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Zhao Y, Zheng X, Tabima JF, Zhu S, Søndreli KL, Hundley H, Bauer D, Barry K, Zhang Y, Schmutz J, Wang Y, LeBoldus JM, Xiong Q. Secreted Effector Proteins of Poplar Leaf Spot and Stem Canker Pathogen Sphaerulina musiva Manipulate Plant Immunity and Contribute to Virulence in Diverse Ways. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2023; 36:779-795. [PMID: 37551980 DOI: 10.1094/mpmi-07-23-0091-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Fungal effectors play critical roles in manipulating plant immune responses and promoting colonization. Sphaerulina musiva is a heterothallic ascomycete fungus that causes Septoria leaf spot and stem canker disease in poplar (Populus spp.) plantations. This disease can result in premature defoliation, branch and stem breakage, increased mortality, and plantation failure. However, little is known about the interaction between S. musiva and poplar. Previous work predicted 142 candidate secreted effector proteins in S. musiva (SmCSEPs), 19 of which were selected for further functional characterization in this study. SmCSEP3 induced plant cell death in Nicotiana benthamiana, while 8 out of 19 tested SmCSEPs suppressed cell death. The signal peptides of these eight SmCSEPs exhibited secretory activity in a yeast signal sequence trap assay. Confocal microscopy revealed that four of these eight SmCSEPs target both the cytoplasm and the nucleus, whereas four predominantly localize to discrete punctate structures. Pathogen challenge assays in N. benthamiana demonstrated that the transient expression of six SmCSEPs promoted Fusarium proliferatum infection. The expression of these six SmCSEP genes were induced during infection. SmCSEP2, SmCSEP13, and SmCSEP25 suppressed chitin-triggered reactive oxygen species burst and callose deposition in N. benthamiana. The candidate secreted effector proteins of S. musiva target multiple compartments in the plant cell and modulate different pattern-triggered immunity pathways. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 "No Rights Reserved" license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2023.
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Affiliation(s)
- Yao Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210095, China
| | - Xinyue Zheng
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Javier F Tabima
- Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331, U.S.A
- Department of Forest Engineering, Resources and Management, College of Forestry, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Sheng Zhu
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Kelsey L Søndreli
- Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Hope Hundley
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, U.S.A
| | - Diane Bauer
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, U.S.A
| | - Kerrie Barry
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, U.S.A
| | - Yaxin Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jeremy Schmutz
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, U.S.A
| | - Yuanchao Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210095, China
| | - Jared M LeBoldus
- Department of Botany and Plant Pathology, College of Agricultural Sciences, Oregon State University, Corvallis, OR 97331, U.S.A
- Department of Biology, Clark University, Worcester, MA 01610, U.S.A
| | - Qin Xiong
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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2
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Tannous J, Sawyer C, Hassan MM, Labbe JL, Eckert C. Establishment of a genome editing tool using CRISPR-Cas9 ribonucleoprotein complexes in the non-model plant pathogen Sphaerulina musiva. Front Genome Ed 2023; 5:1110279. [PMID: 37545762 PMCID: PMC10401582 DOI: 10.3389/fgeed.2023.1110279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 07/06/2023] [Indexed: 08/08/2023] Open
Abstract
CRISPR-Cas9 is a versatile genome editing system widely used since 2013 to introduce site-specific modifications into the genomes of model and non-model species. This technology is used in various applications, from gene knock-outs, knock-ins, and over-expressions to more precise changes, such as the introduction of nucleotides at a targeted locus. CRISPR-Cas9 has been demonstrated to be easy to establish in new species and highly efficient and specific compared to previous gene editing strategies such as Zinc finger nucleases and transcription activator-like effector nucleases. Grand challenges for emerging CRISPR-Cas9 tools in filamentous fungi are developing efficient transformation methods for non-model organisms. In this paper, we have leveraged the establishment of CRISPR-Cas9 genome editing tool that relies on Cas9/sgRNA ribonucleoprotein complexes (RNPs) in the model species Trichoderma reesei and developed the first protocol to efficiently transform the non-model species, Sphaerulina musiva. This fungal pathogen constitutes a real threat to the genus Populus, a foundational bioenergy crop used for biofuel production. Herein, we highlight the general considerations to design sgRNAs and their computational validation. We also describe the use of isolated protoplasts to deliver the CRISPR-Cas9 RNP components in both species and the screening for targeted genome editing events. The development of engineering tools in S. musiva can be used for studying genes involved in diverse processes such as secondary metabolism, establishment, and pathogenicity, among many others, but also for developing genetic mitigation approaches. The approach described here provides guidance for potential development of transformation systems in other non-model spore-bearing ascomycetes.
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Affiliation(s)
- Joanna Tannous
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Cole Sawyer
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, United States
| | - Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Patuakhali, Bangladesh
| | - Jesse L. Labbe
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, United States
| | - Carrie Eckert
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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Ortiz V, Chang HX, Sang H, Jacobs J, Malvick DK, Baird R, Mathew FM, Estévez de Jensen C, Wise KA, Mosquera GM, Chilvers MI. Population genomic analysis reveals geographic structure and climatic diversification for Macrophomina phaseolina isolated from soybean and dry bean across the United States, Puerto Rico, and Colombia. Front Genet 2023; 14:1103969. [PMID: 37351341 PMCID: PMC10282554 DOI: 10.3389/fgene.2023.1103969] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/20/2023] [Indexed: 06/24/2023] Open
Abstract
Macrophomina phaseolina causes charcoal rot, which can significantly reduce yield and seed quality of soybean and dry bean resulting from primarily environmental stressors. Although charcoal rot has been recognized as a warm climate-driven disease of increasing concern under global climate change, knowledge regarding population genetics and climatic variables contributing to the genetic diversity of M. phaseolina is limited. This study conducted genome sequencing for 95 M. phaseolina isolates from soybean and dry bean across the continental United States, Puerto Rico, and Colombia. Inference on the population structure using 76,981 single nucleotide polymorphisms (SNPs) revealed that the isolates exhibited a discrete genetic clustering at the continental level and a continuous genetic differentiation regionally. A majority of isolates from the United States (96%) grouped in a clade with a predominantly clonal genetic structure, while 88% of Puerto Rican and Colombian isolates from dry bean were assigned to a separate clade with higher genetic diversity. A redundancy analysis (RDA) was used to estimate the contributions of climate and spatial structure to genomic variation (11,421 unlinked SNPs). Climate significantly contributed to genomic variation at a continental level with temperature seasonality explaining the most variation while precipitation of warmest quarter explaining the most when spatial structure was accounted for. The loci significantly associated with multivariate climate were found closely to the genes related to fungal stress responses, including transmembrane transport, glycoside hydrolase activity and a heat-shock protein, which may mediate climatic adaptation for M. phaseolina. On the contrary, limited genome-wide differentiation among populations by hosts was observed. These findings highlight the importance of population genetics and identify candidate genes of M. phaseolina that can be used to elucidate the molecular mechanisms that underly climatic adaptation to the changing climate.
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Affiliation(s)
- Viviana Ortiz
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, United States
| | - Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Hyunkyu Sang
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
| | - Janette Jacobs
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
| | - Dean K. Malvick
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Richard Baird
- BCH-EPP Department, Mississippi State University, Mississippi State, MS, United States
| | - Febina M. Mathew
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | | | - Kiersten A. Wise
- Department of Plant Pathology, College of Agriculture, Food and Environment, University of Kentucky, Princeton, KY, United States
| | - Gloria M. Mosquera
- Plant Pathology, Crops for Nutrition and Health, International Center for Tropical Agriculture (CIAT), The Americas Hub, Palmira, Colombia
| | - Martin I. Chilvers
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI, United States
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, United States
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Feau N, Dhillon BD, Sakalidis M, Dale AL, Søndreli KL, Goodwin SB, LeBoldus JM, Hamelin RC. Forest health in the Anthropocene: the emergence of a novel tree disease is associated with poplar cultivation. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220008. [PMID: 36744569 PMCID: PMC9900707 DOI: 10.1098/rstb.2022.0008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Plant domestication and movement are large contributors to the success of new diseases. The introduction of new host species can result in accelerated evolutionary changes in pathogens, affecting long-established coevolutionary dynamics. This has been observed in poplars where severe epidemics of pathogens that were innocuous in their natural pathosystems occurred following host domestication. The North American fungus Sphaerulina musiva is responsible for endemic leaf spots on Populus deltoides. We show that the expansion of poplar cultivation resulted in the emergence of a new lineage of this pathogen that causes stem infections on a new host, P. balsamifera. This suggests a host shift since this is not a known host. Genome analysis of this emerging lineage reveals a mosaic pattern with islands of diversity separated by fixed genome regions, which is consistent with a homoploid hybridization event between two individuals that produced a hybrid swarm. Genome regions of extreme divergence and low diversity are enriched in genes involved in host-pathogen interactions. The specialization of this emerging lineage to a new host and its clonal propagation represents a serious threat to poplars and could affect both natural and planted forests. This work provides a clear example of the changes created by the intensification of tree cultivation that facilitate the emergence of specialized pathogens, jeopardizing the natural equilibrium between hosts and pathogens. This article is part of the theme issue 'Infectious disease ecology and evolution in a changing world'.
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Affiliation(s)
- Nicolas Feau
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, VT6 1Z4,Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, Victoria, BC, Canada, V8Z 1M5
| | - Braham D. Dhillon
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, VT6 1Z4,Department of Plant Pathology, University of Florida - Fort Lauderdale Research and Education Center, Davie, FL 33314, USA
| | - Monique Sakalidis
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, VT6 1Z4,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA,Department of Forestry, Michigan State University, East Lansing, MI 48824, USA
| | - Angela L. Dale
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, VT6 1Z4,GC-New Construction Materials, FPInnovations, Vancouver, BC, Canada, V6T 1Z4
| | - Kelsey L. Søndreli
- Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | | | - Jared M. LeBoldus
- Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA,Forest Engineering, Resources and Management Department, Oregon State University, Corvallis, OR 97331, USA
| | - Richard C. Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, VT6 1Z4,Faculté de Foresterie et Géomatique, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Canada, G1V 0A6
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5
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Dong F, Wang Y, Tang M. Effects of Laccaria bicolor on Gene Expression of Populus trichocarpa Root under Poplar Canker Stress. J Fungi (Basel) 2021; 7:jof7121024. [PMID: 34947006 PMCID: PMC8703858 DOI: 10.3390/jof7121024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 11/24/2021] [Accepted: 11/27/2021] [Indexed: 12/20/2022] Open
Abstract
Poplars can be harmed by poplar canker. Inoculation with mycorrhizal fungi can improve the resistance of poplars to canker, but the molecular mechanism is still unclear. In this study, an aseptic inoculation system of L. bicolor-P. trichocarpa-B. dothidea was constructed, and transcriptome analysis was performed to investigate regulation by L. bicolor of the expression of genes in the roots of P. trichocarpa during the onset of B. dothidea infection, and a total of 3022 differentially expressed genes (DEGs) were identified. Weighted correlation network analysis (WGCNA) was performed on these DEGs, and 661 genes' expressions were considered to be affected by inoculation with L. bicolor and B. dothidea. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that these 661 DEGs were involved in multiple pathways such as signal transduction, reactive oxygen metabolism, and plant-pathogen interaction. Inoculation with L. bicolor changed the gene expression pattern of the roots, evidencing its involvement in the disease resistance response of P. trichocarpa. This research reveals the mechanism of L. bicolor in inducing resistance to canker of P. trichocarpa at the molecular level and provides a theoretical basis for the practical application of mycorrhizal fungi to improve plant disease resistance.
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Affiliation(s)
- Fengxin Dong
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (F.D.); (Y.W.)
| | - Yihan Wang
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (F.D.); (Y.W.)
| | - Ming Tang
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (F.D.); (Y.W.)
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China
- Correspondence: ; Tel.: +86-1370-922-9152
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6
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Dong F, Wang Y, Tang M. Study on the molecular mechanism of Laccaria bicolor helping Populus trichocarpa to resist the infection of Botryosphaeria dothidea. J Appl Microbiol 2021; 132:2220-2233. [PMID: 34779092 DOI: 10.1111/jam.15359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/25/2021] [Accepted: 11/04/2021] [Indexed: 11/30/2022]
Abstract
AIMS This study explored the specific molecular mechanism of Laccaria bicolor to help Populus trichocarpa resist infection by Botryosphaeria dothidea. METHODS AND RESULTS Transcriptome technology was used to sequence P. trichocarpa under disease stress, and a total of 6379 differentially expressed genes (DEGs) were identified. A total of 536 new DEGs were induced by L. bicolor during the infection of B. dothidea. L. bicolor helps to prevent and alleviate the infection of B. dothidea by regulating related genes in the cell wall pathway, signal transduction pathway, disease-resistant protein synthesis pathway and antioxidant enzyme synthesis pathway of P. trichocarpa. CONCLUSION The inoculation of L. bicolor can regulate the expression of genes in the cell wall pathway and enhance the physical defense capabilities of plants. Under disease stress conditions, L. bicolor can regulate signal transduction pathways, disease-resistant related pathways and reactive oxygen species (ROS) clearance pathways to help P. trichocarpa alleviate the disease. SIGNIFICANCE AND IMPACT OF THE STUDY The research reveals the mechanism of L. bicolor inducing resistance to canker of P. trichocarpa from the molecular level and provides a theoretical basis for the practical application of mycorrhizal fungi to improve plant disease resistance.
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Affiliation(s)
- Fengxin Dong
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Yihan Wang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Ming Tang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China.,Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, Guangdong, China
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7
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Hessenauer P, Feau N, Gill U, Schwessinger B, Brar GS, Hamelin RC. Evolution and Adaptation of Forest and Crop Pathogens in the Anthropocene. PHYTOPATHOLOGY 2021; 111:49-67. [PMID: 33200962 DOI: 10.1094/phyto-08-20-0358-fi] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Anthropocene marks the era when human activity is making a significant impact on earth, its ecological and biogeographical systems. The domestication and intensification of agricultural and forest production systems have had a large impact on plant and tree health. Some pathogens benefitted from these human activities and have evolved and adapted in response to the expansion of crop and forest systems, resulting in global outbreaks. Global pathogen genomics data including population genomics and high-quality reference assemblies are crucial for understanding the evolution and adaptation of pathogens. Crops and forest trees have remarkably different characteristics, such as reproductive time and the level of domestication. They also have different production systems for disease management with more intensive management in crops than forest trees. By comparing and contrasting results from pathogen population genomic studies done on widely different agricultural and forest production systems, we can improve our understanding of pathogen evolution and adaptation to different selection pressures. We find that in spite of these differences, similar processes such as hybridization, host jumps, selection, specialization, and clonal expansion are shaping the pathogen populations in both crops and forest trees. We propose some solutions to reduce these impacts and lower the probability of global pathogen outbreaks so that we can envision better management strategies to sustain global food production as well as ecosystem services.
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Affiliation(s)
- Pauline Hessenauer
- Faculty of Forestry, Geography and Geomatics, Laval University, Quebec City, QC, G1V 0A6 Canada
| | - Nicolas Feau
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Upinder Gill
- College of Agriculture, Food Systems, and Natural Resources, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Benjamin Schwessinger
- Research School of Biology, Australian National University, Acton, ACT 2601 Australia
| | - Gurcharn S Brar
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
| | - Richard C Hamelin
- Faculty of Forestry, Geography and Geomatics, Laval University, Quebec City, QC, G1V 0A6 Canada
- Faculty of Forestry, The University of British Columbia, Vancouver, BC, V6T 1Z4 Canada
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8
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Capron A, Feau N, Heinzelmann R, Barnes I, Benowicz A, Bradshaw RE, Dale A, Lewis KJ, Owen TJ, Reich R, Ramsfield TD, Woods AJ, Hamelin RC. Signatures of Post-Glacial Genetic Isolation and Human-Driven Migration in the Dothistroma Needle Blight Pathogen in Western Canada. PHYTOPATHOLOGY 2021; 111:116-127. [PMID: 33112215 DOI: 10.1094/phyto-08-20-0350-fi] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Many current tree improvement programs are incorporating assisted gene flow strategies to match reforestation efforts with future climates. This is the case for the lodgepole pine (Pinus contorta var. latifolia), the most extensively planted tree in western Canada. Knowledge of the structure and origin of pathogen populations associated with this tree would help improve the breeding effort. Recent outbreaks of the Dothistroma needle blight (DNB) pathogen Dothistroma septosporum on lodgepole pine in British Columbia and its discovery in Alberta plantations raised questions about the diversity and population structure of this pathogen in western Canada. Using genotyping-by-sequencing on 119 D. septosporum isolates from 16 natural pine populations and plantations from this area, we identified four genetic lineages, all distinct from the other DNB lineages from outside of North America. Modeling of the population history indicated that these lineages diverged between 31.4 and 7.2 thousand years ago, coinciding with the last glacial maximum and the postglacial recolonization of lodgepole pine in western North America. The lineage found in the Kispiox Valley from British Columbia, where an unprecedented DNB epidemic occurred in the 1990s, was close to demographic equilibrium and displayed a high level of haplotypic diversity. Two lineages found in Alberta and Prince George (British Columbia) showed departure from random mating and contemporary gene flow, likely resulting from pine breeding activities and material exchanges in these areas. The increased movement of planting material could have some major consequences by facilitating secondary contact between genetically isolated DNB lineages, possibly resulting in new epidemics.
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Affiliation(s)
- Arnaud Capron
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Nicolas Feau
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Renate Heinzelmann
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Andy Benowicz
- Alberta Agriculture and Forestry, 9920-108 Street, Edmonton, AB, T5K 2M4, Canada
| | - Rosie E Bradshaw
- School of Fundamental Sciences, Massey University, Palmerston North, 4410, New Zealand
| | - Angela Dale
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- SC-New Construction Materials, FPInnovations, Vancouver, BC, V6T 1Z4, Canada
| | - Kathy J Lewis
- Ecosystem Science and Management Program, University of Northern British Columbia, Prince George, BC, V2N 4Z9, Canada
| | - Timothy J Owen
- Ecosystem Science and Management Program, University of Northern British Columbia, Prince George, BC, V2N 4Z9, Canada
| | - Richard Reich
- Natural Resources and Forest Technology, College of New Caledonia, Prince George, BC, V2N 1P8, Canada
| | - Tod D Ramsfield
- Natural Resources Canada, Canadian Forest Service, 5320 - 122 St., Edmonton, AB, T6H 3S5, Canada
| | - Alex J Woods
- BC Ministry of Forests Lands and Natural Resource Operations and Rural Development, Skeena Region, Smithers, BC, V0J 2N0, Canada
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Faculté de foresterie et géomatique, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, QC, G1V0A6, Canada
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9
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Tabima JF, Gonen L, Gómez-Gallego M, Panda P, Grünwald NJ, Hansen EM, McDougal R, LeBoldus JM, Williams NM. Molecular Phylogenomics and Population Structure of Phytophthora pluvialis. PHYTOPATHOLOGY 2021; 111:108-115. [PMID: 33048632 DOI: 10.1094/phyto-06-20-0232-fi] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Phytophthora pluvialis is an oomycete that was first isolated from soil, water, and tree foliage in mixed Douglas-fir-tanoak forests of the U.S. Pacific Northwest (PNW). It was then identified as the causal agent of red needle cast of radiata pine (Pinus radiata) in New Zealand (NZ). Genotyping-by-sequencing was used to obtain 1,543 single nucleotide polymorphisms across 145 P. pluvialis isolates to characterize the population structure in the PNW and NZ. We tested the hypothesis that P. pluvialis was introduced to NZ from the PNW using genetic distance measurements and population structure analyses among locations between countries. The low genetic distance, population heterozygosity, and lack of geographic structure in NZ suggest a single colonization event from the United States followed by clonal expansion in NZ. The PNW Coast Range was proposed as a presumptive center of origin of the currently known distribution of P. pluvialis based on its geographic range and position as the central cluster in a minimum spanning network. The Coastal cluster of isolates were located at the root of every U.S. cluster and emerged earlier than all NZ clusters. The Coastal cluster had the highest degree of heterozygosity (Hs = 0.254) and median pairwise genetic distance (0.093) relative to any other cluster. Finally, the rapid host diversification between closely related isolates of P. pluvialis in NZ indicate that this pathogen has the potential to infect a broader range of hosts than is currently recognized.
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Affiliation(s)
- Javier F Tabima
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331, U.S.A
- Department of Biology, Clark University, The Lasry Center for Bioscience, Worcester, MA 01610, U.S.A
| | - Lilah Gonen
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331, U.S.A
| | - Mireia Gómez-Gallego
- New Zealand Forest Research Institute (Scion), 49 Sala Street, Te Papa Tipu Innovation Park, Private Bag 3020, Rotorua 3046, New Zealand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Box 7026, 750 07 Uppsala, Sweden
- UMR IAM-Interactions Arbres-Microorganismes, Université de Lorraine, INRAE, Nancy 54000, France
| | - Preeti Panda
- New Zealand Forest Research Institute (Scion), 49 Sala Street, Te Papa Tipu Innovation Park, Private Bag 3020, Rotorua 3046, New Zealand
- Department of Pathogen Ecology and Control, Plant and Food Research, Private Bag 1401, Havelock North 4130, New Zealand
| | - Niklaus J Grünwald
- USDA Agricultural Research Service, Horticultural Research Unit, 3420 NW Orchard Ave., Corvallis, OR 97331, U.S.A
| | - Everett M Hansen
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331, U.S.A
| | - Rebecca McDougal
- New Zealand Forest Research Institute (Scion), 49 Sala Street, Te Papa Tipu Innovation Park, Private Bag 3020, Rotorua 3046, New Zealand
| | - Jared M LeBoldus
- Department of Botany and Plant Pathology, Oregon State University, 2082 Cordley Hall, Corvallis, OR 97331, U.S.A
- Department of Forest Engineering, Resources and Management, Oregon State University, Peavy Forest Science Center, Corvallis, OR 97331, U.S.A
| | - Nari M Williams
- New Zealand Forest Research Institute (Scion), 49 Sala Street, Te Papa Tipu Innovation Park, Private Bag 3020, Rotorua 3046, New Zealand
- Department of Pathogen Ecology and Control, Plant and Food Research, Private Bag 1401, Havelock North 4130, New Zealand
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