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Ding Q, Ren X, Li R, Chan L, Ho VWS, Bi Y, Xie D, Zhao Z. Highly efficient transgenesis with miniMos in Caenorhabditis briggsae. G3 (BETHESDA, MD.) 2022; 12:jkac254. [PMID: 36171682 PMCID: PMC9713419 DOI: 10.1093/g3journal/jkac254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/29/2022] [Indexed: 06/13/2023]
Abstract
Caenorhabditis briggsae as a companion species for Caenorhabditis elegans has played an increasingly important role in study of evolution of development and genome and gene regulation. Aided by the isolation of its sister spices, it has recently been established as a model for speciation study. To take full advantage of the species for comparative study, an effective transgenesis method especially those with single-copy insertion is important for functional comparison. Here, we improved a transposon-based transgenesis methodology that had been originally developed in C. elegans but worked marginally in C. briggsae. By incorporation of a heat shock step, the transgenesis efficiency in C. briggsae with a single-copy insertion is comparable to that in C. elegans. We used the method to generate 54 independent insertions mostly consisting of a mCherry tag over the C. briggsae genome. We demonstrated the use of the tags in identifying interacting loci responsible for hybrid male sterility between C. briggsae and Caenorhabditis nigoni when combined with the GFP tags we generated previously. Finally, we demonstrated that C. briggsae tolerates the C. elegans toxin, PEEL-1, but not SUP-35, making the latter a potential negative selection marker against extrachromosomal array.
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Affiliation(s)
- Qiutao Ding
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Xiaoliang Ren
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Luyan Chan
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Vincy W S Ho
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yu Bi
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Dongying Xie
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong SAR, China
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Ogaji YO, Lee RC, Sawbridge TI, Cocks BG, Daetwyler HD, Kaur S. De Novo Long-Read Whole-Genome Assemblies and the Comparative Pan-Genome Analysis of Ascochyta Blight Pathogens Affecting Field Pea. J Fungi (Basel) 2022; 8:884. [PMID: 36012871 PMCID: PMC9410150 DOI: 10.3390/jof8080884] [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: 06/22/2022] [Revised: 08/12/2022] [Accepted: 08/15/2022] [Indexed: 11/16/2022] Open
Abstract
Ascochyta Blight (AB) is a major disease of many cool-season legumes globally. In field pea, three fungal pathogens have been identified to be responsible for this disease in Australia, namely Peyronellaea pinodes, Peyronellaea pinodella and Phoma koolunga. Limited genomic resources for these pathogens have been generated, which has hampered the implementation of effective management strategies and breeding for resistant cultivars. Using Oxford Nanopore long-read sequencing, we report the first high-quality, fully annotated, near-chromosome-level nuclear and mitochondrial genome assemblies for 18 isolates from the Australian AB complex. Comparative genome analysis was performed to elucidate the differences and similarities between species and isolates using phylogenetic relationships and functional diversity. Our data indicated that P. pinodella and P. koolunga are heterothallic, while P. pinodes is homothallic. More homology and orthologous gene clusters are shared between P. pinodes and P. pinodella compared to P. koolunga. The analysis of the repetitive DNA content showed differences in the transposable repeat composition in the genomes and their expression in the transcriptomes. Significant repeat expansion in P. koolunga's genome was seen, with strong repeat-induced point mutation (RIP) activity being evident. Phylogenetic analysis revealed that genetic diversity can be exploited for species marker development. This study provided the much-needed genetic resources and characterization of the AB species to further drive research in key areas such as disease epidemiology and host-pathogen interactions.
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Affiliation(s)
- Yvonne O. Ogaji
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Robert C. Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Perth, WA 6102, Australia
| | - Tim I. Sawbridge
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Benjamin G. Cocks
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Hans D. Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Melbourne, VIC 3086, Australia
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Melbourne, VIC 3083, Australia
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GSNOR Contributes to Demethylation and Expression of Transposable Elements and Stress-Responsive Genes. Antioxidants (Basel) 2021; 10:antiox10071128. [PMID: 34356361 PMCID: PMC8301139 DOI: 10.3390/antiox10071128] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 12/19/2022] Open
Abstract
In the past, reactive nitrogen species (RNS) were supposed to be stress-induced by-products of disturbed metabolism that cause oxidative damage to biomolecules. However, emerging evidence demonstrates a substantial role of RNS as endogenous signals in eukaryotes. In plants, S-nitrosoglutathione (GSNO) is the dominant RNS and serves as the •NO donor for S-nitrosation of diverse effector proteins. Remarkably, the endogenous GSNO level is tightly controlled by S-nitrosoglutathione reductase (GSNOR) that irreversibly inactivates the glutathione-bound NO to ammonium. Exogenous feeding of diverse RNS, including GSNO, affected chromatin accessibility and transcription of stress-related genes, but the triggering function of RNS on these regulatory processes remained elusive. Here, we show that GSNO reductase-deficient plants (gsnor1-3) accumulate S-adenosylmethionine (SAM), the principal methyl donor for methylation of DNA and histones. This SAM accumulation triggered a substantial increase in the methylation index (MI = [SAM]/[S-adenosylhomocysteine]), indicating the transmethylation activity and histone methylation status in higher eukaryotes. Indeed, a mass spectrometry-based global histone profiling approach demonstrated a significant global increase in H3K9me2, which was independently verified by immunological detection using a selective antibody. Since H3K9me2-modified regions tightly correlate with methylated DNA regions, we also determined the DNA methylation status of gsnor1-3 plants by whole-genome bisulfite sequencing. DNA methylation in the CG, CHG, and CHH contexts in gsnor1-3 was significantly enhanced compared to the wild type. We propose that GSNOR1 activity affects chromatin accessibility by controlling the transmethylation activity (MI) required for maintaining DNA methylation and the level of the repressive chromatin mark H3K9me2.
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Torres DE, Thomma BPHJ, Seidl MF. Transposable Elements Contribute to Genome Dynamics and Gene Expression Variation in the Fungal Plant Pathogen Verticillium dahliae. Genome Biol Evol 2021; 13:evab135. [PMID: 34100895 PMCID: PMC8290119 DOI: 10.1093/gbe/evab135] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
Transposable elements (TEs) are a major source of genetic and regulatory variation in their host genome and are consequently thought to play important roles in evolution. Many fungal and oomycete plant pathogens have evolved dynamic and TE-rich genomic regions containing genes that are implicated in host colonization and adaptation. TEs embedded in these regions have typically been thought to accelerate the evolution of these genomic compartments, but little is known about their dynamics in strains that harbor them. Here, we used whole-genome sequencing data of 42 strains of the fungal plant pathogen Verticillium dahliae to systematically identify polymorphic TEs that may be implicated in genomic as well as in gene expression variation. We identified 2,523 TE polymorphisms and characterize a subset of 8% of the TEs as polymorphic elements that are evolutionary younger, less methylated, and more highly expressed when compared with the remaining 92% of the total TE complement. As expected, the polyrmorphic TEs are enriched in the adaptive genomic regions. Besides, we observed an association of polymorphic TEs with pathogenicity-related genes that localize nearby and that display high expression levels. Collectively, our analyses demonstrate that TE dynamics in V. dahliae contributes to genomic variation, correlates with expression of pathogenicity-related genes, and potentially impacts the evolution of adaptive genomic regions.
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Affiliation(s)
- David E Torres
- Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, The Netherlands
- Laboratory of Phytopathology, Wageningen University and Research, The Netherlands
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University and Research, The Netherlands
- Cluster of Excellence on Plant Sciences (CEPLAS), Institute for Plant Sciences, University of Cologne, Germany
| | - Michael F Seidl
- Theoretical Biology and Bioinformatics Group, Department of Biology, Utrecht University, The Netherlands
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Atighi MR, Verstraeten B, De Meyer T, Kyndt T. Genome-wide DNA hypomethylation shapes nematode pattern-triggered immunity in plants. THE NEW PHYTOLOGIST 2020; 227:545-558. [PMID: 32162327 PMCID: PMC7317725 DOI: 10.1111/nph.16532] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/26/2020] [Indexed: 05/22/2023]
Abstract
A role for DNA hypomethylation has recently been suggested in the interaction between bacteria and plants; it is unclear whether this phenomenon reflects a conserved response. Treatment of plants of monocot rice and dicot tomato with nematode-associated molecular patterns from different nematode species or bacterial pathogen-associated molecular pattern flg22 revealed global DNA hypomethylation. A similar hypomethylation response was observed during early gall induction by Meloidogyne graminicola in rice. Evidence for the causal impact of hypomethylation on immunity was revealed by a significantly reduced plant susceptibility upon treatment with DNA methylation inhibitor 5-azacytidine. Whole-genome bisulphite sequencing of young galls revealed massive hypomethylation in the CHH context, while not for CG or CHG nucleotide contexts. Further, CHH hypomethylated regions were predominantly associated with gene promoter regions, which was not correlated with activated gene expression at the same time point but, rather, was correlated with a delayed transcriptional gene activation. Finally, the relevance of CHH hypomethylation in plant defence was confirmed in rice mutants of the RNA-directed DNA methylation pathway and DECREASED DNA METHYLATION 1. We demonstrated that DNA hypomethylation is associated with reduced susceptibility in rice towards root-parasitic nematodes and is likely to be part of the basal pattern-triggered immunity response in plants.
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Affiliation(s)
| | | | - Tim De Meyer
- Department of Data Analysis & Mathematical ModellingGhent UniversityB‐9000GhentBelgium
| | - Tina Kyndt
- Department of BiotechnologyGhent UniversityB‐9000GhentBelgium
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6
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Intraspecific Diversity in the Cold Stress Response of Transposable Elements in the Diatom Leptocylindrus aporus. Genes (Basel) 2019; 11:genes11010009. [PMID: 31861932 PMCID: PMC7017206 DOI: 10.3390/genes11010009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 12/19/2019] [Indexed: 01/18/2023] Open
Abstract
Transposable elements (TEs), activated as a response to unfavorable conditions, have been proposed to contribute to the generation of genetic and phenotypic diversity in diatoms. Here we explore the transcriptome of three warm water strains of the diatom Leptocylindrus aporus, and the possible involvement of TEs in their response to changing temperature conditions. At low temperature (13 °C) several stress response proteins were overexpressed, confirming low temperature to be unfavorable for L. aporus, while TE-related transcripts of the LTR retrotransposon superfamily were the most enriched transcripts. Their expression levels, as well as most of the stress-related proteins, were found to vary significantly among strains, and even within the same strains analysed at different times. The lack of overexpression after many months of culturing suggests a possible role of physiological plasticity in response to growth under controlled laboratory conditions. While further investigation on the possible central role of TEs in the diatom stress response is warranted, the strain-specific responses and possible role of in-culture evolution draw attention to the interplay between the high intraspecific variability and the physiological plasticity of diatoms, which can both contribute to the adaptation of a species to a wide range of conditions in the marine environment.
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Viana Ferreira AM, Marajó L, Matoso DA, Ribeiro LB, Feldberg E. Chromosomal Mapping of Rex Retrotransposons in Tambaqui (Colossoma macropomum Cuvier, 1818) Exposed to Three Climate Change Scenarios. Cytogenet Genome Res 2019; 159:39-47. [PMID: 31593951 DOI: 10.1159/000502926] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2019] [Indexed: 11/19/2022] Open
Abstract
Greenhouse gas emissions are known to influence the planet's temperature, mainly due to human activities. To allow hypothesis testing, as well as to seek viable alternatives for mitigation, the Intergovernmental Panel on Climate Change (IPCC) suggested 3 main scenarios for changes projected for the year 2100. In this paper, we subjected Colossoma macropomum Cuvier, 1818 (tambaqui) individuals in a microcosm to IPCC scenarios B1 (mild), A1B (intermediate), and A2 (extreme) to test possible impacts on their genome. We found chromosome heterochromatinization in specimens exposed to the A2 scenario, where terminal blocks and interstitial bands were detected on several chromosome pairs. The behavior of Rex1 and Rex3 sequences differed between the test scenarios. Hybridization of Rex1 resulted in diffuse signals which showed a gradual increase in the tested scenarios. For Rex3, an increase was observed in the A2 scenario with blocks on several chromosomes, some of which coincided with heterochromatin. Heterochromatinization is an epigenetic process, which may have occurred as a mechanism for regulating Rex3 activity. The signal pattern of Rex6 did not change, suggesting that other mechanisms are acting to regulate its activity.
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8
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Volkova PY, Geras'kin SA, Horemans N, Makarenko ES, Saenen E, Duarte GT, Nauts R, Bondarenko VS, Jacobs G, Voorspoels S, Kudin M. Chronic radiation exposure as an ecological factor: Hypermethylation and genetic differentiation in irradiated Scots pine populations. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 232:105-112. [PMID: 28931465 DOI: 10.1016/j.envpol.2017.08.123] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/14/2017] [Accepted: 08/24/2017] [Indexed: 05/18/2023]
Abstract
Genetic and epigenetic changes were investigated in chronically irradiated Scots pine (Pinus sylvestris L.) populations from territories that were heavily contaminated by radionuclides as result of the Chernobyl Nuclear Power Plant accident. In comparison to the reference site, the genetic diversity revealed by electrophoretic mobility of AFLPs was found to be significantly higher at the radioactively contaminated areas. In addition, the genome of pine trees was significantly hypermethylated at 4 of the 7 affected sites.
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Affiliation(s)
- P Yu Volkova
- Institute of Radiology and Agroecology, 249030, Obninsk, Russian Federation.
| | - S A Geras'kin
- Institute of Radiology and Agroecology, 249030, Obninsk, Russian Federation
| | - N Horemans
- Belgian Nuclear Research Centre SCK•CEN, Biosphere Impact Studies, Boeretang 200, 2400, Mol, Belgium
| | - E S Makarenko
- Institute of Radiology and Agroecology, 249030, Obninsk, Russian Federation
| | - E Saenen
- Belgian Nuclear Research Centre SCK•CEN, Biosphere Impact Studies, Boeretang 200, 2400, Mol, Belgium
| | - G T Duarte
- Institute of Radiology and Agroecology, 249030, Obninsk, Russian Federation
| | - R Nauts
- Belgian Nuclear Research Centre SCK•CEN, Biosphere Impact Studies, Boeretang 200, 2400, Mol, Belgium
| | - V S Bondarenko
- Institute of Radiology and Agroecology, 249030, Obninsk, Russian Federation
| | - G Jacobs
- Flemish Institute for Technological Research (VITO NV), Boeretang 200, 2400 Mol, Belgium
| | - S Voorspoels
- Flemish Institute for Technological Research (VITO NV), Boeretang 200, 2400 Mol, Belgium
| | - M Kudin
- Polessye State Radiation Ecological Reserve, 247618, Belarus
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9
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Negi P, Rai AN, Suprasanna P. Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response. FRONTIERS IN PLANT SCIENCE 2016; 7:1448. [PMID: 27777577 PMCID: PMC5056178 DOI: 10.3389/fpls.2016.01448] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 09/12/2016] [Indexed: 05/02/2023]
Abstract
The recognition of a positive correlation between organism genome size with its transposable element (TE) content, represents a key discovery of the field of genome biology. Considerable evidence accumulated since then suggests the involvement of TEs in genome structure, evolution and function. The global genome reorganization brought about by transposon activity might play an adaptive/regulatory role in the host response to environmental challenges, reminiscent of McClintock's original 'Controlling Element' hypothesis. This regulatory aspect of TEs is also garnering support in light of the recent evidences, which project TEs as "distributed genomic control modules." According to this view, TEs are capable of actively reprogramming host genes circuits and ultimately fine-tuning the host response to specific environmental stimuli. Moreover, the stress-induced changes in epigenetic status of TE activity may allow TEs to propagate their stress responsive elements to host genes; the resulting genome fluidity can permit phenotypic plasticity and adaptation to stress. Given their predominating presence in the plant genomes, nested organization in the genic regions and potential regulatory role in stress response, TEs hold unexplored potential for crop improvement programs. This review intends to present the current information about the roles played by TEs in plant genome organization, evolution, and function and highlight the regulatory mechanisms in plant stress responses. We will also briefly discuss the connection between TE activity, host epigenetic response and phenotypic plasticity as a critical link for traversing the translational bridge from a purely basic study of TEs, to the applied field of stress adaptation and crop improvement.
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Affiliation(s)
| | | | - Penna Suprasanna
- Plant Stress Physiology and Biotechnology Section, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research CentreTrombay, India
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Goldfarb M, Santana MF, Salomão TMF, Queiroz MVD, Barros EGD. Evidence of ectopic recombination and a repeat-induced point (RIP) mutation in the genome of Sclerotinia sclerotiorum, the agent responsible for white mold. Genet Mol Biol 2016; 39:426-30. [PMID: 27560652 PMCID: PMC5004834 DOI: 10.1590/1678-4685-gmb-2015-0241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Accepted: 12/20/2015] [Indexed: 12/24/2022] Open
Abstract
Two retrotransposons from the superfamilies Copia and
Gypsy named as Copia-LTR_SS and
Gypsy-LTR_SS, respectively, were identified in
the genomic bank of Sclerotinia sclerotiorum. These transposable
elements (TEs) contained direct and preserved long terminal repeats (LTR). Domains
related to codified regions for gag protein, integrase, reverse transcriptase and
RNAse H were identified in Copia-LTR_SS, whereas in
Gypsy-LTR_SS only domains for gag, reverse
transcriptase and RNAse H were found. The abundance of identified LTR-Solo suggested
possible genetic recombination events in the S. sclerotiorum genome.
Furthermore, alignment of the sequences for LTR elements from each superfamily
suggested the presence of a RIP (repeat-induced point mutation) silencing mechanism
that may directly affect the evolution of this species.
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Affiliation(s)
- Míriam Goldfarb
- Laboratório de Biologia Molecular de Plantas, Instituto de Biotecnologia Aplicada (BIOAGRO), Universidade Federal de Viçosa (UFV), 36570-000, Viçosa, MG, Brazil
| | - Mateus Ferreira Santana
- Laboratório de Genética Molecular e de Microrganismo, Instituto de Biotecnologia Aplicada (BIOAGRO), Universidade Federal de Viçosa (UFV), 36570-000, Viçosa, MG, Brazil
| | - Tânia Maria Fernandes Salomão
- Laboratório de Biologia Molecular de Insetos, Departamento de Biologia Geral, Universidade Federal de Viçosa (UFV), 36570-000, Viçosa, MG, Brazil
| | - Marisa Vieira de Queiroz
- Laboratório de Genética Molecular e de Microrganismo, Instituto de Biotecnologia Aplicada (BIOAGRO), Universidade Federal de Viçosa (UFV), 36570-000, Viçosa, MG, Brazil
| | - Everaldo Gonçalves de Barros
- Laboratório de Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, 70790-160, Brasília, DF, Brazil
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Abstract
Most reviews of climate change are epidemiological, focusing on impact assessment and risk mapping. However, there are many reports of the effects of environmental stress factors on defense mechanisms in plants against pathogens. We review those representative of key climate change-related stresses to determine whether there are any patterns or trends in adaptation responses. We recognize the complexity of climate change itself and the multitrophic nature of the complex biological interactions of plants, microbes, soil, and the environment and, therefore, the difficulty of reductionist dissection approaches to resolving the problems. We review host defense genes, germplasm, and environmental interactions in different types of organisms but find no significant group-specific trends. Similarly, we review by host defense mechanism type and by host-pathogen trophic relationship but identify no dominating mechanism for stress response. However, we do identify core stress response mechanisms playing key roles in multiple response pathways whether to biotic or abiotic stress. We suggest that these should be central to mechanistic climate change plant defense research. We also recognize biodiversity, heterogeneity, and the need for understanding stress in a true systems biology approach as being essential components of progressing our understanding of and response to climate change.
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Rey O, Danchin E, Mirouze M, Loot C, Blanchet S. Adaptation to Global Change: A Transposable Element-Epigenetics Perspective. Trends Ecol Evol 2016; 31:514-526. [PMID: 27080578 DOI: 10.1016/j.tree.2016.03.013] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 12/21/2022]
Abstract
Understanding how organisms cope with global change is a major scientific challenge. The molecular pathways underlying rapid adaptive phenotypic responses to global change remain poorly understood. Here, we highlight the relevance of two environment-sensitive molecular elements: transposable elements (TEs) and epigenetic components (ECs). We first outline the sensitivity of these elements to global change stressors and review how they interact with each other. We then propose an integrative molecular engine coupling TEs and ECs and allowing organisms to fine-tune phenotypes in a real-time fashion, adjust the production of phenotypic and genetic variation, and produce heritable phenotypes with different levels of transmission fidelity. We finally discuss the implications of this molecular engine in the context of global change.
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Affiliation(s)
- Olivier Rey
- CNRS, UPS, Station d'Écologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France; Department of Biosciences, College of Science, Swansea University, Swansea SA2 8PP, UK.
| | - Etienne Danchin
- CNRS, UPS, ENFA, Évolution & Diversité Biologique (EDB) UMR 5174, 118 Route de Narbonne, 31062 Toulouse, Cedex 9, France; Université Paul Sabatier, Évolution & Diversité Biologique (EDB), 31062 Toulouse, Cedex 9, France
| | - Marie Mirouze
- Institut de Recherche pour le Développement, UMR232 DIADE Diversité Adaptation et Développement des Plantes, Laboratoire Génome et Développement des Plantes, 58 avenue Paul Alduy, 66860 Perpignan, France
| | - Céline Loot
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Paris, France; CNRS UMR3525, Paris, France
| | - Simon Blanchet
- CNRS, UPS, Station d'Écologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France; CNRS, UPS, ENFA, Évolution & Diversité Biologique (EDB) UMR 5174, 118 Route de Narbonne, 31062 Toulouse, Cedex 9, France.
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Funikov SY, Ryazansky SS, Zelentsova ES, Popenko VI, Leonova OG, Garbuz DG, Evgen'ev MB, Zatsepina OG. The peculiarities of piRNA expression upon heat shock exposure in Drosophila melanogaster. Mob Genet Elements 2015; 5:72-80. [PMID: 26904377 DOI: 10.1080/2159256x.2015.1086502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 08/15/2015] [Accepted: 08/18/2015] [Indexed: 01/05/2023] Open
Abstract
Different types of stress including heat shock may induce genomic instability, due to the derepression and amplification of mobile elements (MEs). It remains unclear, however, whether piRNA-machinery regulating ME expression functions normally under stressful conditions. The aim of this study was to explore the features of piRNA expression after heat shock (HS) exposure in Drosophila melanogaster. We also evaluated functioning of piRNA-machinery in the absence of major stress protein Hsp70 in this species. We analyzed the deep sequence data of piRNA expression after HS treatment and demonstrated that it modulates the expression of certain double-stranded germinal piRNA-clusters. Notable, we demonstrated significant changes in piRNA levels targeting a group of MEs after HS only in the strain containing normal set of hsp70 genes. Surprisingly, we failed to detect any correlation between the levels of piRNAs and the transcription of complementary MEs in the studied strains. We propose that modulation of certain piRNA-clusters expression upon HS exposure in D. melanogaster occurs due to HS-induced altering of chromatin state at certain chromosome regions.
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Affiliation(s)
- S Yu Funikov
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences ; Moscow, Russia
| | - S S Ryazansky
- Institute of Molecular Genetics; Russian Academy of Sciences ; Moscow, Russia
| | - E S Zelentsova
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences ; Moscow, Russia
| | - V I Popenko
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences ; Moscow, Russia
| | - O G Leonova
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences ; Moscow, Russia
| | - D G Garbuz
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences ; Moscow, Russia
| | - M B Evgen'ev
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences ; Moscow, Russia
| | - O G Zatsepina
- Engelhardt Institute of Molecular Biology; Russian Academy of Sciences ; Moscow, Russia
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14
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MpSaci is a widespread gypsy-Ty3 retrotransposon highly represented by non-autonomous copies in the Moniliophthora perniciosa genome. Curr Genet 2015; 61:185-202. [DOI: 10.1007/s00294-014-0469-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 11/21/2014] [Accepted: 12/22/2014] [Indexed: 11/25/2022]
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Comeau AM, Dufour J, Bouvet GF, Jacobi V, Nigg M, Henrissat B, Laroche J, Levesque RC, Bernier L. Functional annotation of the Ophiostoma novo-ulmi genome: insights into the phytopathogenicity of the fungal agent of Dutch elm disease. Genome Biol Evol 2014; 7:410-30. [PMID: 25539722 PMCID: PMC4350166 DOI: 10.1093/gbe/evu281] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2014] [Indexed: 12/18/2022] Open
Abstract
The ascomycete fungus Ophiostoma novo-ulmi is responsible for the pandemic of Dutch elm disease that has been ravaging Europe and North America for 50 years. We proceeded to annotate the genome of the O. novo-ulmi strain H327 that was sequenced in 2012. The 31.784-Mb nuclear genome (50.1% GC) is organized into 8 chromosomes containing a total of 8,640 protein-coding genes that we validated with RNA sequencing analysis. Approximately 53% of these genes have their closest match to Grosmannia clavigera kw1407, followed by 36% in other close Sordariomycetes, 5% in other Pezizomycotina, and surprisingly few (5%) orphans. A relatively small portion (∼3.4%) of the genome is occupied by repeat sequences; however, the mechanism of repeat-induced point mutation appears active in this genome. Approximately 76% of the proteins could be assigned functions using Gene Ontology analysis; we identified 311 carbohydrate-active enzymes, 48 cytochrome P450s, and 1,731 proteins potentially involved in pathogen-host interaction, along with 7 clusters of fungal secondary metabolites. Complementary mating-type locus sequencing, mating tests, and culturing in the presence of elm terpenes were conducted. Our analysis identified a specific genetic arsenal impacting the sexual and vegetative growth, phytopathogenicity, and signaling/plant-defense-degradation relationship between O. novo-ulmi and its elm host and insect vectors.
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Affiliation(s)
- André M Comeau
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada Present address: Department of Pharmacology, Dalhousie University, Halifax, NS, Canada
| | - Josée Dufour
- Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada
| | - Guillaume F Bouvet
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, Québec, Canada
| | - Volker Jacobi
- Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada
| | - Martha Nigg
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada
| | - Bernard Henrissat
- Centre National de la Recherche Scientifique (CNRS), UMR7257, Université Aix-Marseille, France Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Jérôme Laroche
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada
| | - Roger C Levesque
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada Département de Microbiologie-Infectiologie et Immunologie, Faculté de Médecine, Université Laval, Québec, Québec, Canada
| | - Louis Bernier
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Québec, Canada Centre d'Étude de la Forêt (CEF), Université Laval, Québec, Québec, Canada
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Santana MF, Silva JCF, Mizubuti ESG, Araújo EF, Queiroz MV. Analysis of Tc1-Mariner elements in Sclerotinia sclerotiorum suggests recent activity and flexible transposases. BMC Microbiol 2014; 14:256. [PMID: 25281292 PMCID: PMC4188875 DOI: 10.1186/s12866-014-0256-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 09/25/2014] [Indexed: 12/12/2022] Open
Abstract
Background Sclerotinia sclerotiorum is a necrotrophic fungus that is pathogenic to many plants. Genomic analysis of its revealed transposable element expansion that has strongly influenced the evolutionary trajectory of several species. Transposons from the Tc1-Mariner superfamily are thought to be ubiquitous components of fungal genomes and are generally found in low copy numbers with large numbers of deleterious mutations in their transposase coding sequence. Results This study shows that the genome of S. sclerotiorum has a large number of copies of Tc1-Mariner transposons, and in silico analysis shows evidence that they were recently active. This finding was confirmed by expressed sequence tag (EST) analysis. Fourteen new Tc1-Mariner transposon families that were distributed throughout the genome were identified, and in some cases, due to the excision/retention of introns, different transcripts were observed for the same family, which might be the result of an efficient strategy to circumvent mutations that generate premature stop codons in the RNA sequence. In addition, the presence of these introns shows that the transposase protein has a flexible coding sequence and, consequently, conformation. No evidence for RIP-like gene silencing mechanisms, which are commonly found in fungi, was found in the identified Tc1-Mariner elements, and analysis of the genomic insertion sites of these elements showed that they were widely distributed throughout the genome with some copies located near the 3′ regions of genes. In particular, EST analysis demonstrated that one of these copies was co-expressed with a gene, which showed the potential for these elements to undergo exaptation. Conclusions Fourteen novel Tc1-Mariner families were characterized. Some families had evidence of introns, which might or might not be excised depending on the family or element in question, and this finding demonstrates a possible strategy for overcoming possible mutations that generate premature stop codons in a RNA sequence. Tc1-Mariner elements likely play an important role in the structure and evolution of the S. sclerotiorum genome.
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Santana MF, Silva JCF, Mizubuti ESG, Araújo EF, Condon BJ, Turgeon BG, Queiroz MV. Characterization and potential evolutionary impact of transposable elements in the genome of Cochliobolus heterostrophus. BMC Genomics 2014; 15:536. [PMID: 24973942 PMCID: PMC4112212 DOI: 10.1186/1471-2164-15-536] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 06/17/2014] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Cochliobolus heterostrophus is a dothideomycete that causes Southern Corn Leaf Blight disease. There are two races, race O and race T that differ by the absence (race O) and presence (race T) of ~ 1.2-Mb of DNA encoding genes responsible for the production of T-toxin, which makes race T much more virulent than race O. The presence of repetitive elements in fungal genomes is considered to be an important source of genetic variability between different species. RESULTS A detailed analysis of class I and II TEs identified in the near complete genome sequence of race O was performed. In total in race O, 12 new families of transposons were identified. In silico evidence of recent activity was found for many of the transposons and analyses of expressed sequence tags (ESTs) demonstrated that these elements were actively transcribed. Various potentially active TEs were found near coding regions and may modify the expression and structure of these genes by acting as ectopic recombination sites. Transposons were found on scaffolds carrying polyketide synthase encoding genes, responsible for production of T-toxin in race T. Strong evidence of ectopic recombination was found, demonstrating that TEs can play an important role in the modulation of genome architecture of this species. The Repeat Induced Point mutation (RIP) silencing mechanism was shown to have high specificity in C. heterostrophus, acting only on transposons near coding regions. CONCLUSIONS New families of transposons were identified. In C. heterostrophus, the RIP silencing mechanism is efficient and selective. The co-localization of effector genes and TEs, therefore, exposes those genes to high rates of point mutations. This may accelerate the rate of evolution of these genes, providing a potential advantage for the host. Additionally, it was shown that ectopic recombination promoted by TEs appears to be the major event in the genome reorganization of this species and that a large number of elements are still potentially active. So, this study provides information about the potential impact of TEs on the evolution of C. heterostrophus.
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Affiliation(s)
- Mateus F Santana
- />Laboratório de Genética Molecular e de Micro-organismo, Universidade Federal de Viçosa, Viçosa, Brazil
| | - José CF Silva
- />Instituto Nacional de Ciência e Tecnologia em Interações Planta-Praga, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Eduardo SG Mizubuti
- />Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Elza F Araújo
- />Laboratório de Genética Molecular e de Micro-organismo, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Bradford J Condon
- />Department of Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, USA
| | - B Gillian Turgeon
- />Department of Plant Pathology & Plant-Microbe Biology, Cornell University, Ithaca, USA
| | - Marisa V Queiroz
- />Laboratório de Genética Molecular e de Micro-organismo, Universidade Federal de Viçosa, Viçosa, Brazil
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García Guerreiro MP. What makes transposable elements move in the Drosophila genome? Heredity (Edinb) 2012; 108:461-8. [PMID: 21971178 PMCID: PMC3330689 DOI: 10.1038/hdy.2011.89] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 08/22/2011] [Accepted: 08/25/2011] [Indexed: 11/08/2022] Open
Abstract
Transposable elements (TEs), by their capacity of moving and inducing mutations in the genome, are considered important drivers of species evolution. The successful invasions of TEs in genomes, despite their mutational properties, are an apparent paradox. TEs' transposition is usually strongly regulated to low value, but in some cases these elements can also show high transposition rates, which has been associated sometimes to changes in environmental conditions. It is evident that factors susceptible to induce transpositions in natural populations contribute to TE perpetuation. Different factors were proposed as causative agents of TE mobilization in a wide range of organisms: biotic and abiotic stresses, inter- and intraspecific crosses and populational factors. However, there is no clear evidence of the factors capable of inducing TE mobilization in Drosophila, and data on laboratory stocks show contradictory results. The aim of this review is to have an update critical revision about mechanisms promoting transposition of TEs in Drosophila, and to provide to the readers a global vision of the dynamics of these genomic elements in the Drosophila genome.
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Affiliation(s)
- M P García Guerreiro
- Grup de Biologia Evolutiva, Departament de Genètica i Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
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The transposon impala is activated by low temperatures: use of a controlled transposition system to identify genes critical for viability of Aspergillus fumigatus. EUKARYOTIC CELL 2010; 9:438-48. [PMID: 20097738 DOI: 10.1128/ec.00324-09] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Genes that are essential for viability represent potential targets for the development of anti-infective agents. However, relatively few have been determined in the filamentous fungal pathogen Aspergillus fumigatus. A novel solution employing parasexual genetics coupled with transposon mutagenesis using the Fusarium oxysporum transposon impala had previously enabled the identification of 20 essential genes from A. fumigatus; however, further use of this system required a better understanding of the mode of action of the transposon itself. Examination of a range of conditions indicated that impala is activated by prolonged exposure to low temperatures. This newly identified property was then harnessed to identify 96 loci that are critical for viability in A. fumigatus, including genes required for RNA metabolism, organelle organization, protein transport, ribosome biogenesis, and transcription, as well as a number of noncoding RNAs. A number of these genes represent potential targets for much-needed novel antifungal drugs.
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Zeh DW, Zeh JA, Ishida Y. Transposable elements and an epigenetic basis for punctuated equilibria. Bioessays 2009; 31:715-26. [DOI: 10.1002/bies.200900026] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Gregory PJ, Johnson SN, Newton AC, Ingram JSI. Integrating pests and pathogens into the climate change/food security debate. JOURNAL OF EXPERIMENTAL BOTANY 2009; 60:2827-38. [PMID: 19380424 DOI: 10.1093/jxb/erp080] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
While many studies have demonstrated the sensitivities of plants and of crop yield to a changing climate, a major challenge for the agricultural research community is to relate these findings to the broader societal concern with food security. This paper reviews the direct effects of climate on both crop growth and yield and on plant pests and pathogens and the interactions that may occur between crops, pests, and pathogens under changed climate. Finally, we consider the contribution that better understanding of the roles of pests and pathogens in crop production systems might make to enhanced food security. Evidence for the measured climate change on crops and their associated pests and pathogens is starting to be documented. Globally atmospheric [CO(2)] has increased, and in northern latitudes mean temperature at many locations has increased by about 1.0-1.4 degrees C with accompanying changes in pest and pathogen incidence and to farming practices. Many pests and pathogens exhibit considerable capacity for generating, recombining, and selecting fit combinations of variants in key pathogenicity, fitness, and aggressiveness traits that there is little doubt that any new opportunities resulting from climate change will be exploited by them. However, the interactions between crops and pests and pathogens are complex and poorly understood in the context of climate change. More mechanistic inclusion of pests and pathogen effects in crop models would lead to more realistic predictions of crop production on a regional scale and thereby assist in the development of more robust regional food security policies.
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Affiliation(s)
- Peter J Gregory
- Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK.
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Plourde KV, Jacobi V, Bernier L. Use of insertional mutagenesis to tag putative parasitic fitness genes in the Dutch elm disease fungus Ophiostoma novo-ulmi subsp. novo-ulmi. Can J Microbiol 2008; 54:797-802. [PMID: 18772944 DOI: 10.1139/w08-068] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We used insertional mutagenesis to produce genetically tagged mutants of the Dutch elm disease fungus Ophiostoma novo-ulmi subsp. novo-ulmi. We first optimized transformation of O. novo-ulmi protoplasts by the restriction enzyme mediated integration method. A concentration of 80 U of HindIII with 108 fungal protoplasts and 5 microg of plasmid DNA was the most efficient for generating a high number of O. novo-ulmi mutants carrying a single insertion in their genome. Mycelium- and yeast-like growth kinetics of 24 O. novo-ulmi mutants were evaluated in vitro. Flanking sequences were successfully recovered in 8% of the transformants analyzed. Some mutant phenotypes appeared to result from gene disruption events, whereas others likely involved modifications of noncoding regions. Several nuclear loci that control vegetative growth and could potentially impact parasitic fitness were successfully tagged.
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Affiliation(s)
- Karine V Plourde
- Centre d'Etude de la Forêt, Faculté de Foresterie et de Géomatique, Université Laval, Québec, QCG1V0A6, Canada.
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Dufresne M, Lee TVD, M’Barek SB, Xu X, Zhang X, Liu T, Waalwijk C, Zhang W, Kema GH, Daboussi MJ. Transposon-tagging identifies novel pathogenicity genes in Fusarium graminearum. Fungal Genet Biol 2008; 45:1552-61. [DOI: 10.1016/j.fgb.2008.09.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2008] [Revised: 07/31/2008] [Accepted: 09/03/2008] [Indexed: 01/14/2023]
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