasteelpark Arenberg 31-2435, BE-3001 Leuven, Belgium
| | - James Buckley
- grid.11201.330000 0001 2219 0747School of Biological and Marine Sciences, University of Plymouth, Plymouth, PL1 2BT UK
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32
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Hämälä T, Ning W, Kuittinen H, Aryamanesh N, Savolainen O. Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of Arabidopsis lyrata. eLife 2022; 11:83115. [PMID: 36306157 PMCID: PMC9616567 DOI: 10.7554/elife.83115] [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: 08/31/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022] Open
Abstract
Understanding what factors influence plastic and genetic variation is valuable for predicting how organisms respond to changes in the selective environment. Here, using gene expression and DNA methylation as molecular phenotypes, we study environmentally induced variation among Arabidopsis lyrata plants grown at lowland and alpine field sites. Our results show that gene expression is highly plastic, as many more genes are differentially expressed between the field sites than between populations. These environmentally responsive genes evolve under strong selective constraint – the strength of purifying selection on the coding sequence is high, while the rate of adaptive evolution is low. We find, however, that positive selection on cis-regulatory variants has likely contributed to the maintenance of genetically variable environmental responses, but such variants segregate only between distantly related populations. In contrast to gene expression, DNA methylation at genic regions is largely insensitive to the environment, and plastic methylation changes are not associated with differential gene expression. Besides genes, we detect environmental effects at transposable elements (TEs): TEs at the high-altitude field site have higher expression and methylation levels, suggestive of a broad-scale TE activation. Compared to the lowland population, plants native to the alpine environment harbor an excess of recent TE insertions, and we observe that specific TE families are enriched within environmentally responsive genes. Our findings provide insight into selective forces shaping plastic and genetic variation. We also highlight how plastic responses at TEs can rapidly create novel heritable variation in stressful conditions.
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Affiliation(s)
- Tuomas Hämälä
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Weixuan Ning
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Helmi Kuittinen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Nader Aryamanesh
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Outi Savolainen
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
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33
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Klein SP, Anderson SN. The evolution and function of transposons in epigenetic regulation in response to the environment. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102277. [PMID: 35961279 DOI: 10.1016/j.pbi.2022.102277] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/21/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Transposable elements (TEs) make up a major proportion of plant genomes. Despite their prevalence genome-wide, TEs are often tossed aside as "junk DNA" since they rarely cause phenotypes, and epigenetic mechanisms silence TEs to prevent them from causing deleterious mutations through movement. While this bleak picture of TEs in genomes is true on average, a growing number of examples across many plant species point to TEs as drivers of phenotypic diversity and novel stress responses. Examples of TE-influenced phenotypes illustrate the many ways that novel transposition events can alter local gene expression and how this relates to potential variation in plant responses to environmental stress. Since TE families and insertions at the locus level lack evolutionary conservation, advancements in the field will require TE experts across diverse species to identify and utilize TE variation in their own systems as a means of crop improvement.
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Affiliation(s)
- Stephanie P Klein
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Sarah N Anderson
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.
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34
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Thieme M, Brêchet A, Bourgeois Y, Keller B, Bucher E, Roulin AC. Experimentally heat-induced transposition increases drought tolerance in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2022; 236:182-194. [PMID: 35715973 PMCID: PMC9544478 DOI: 10.1111/nph.18322] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 06/10/2022] [Indexed: 05/14/2023]
Abstract
Eukaryotic genomes contain a vast diversity of transposable elements (TEs). Formerly often described as selfish and parasitic DNA sequences, TEs are now recognised as a source of genetic diversity and powerful drivers of evolution. However, because their mobility is tightly controlled by the host, studies experimentally assessing how fast TEs may mediate the emergence of adaptive traits are scarce. We exposed Arabidopsis thaliana high-copy TE lines (hcLines) with up to c. eight-fold increased copy numbers of the heat-responsive ONSEN TE to drought as a straightforward and ecologically highly relevant selection pressure. We provide evidence for increased drought tolerance in five out of the 23 tested hcLines and further pinpoint one of the causative mutations to an exonic insertion of ONSEN in the ribose-5-phosphate-isomerase 2 gene. The resulting loss-of-function mutation caused a decreased rate of photosynthesis, plant size and water consumption. Overall, we show that the heat-induced transposition of a low-copy TE increases phenotypic diversity and leads to the emergence of drought-tolerant individuals in A. thaliana. This is one of the rare empirical examples substantiating the adaptive potential of mobilised stress-responsive TEs in eukaryotes. Our work demonstrates the potential of TE-mediated loss-of-function mutations in stress adaptation.
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Affiliation(s)
- Michael Thieme
- Department of Plant and Microbial BiologyUniversity of Zurich8008ZürichSwitzerland
| | - Arthur Brêchet
- Department of Environmental Sciences – BotanyUniversity of Basel4056BaselSwitzerland
| | - Yann Bourgeois
- School of Biological SciencesUniversity of PortsmouthPO1 2DTPortsmouthUK
| | - Bettina Keller
- Department of Plant and Microbial BiologyUniversity of Zurich8008ZürichSwitzerland
| | | | - Anne C. Roulin
- Department of Plant and Microbial BiologyUniversity of Zurich8008ZürichSwitzerland
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35
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Abstract
Transposons were once thought to be junk repetitive DNA in the genome. However, their importance gradually became apparent as it became clear that they regulate gene expression, which is essential for organisms to survive, and that they are important factors in the driving force of evolution. Since there are multiple transposons in the genomes of all organisms, transposons have likely been activated and increased in copy number throughout their long history. This review focuses on environmental stress as a factor in transposon activation, paying particular attention to transposons in plants that are activated by environmental stresses. It is now known that plants respond to environmental stress in various ways, and correspondingly, many transposons respond to stress. The relationship between environmental stress and transposons is reviewed, including the mechanisms of their activation and the effects of transposon activation on host plants.
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36
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De Kort H, Toivainen T, Van Nieuwerburgh F, Andrés J, Hytönen TP, Honnay O. Signatures of polygenic adaptation align with genome-wide methylation patterns in wild strawberry plants. THE NEW PHYTOLOGIST 2022; 235:1501-1514. [PMID: 35575945 DOI: 10.1111/nph.18225] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Epigenetic inheritance can drive adaptive evolution independently of DNA sequence variation. However, to what extent epigenetic variation represents an autonomous evolutionary force remains largely elusive. Through gene ontology and comparative analyses of genomic and epigenomic variation of wild strawberry plants raised in distinct drought settings, we characterised genome-wide covariation between single nucleotide polymorphisms (SNPs) and differentially methylated cytosines (DMCs). Covariation between SNPs and DMCs was independent of genomic proximity, but instead associated with fitness-related processes such as stress responses, genome regulation and reproduction. We expected this functional SNP-DMC covariation to be driven by adaptive evolution canalising SNP and DMC variation, but instead observed significantly lower covariation with DMCs for adaptive rather than for neutral SNPs. Drought-induced DMCs frequently co-varied with tens of SNPs, suggesting high genomic redundancy as a broad potential basis for polygenic adaptation of gene expression. Our findings suggest that stress-responsive DMCs initially co-vary with many SNPs under increased environmental stress, and that natural selection acting upon several of these SNPs subsequently reduces standing covariation with stress-responsive DMCs. Our study supports DNA methylation profiles that represent complex quantitative traits rather than autonomous evolutionary forces. We provide a conceptual framework for polygenic regulation and adaptation shaping genome-wide methylation patterns in plants.
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Affiliation(s)
- Hanne De Kort
- Plant Conservation and Population Biology, University of Leuven, Kasteelpark Arenberg 31-2435, BE-3001, Leuven, Belgium
| | - Tuomas Toivainen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Latokartanonkaari 7, 00790, Helsinki, Finland
| | | | - Javier Andrés
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Latokartanonkaari 7, 00790, Helsinki, Finland
| | - Timo P Hytönen
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Latokartanonkaari 7, 00790, Helsinki, Finland
| | - Olivier Honnay
- Plant Conservation and Population Biology, University of Leuven, Kasteelpark Arenberg 31-2435, BE-3001, Leuven, Belgium
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Veitia RA. Who ever thought genetic mutations were random? TRENDS IN PLANT SCIENCE 2022; 27:733-735. [PMID: 35307269 DOI: 10.1016/j.tplants.2022.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/28/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
In a recent study of de novo mutations in arabidopsis (Arabidopsis thaliana), Monroe et al. found a lower mutation frequency inside gene bodies and certain essential genes, shattering the long-standing idea that mutations are entirely random across the genome. Here I highlight the molecular nonrandomness of mutations and the type of gene affected.
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Affiliation(s)
- Reiner A Veitia
- Université de Paris, Paris 752052, France; Institut Jacques Monod, CNRS UMR7592, Paris 75013, France; Université Paris Saclay, 91190 Gif-sur-Yvette, France; Institut de Biologie François Jacob, Commissariat à l'Energie Atomique et aux Energies Alternatives/CEA, 92 265 Fontenay aux Roses, France.
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38
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Cai X, Lin R, Liang J, King GJ, Wu J, Wang X. Transposable element insertion: a hidden major source of domesticated phenotypic variation in Brassica rapa. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1298-1310. [PMID: 35278263 PMCID: PMC9241368 DOI: 10.1111/pbi.13807] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/16/2022] [Accepted: 03/01/2022] [Indexed: 05/20/2023]
Abstract
Transposable element (TE) is prevalent in plant genomes. However, studies on their impact on phenotypic evolution in crop plants are relatively rare, because systematically identifying TE insertions within a species has been a challenge. Here, we present a novel approach for uncovering TE insertion polymorphisms (TIPs) using pan-genome analysis combined with population-scale resequencing, and we adopt this pipeline to retrieve TIPs in a Brassica rapa germplasm collection. We found that 23% of genes within the reference Chiifu-401-42 genome harbored TIPs. TIPs tended to have large transcriptional effects, including modifying gene expression levels and altering gene structure by introducing new introns. Among 524 diverse accessions, TIPs broadly influenced genes related to traits and acted a crucial role in the domestication of B. rapa morphotypes. As examples, four specific TIP-containing genes were found to be candidates that potentially involved in various climatic conditions, promoting the formation of diverse vegetable crops in B. rapa. Our work reveals the hitherto hidden TIPs implicated in agronomic traits and highlights their widespread utility in studies of crop domestication.
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Affiliation(s)
- Xu Cai
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Runmao Lin
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Jianli Liang
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Graham J. King
- Southern Cross Plant ScienceSouthern Cross UniversityLismoreNSWAustralia
| | - Jian Wu
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
| | - Xiaowu Wang
- Institute of Vegetables and FlowersChinese Academy of Agricultural SciencesBeijingChina
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Kwolek K, Kędzierska P, Hankiewicz M, Mirouze M, Panaud O, Grzebelus D, Macko‐Podgórni A. Diverse and mobile: eccDNA-based identification of carrot low-copy-number LTR retrotransposons active in callus cultures. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1811-1828. [PMID: 35426957 PMCID: PMC9324142 DOI: 10.1111/tpj.15773] [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: 12/21/2021] [Revised: 03/15/2022] [Accepted: 03/29/2022] [Indexed: 05/28/2023]
Abstract
Long terminal repeat retrotransposons (LTR-RTs) are mobilized via an RNA intermediate using a 'copy and paste' mechanism, and account for the majority of repetitive DNA in plant genomes. As a side effect of mobilization, the formation of LTR-RT-derived extrachromosomal circular DNAs (eccDNAs) occurs. Thus, high-throughput sequencing of eccDNA can be used to identify active LTR-RTs in plant genomes. Despite the release of a reference genome assembly, carrot LTR-RTs have not yet been thoroughly characterized. LTR-RTs are abundant and diverse in the carrot genome. We identified 5976 carrot LTR-RTs, 2053 and 1660 of which were attributed to Copia and Gypsy superfamilies, respectively. They were further classified into lineages, families and subfamilies. More diverse LTR-RT lineages, i.e. lineages comprising many low-copy-number subfamilies, were more frequently associated with genic regions. Certain LTR-RT lineages have been recently active in Daucus carota. In particular, low-copy-number LTR-RT subfamilies, e.g. those belonging to the DcAle lineage, have significantly contributed to carrot genome diversity as a result of continuing activity. We utilized eccDNA sequencing to identify and characterize two DcAle subfamilies, Alex1 and Alex3, active in carrot callus. We documented 14 and 32 de novo insertions of Alex1 and Alex3, respectively, which were positioned in non-repetitive regions.
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Affiliation(s)
- Kornelia Kwolek
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
| | - Patrycja Kędzierska
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
| | - Magdalena Hankiewicz
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
| | - Marie Mirouze
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVDUniversité de PerpignanVia Domitia, 52 Avenue Paul Alduy66 860Perpignan CedexFrance
- IRD, EMR IRD‐CNRS‐UPVD ‘MANGO’Université de PerpignanPerpignanFrance
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVDUniversité de PerpignanVia Domitia, 52 Avenue Paul Alduy66 860Perpignan CedexFrance
| | - Dariusz Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
| | - Alicja Macko‐Podgórni
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
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40
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Chen TH, Winefield C. Comprehensive analysis of both long and short read transcriptomes of a clonal and a seed-propagated model species reveal the prerequisites for transcriptional activation of autonomous and non-autonomous transposons in plants. Mob DNA 2022; 13:16. [PMID: 35549762 PMCID: PMC9097378 DOI: 10.1186/s13100-022-00271-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 04/13/2022] [Indexed: 11/29/2022] Open
Abstract
Background Transposable element (TE) transcription is a precursor to its mobilisation in host genomes. However, the characteristics of expressed TE loci, the identification of self-competent transposon loci contributing to new insertions, and the genomic conditions permitting their mobilisation remain largely unknown. Results Using Vitis vinifera embryogenic callus, we explored the impact of biotic stressors on transposon transcription through the exposure of the callus to live cultures of an endemic grapevine yeast, Hanseniaspora uvarum. We found that only 1.7–2.5% of total annotated TE loci were transcribed, of which 5–10% of these were full-length, and the expressed TE loci exhibited a strong location bias towards expressed genes. These trends in transposon transcription were also observed in RNA-seq data from Arabidopsis thaliana wild-type plants but not in epigenetically compromised Arabidopsis ddm1 mutants. Moreover, differentially expressed TE loci in the grapevine tended to share expression patterns with co-localised differentially expressed genes. Utilising nanopore cDNA sequencing, we found a strong correlation between the inclusion of intronic TEs in gene transcripts and the presence of premature termination codons in these transcripts. Finally, we identified low levels of full-length transcripts deriving from structurally intact TE loci in the grapevine model. Conclusion Our observations in two disparate plant models representing clonally and seed propagated plant species reveal a closely connected transcriptional relationship between TEs and co-localised genes, particularly when epigenetic silencing is not compromised. We found that the stress treatment alone was insufficient to induce large-scale full-length transcription from structurally intact TE loci, a necessity for non-autonomous and autonomous mobilisation. Supplementary Information The online version contains supplementary material available at 10.1186/s13100-022-00271-5.
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Affiliation(s)
- Ting-Hsuan Chen
- Department of Wine, Food, and Molecular Biosciences, Lincoln University, Lincoln, 7647, New Zealand.,Present address: The New Zealand Institute for Plant and Food Research Ltd, Lincoln, 7608, New Zealand
| | - Christopher Winefield
- Department of Wine, Food, and Molecular Biosciences, Lincoln University, Lincoln, 7647, New Zealand.
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Sasaki T, Ro K, Caillieux E, Manabe R, Bohl-Viallefond G, Baduel P, Colot V, Kakutani T, Quadrana L. Fast co-evolution of anti-silencing systems shapes the invasiveness of Mu-like DNA transposons in eudicots. EMBO J 2022; 41:e110070. [PMID: 35285528 PMCID: PMC9016345 DOI: 10.15252/embj.2021110070] [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: 10/28/2021] [Revised: 02/10/2022] [Accepted: 02/15/2022] [Indexed: 01/09/2023] Open
Abstract
Transposable elements (TEs) constitute a major threat to genome stability and are therefore typically silenced by epigenetic mechanisms. In response, some TEs have evolved counteracting systems to suppress epigenetic silencing. In the model plant Arabidopsis thaliana, two such anti-silencing systems have been identified and found to be mediated by the VANC DNA-binding proteins encoded by VANDAL transposons. Here, we show that anti-silencing systems have rapidly diversified since their origin in eudicots by gaining and losing VANC-containing domains, such as DUF1985, DUF287, and Ulp1, as well as target sequence motifs. We further demonstrate that these motifs determine anti-silencing specificity by sequence, density, and helical periodicity. Moreover, such rapid diversification yielded at least 10 distinct VANC-induced anti-silencing systems in Arabidopsis. Strikingly, anti-silencing of non-autonomous VANDALs, which can act as reservoirs of 24-nt small RNAs, is critical to prevent the demise of cognate autonomous TEs and to ensure their propagation. Our findings illustrate how complex co-evolutionary dynamics between TEs and host suppression pathways have shaped the emergence of new epigenetic control mechanisms.
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Affiliation(s)
- Taku Sasaki
- Department of Biological Sciences, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kyudo Ro
- Department of Biological Sciences, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Erwann Caillieux
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Riku Manabe
- Department of Biological Sciences, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Grégoire Bohl-Viallefond
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Pierre Baduel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, Paris, France
| | - Tetsuji Kakutani
- Department of Biological Sciences, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, Paris, France
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Specificities and Dynamics of Transposable Elements in Land Plants. BIOLOGY 2022; 11:biology11040488. [PMID: 35453688 PMCID: PMC9033089 DOI: 10.3390/biology11040488] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/10/2022] [Accepted: 03/18/2022] [Indexed: 01/27/2023]
Abstract
Simple Summary Transposable elements are dynamic components of plant genomes, and display a high diversity of lineages and distribution as the result of evolutionary driving forces and overlapping mechanisms of genetic and epigenetic regulation. They are now regarded as main contributors for genome evolution and function, and important regulators of endogenous gene expression. In this review, we survey recent progress and current challenges in the identification and classification of transposon lineages in complex plant genomes, highlighting the molecular specificities that may explain the expansion and diversification of mobile genetic elements in land plants. Abstract Transposable elements (TEs) are important components of most plant genomes. These mobile repetitive sequences are highly diverse in terms of abundance, structure, transposition mechanisms, activity and insertion specificities across plant species. This review will survey the different mechanisms that may explain the variability of TE patterns in land plants, highlighting the tight connection between TE dynamics and host genome specificities, and their co-evolution to face and adapt to a changing environment. We present the current TE classification in land plants, and describe the different levels of genetic and epigenetic controls originating from the plant, the TE itself, or external environmental factors. Such overlapping mechanisms of TE regulation might be responsible for the high diversity and dynamics of plant TEs observed in nature.
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DNA methylation-free Arabidopsis reveals crucial roles of DNA methylation in regulating gene expression and development. Nat Commun 2022; 13:1335. [PMID: 35288562 PMCID: PMC8921224 DOI: 10.1038/s41467-022-28940-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/16/2022] [Indexed: 12/17/2022] Open
Abstract
A contribution of DNA methylation to defense against invading nucleic acids and maintenance of genome integrity is uncontested; however, our understanding of the extent of involvement of this epigenetic mark in genome-wide gene regulation and plant developmental control is incomplete. Here, we knock out all five known DNA methyltransferases in Arabidopsis, generating DNA methylation-free plants. This quintuple mutant exhibits a suite of developmental defects, unequivocally demonstrating that DNA methylation is essential for multiple aspects of plant development. We show that CG methylation and non-CG methylation are required for a plethora of biological processes, including pavement cell shape, endoreduplication, cell death, flowering, trichome morphology, vasculature and meristem development, and root cell fate determination. Moreover, we find that DNA methylation has a strong dose-dependent effect on gene expression and repression of transposable elements. Taken together, our results demonstrate that DNA methylation is dispensable for Arabidopsis survival but essential for the proper regulation of multiple biological processes. Our understanding of the extent of involvement of DNA methylation in genome-wide gene regulation and plant developmental control is incomplete. Here, the authors knock out all five known DNA methyltransferases and show the developmental and gene expression changes in the DNA methylation-free Arabidopsis plants.
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44
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Catlin NS, Josephs EB. The important contribution of transposable elements to phenotypic variation and evolution. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102140. [PMID: 34883307 DOI: 10.1016/j.pbi.2021.102140] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/04/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
Transposable elements (TEs) are responsible for significant genomic variation in plants. Our understanding of the evolutionary forces shaping TE polymorphism has lagged behind other mutations because of the difficulty of accurately identifying TE polymorphism in short-read population genomic data. However, new approaches allow us to quantify TE polymorphisms in population datasets and address fundamental questions about the evolution of these polymorphisms. Here, we discuss how insertional biases shape where, when, and how often TEs insert throughout the genome. Next, we examine mechanisms by which TEs can affect phenotype. Finally, we evaluate current evidence for selection on TE polymorphisms. All together, it is clear that TEs are important, but underappreciated, contributors to intraspecific phenotypic variation, and that understanding the dynamics governing TE polymorphism is crucial for evolutionary biologists interested in the maintenance of variation.
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Affiliation(s)
- Nathan S Catlin
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA.
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA; Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, 48824, USA
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45
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Monroe JG, Srikant T, Carbonell-Bejerano P, Becker C, Lensink M, Exposito-Alonso M, Klein M, Hildebrandt J, Neumann M, Kliebenstein D, Weng ML, Imbert E, Ågren J, Rutter MT, Fenster CB, Weigel D. Mutation bias reflects natural selection in Arabidopsis thaliana. Nature 2022; 602:101-105. [PMID: 35022609 PMCID: PMC8810380 DOI: 10.1038/s41586-021-04269-6] [Citation(s) in RCA: 144] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/17/2021] [Indexed: 12/24/2022]
Abstract
Since the first half of the twentieth century, evolutionary theory has been dominated by the idea that mutations occur randomly with respect to their consequences1. Here we test this assumption with large surveys of de novo mutations in the plant Arabidopsis thaliana. In contrast to expectations, we find that mutations occur less often in functionally constrained regions of the genome-mutation frequency is reduced by half inside gene bodies and by two-thirds in essential genes. With independent genomic mutation datasets, including from the largest Arabidopsis mutation accumulation experiment conducted to date, we demonstrate that epigenomic and physical features explain over 90% of variance in the genome-wide pattern of mutation bias surrounding genes. Observed mutation frequencies around genes in turn accurately predict patterns of genetic polymorphisms in natural Arabidopsis accessions (r = 0.96). That mutation bias is the primary force behind patterns of sequence evolution around genes in natural accessions is supported by analyses of allele frequencies. Finally, we find that genes subject to stronger purifying selection have a lower mutation rate. We conclude that epigenome-associated mutation bias2 reduces the occurrence of deleterious mutations in Arabidopsis, challenging the prevailing paradigm that mutation is a directionless force in evolution.
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Affiliation(s)
- J Grey Monroe
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
- Department of Plant Sciences, University of California Davis, Davis, CA, USA.
| | - Thanvi Srikant
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | | | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Faculty of Biology, Ludwig Maximilian University, Martinsried, Germany
| | - Mariele Lensink
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Marie Klein
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Julia Hildebrandt
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Manuela Neumann
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Daniel Kliebenstein
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Mao-Lun Weng
- Department of Biology, Westfield State University, Westfield, MA, USA
| | - Eric Imbert
- ISEM, University of Montpellier, Montpellier, France
| | - Jon Ågren
- Department of Ecology and Genetics, EBC, Uppsala University, Uppsala, Sweden
| | - Matthew T Rutter
- Department of Biology, College of Charleston, Charleston, SC, USA
| | - Charles B Fenster
- Oak Lake Field Station, South Dakota State University, Brookings, SD, USA
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
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46
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Blasio F, Prieto P, Pradillo M, Naranjo T. Genomic and Meiotic Changes Accompanying Polyploidization. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11010125. [PMID: 35009128 PMCID: PMC8747196 DOI: 10.3390/plants11010125] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/24/2021] [Accepted: 12/29/2021] [Indexed: 05/04/2023]
Abstract
Hybridization and polyploidy have been considered as significant evolutionary forces in adaptation and speciation, especially among plants. Interspecific gene flow generates novel genetic variants adaptable to different environments, but it is also a gene introgression mechanism in crops to increase their agronomical yield. An estimate of 9% of interspecific hybridization has been reported although the frequency varies among taxa. Homoploid hybrid speciation is rare compared to allopolyploidy. Chromosome doubling after hybridization is the result of cellular defects produced mainly during meiosis. Unreduced gametes, which are formed at an average frequency of 2.52% across species, are the result of altered spindle organization or orientation, disturbed kinetochore functioning, abnormal cytokinesis, or loss of any meiotic division. Meiotic changes and their genetic basis, leading to the cytological diploidization of allopolyploids, are just beginning to be understood especially in wheat. However, the nature and mode of action of homoeologous recombination suppressor genes are poorly understood in other allopolyploids. The merger of two independent genomes causes a deep modification of their architecture, gene expression, and molecular interactions leading to the phenotype. We provide an overview of genomic changes and transcriptomic modifications that particularly occur at the early stages of allopolyploid formation.
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Affiliation(s)
- Francesco Blasio
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (F.B.); (M.P.)
| | - Pilar Prieto
- Plant Breeding Department, Institute for Sustainable Agriculture, Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, Apartado 4048, 14080 Cordova, Spain;
| | - Mónica Pradillo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (F.B.); (M.P.)
| | - Tomás Naranjo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Biología, Universidad Complutense de Madrid, 28040 Madrid, Spain; (F.B.); (M.P.)
- Correspondence:
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Hüther P, Hagmann J, Nunn A, Kakoulidou I, Pisupati R, Langenberger D, Weigel D, Johannes F, Schultheiss SJ, Becker C. MethylScore, a pipeline for accurate and context-aware identification of differentially methylated regions from population-scale plant whole-genome bisulfite sequencing data. QUANTITATIVE PLANT BIOLOGY 2022; 3:e19. [PMID: 37077980 PMCID: PMC10095865 DOI: 10.1017/qpb.2022.14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 05/03/2023]
Abstract
Whole-genome bisulfite sequencing (WGBS) is the standard method for profiling DNA methylation at single-nucleotide resolution. Different tools have been developed to extract differentially methylated regions (DMRs), often built upon assumptions from mammalian data. Here, we present MethylScore, a pipeline to analyse WGBS data and to account for the substantially more complex and variable nature of plant DNA methylation. MethylScore uses an unsupervised machine learning approach to segment the genome by classification into states of high and low methylation. It processes data from genomic alignments to DMR output and is designed to be usable by novice and expert users alike. We show how MethylScore can identify DMRs from hundreds of samples and how its data-driven approach can stratify associated samples without prior information. We identify DMRs in the A. thaliana 1,001 Genomes dataset to unveil known and unknown genotype-epigenotype associations .
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Affiliation(s)
- Patrick Hüther
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
| | | | - Adam Nunn
- ecSeq Bioinformatics GmbH, 04103 Leipzig, Germany
- Department of Computer Science, Leipzig University, 04107 Leipzig, Germany
| | - Ioanna Kakoulidou
- Department of Plant Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Rahul Pisupati
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
| | | | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Frank Johannes
- Department of Plant Sciences, Technical University of Munich, 85354 Freising, Germany
- Institute for Advanced Study, Technical University of Munich, 85748 Garching, Germany
| | | | - Claude Becker
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030 Vienna, Austria
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152 Martinsried, Germany
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48
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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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Tossi VE, Martínez Tosar LJ, Laino LE, Iannicelli J, Regalado JJ, Escandón AS, Baroli I, Causin HF, Pitta-Álvarez SI. Impact of polyploidy on plant tolerance to abiotic and biotic stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:869423. [PMID: 36072313 PMCID: PMC9441891 DOI: 10.3389/fpls.2022.869423] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 07/25/2022] [Indexed: 05/04/2023]
Abstract
Polyploidy, defined as the coexistence of three or more complete sets of chromosomes in an organism's cells, is considered as a pivotal moving force in the evolutionary history of vascular plants and has played a major role in the domestication of several crops. In the last decades, improved cultivars of economically important species have been developed artificially by inducing autopolyploidy with chemical agents. Studies on diverse species have shown that the anatomical and physiological changes generated by either natural or artificial polyploidization can increase tolerance to abiotic and biotic stresses as well as disease resistance, which may positively impact on plant growth and net production. The aim of this work is to review the current literature regarding the link between plant ploidy level and tolerance to abiotic and biotic stressors, with an emphasis on the physiological and molecular mechanisms responsible for these effects, as well as their impact on the growth and development of both natural and artificially generated polyploids, during exposure to adverse environmental conditions. We focused on the analysis of those types of stressors in which more progress has been made in the knowledge of the putative morpho-physiological and/or molecular mechanisms involved, revealing both the factors in common, as well as those that need to be addressed in future research.
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Affiliation(s)
- Vanesa E. Tossi
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - Leandro J. Martínez Tosar
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Departamento de Biotecnología, Alimentos, Agro y Ambiental (DEBAL), Facultad de Ingeniería y Ciencias Exactas, Universidad Argentina de la Empresa (UADE), Buenos Aires, Argentina
| | - Leandro E. Laino
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - Jesica Iannicelli
- Instituto Nacional de Tecnología, Agropecuaria (INTA), Instituto de Genética “Ewald A. Favret”, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Biodiversidad y Biología Experimental (IBBEA), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - José Javier Regalado
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
| | - Alejandro Salvio Escandón
- Instituto Nacional de Tecnología, Agropecuaria (INTA), Instituto de Genética “Ewald A. Favret”, Buenos Aires, Argentina
| | - Irene Baroli
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Biodiversidad y Biología Experimental (IBBEA), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Irene Baroli,
| | - Humberto Fabio Causin
- Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Humberto Fabio Causin,
| | - Sandra Irene Pitta-Álvarez
- Laboratorio de Cultivo Experimental de Plantas y Microalgas, Departamento de Biodiversidad y Biología Experimental (DBBE), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad de Buenos Aires, Instituto de Micología y Botánica (INMIBO), Ciudad Universitaria, Int. Güiraldes y Cantilo, Buenos Aires, Argentina
- *Correspondence: Sandra Irene Pitta-Álvarez, ;
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Dal Grande F, Jamilloux V, Choisne N, Calchera A, Rolshausen G, Petersen M, Schulz M, Nilsson MA, Schmitt I. Transposable Elements in the Genome of the Lichen-Forming Fungus Umbilicaria pustulata and Their Distribution in Different Climate Zones along Elevation. BIOLOGY 2021; 11:biology11010024. [PMID: 35053022 PMCID: PMC8773270 DOI: 10.3390/biology11010024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022]
Abstract
Transposable elements (TEs) are an important source of genome plasticity across the tree of life. Drift and natural selection are important forces shaping TE distribution and accumulation. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host's ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold temperate. We trace the occurrence of the newly identified TEs in populations along three elevation gradients using a Pool-Seq approach to identify TE insertions of potential adaptive significance. We found that TEs cover 21.26% of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. We identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. This pioneering study of the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution.
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Affiliation(s)
- Francesco Dal Grande
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Correspondence: ; Tel.: +49-(0)69-7542-1856
| | - Véronique Jamilloux
- INRAE URGI, Centre de Versailles, Bâtiment 18, Route de Saint Cyr, 78026 Versailles, France; (V.J.); (N.C.)
| | - Nathalie Choisne
- INRAE URGI, Centre de Versailles, Bâtiment 18, Route de Saint Cyr, 78026 Versailles, France; (V.J.); (N.C.)
| | - Anjuli Calchera
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
| | - Gregor Rolshausen
- Senckenberg Center for Wildlife Genetics, Clamecystrasse 12, 63571 Gelnhausen, Germany;
| | - Malte Petersen
- Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany;
| | - Meike Schulz
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
| | - Maria A. Nilsson
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Imke Schmitt
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; (A.C.); (M.S.); (M.A.N.); (I.S.)
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
- Institut für Ökologie, Evolution und Diversität, Goethe-Universität Frankfurt, Max-von-Laue-Strasse. 9, 60438 Frankfurt am Main, Germany
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