1
|
Syazwan SA, Mohd-Farid A, Yih Lee S, Mohamed R. Comparative analysis of mitochondrial genomes in Ceratocystis fimbriata complex across diverse hosts. Gene 2024; 921:148539. [PMID: 38710292 DOI: 10.1016/j.gene.2024.148539] [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: 01/08/2024] [Revised: 04/16/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
The decline ofAcacia mangiumWilld. in Malaysia, especially in Sabah since 2010, is primarily due to Ceratocystiswilt and canker disease (CWCD) caused by theCeratocystis fimbriataEllis & Halst. complex. This study was aimed to investigate the mitochondrial genome architecture of two differentC. fimbriatacomplex isolates from Malaysia: one fromA. mangiumin Pahang (FRIM1162) and another fromEucalyptus pellitain Sarawak (FRIM1441). This research employed Next-Generation Sequencing (NGS) to contrast genomes from diverse hosts with nine additional mitochondrial sequences, identifying significant genetic diversity and mutational hotspots in the mitochondrial genome alignment. The mitochondrial genome-based phylogenetic analysis revealed a significant genetic relationship between the studied isolates and theC. fimbriatacomplex in the South American Subclade, indicating that theC. fimbriatacomplex discovered in Malaysia isC. manginecans. The comparative mitochondrial genome demonstrates the adaptability of the complex due to mobile genetic components and genomic rearrangements in the studiedfungal isolates. This research enhances our knowledge of the genetic diversity and evolutionary patterns within theC. fimbriatacomplex, aiding in a deeper understanding of fungal disease development and host adaption processes. The acquired insights are crucial for creating specific management strategies for CWCD, improving the overall understanding of fungal disease evolution and control.
Collapse
Affiliation(s)
- Samsuddin Ahmad Syazwan
- Mycology and Pathology Branch, Forest Health and Conservation Programme, Forest Biodiversity Division, Forest Research Institute Malaysia, 52109 Kepong, Selangor, Malaysia; Department of Forest Science and Biodiversity, Faculty of Forestry and Environment, 43400 Serdang, Selangor, Malaysia.
| | - Ahmad Mohd-Farid
- Mycology and Pathology Branch, Forest Health and Conservation Programme, Forest Biodiversity Division, Forest Research Institute Malaysia, 52109 Kepong, Selangor, Malaysia.
| | - Shiou Yih Lee
- Faculty of Health and Life Sciences, INTI International University, 71800 Nilai, Negeri Sembilan, Malaysia.
| | - Rozi Mohamed
- Department of Forest Science and Biodiversity, Faculty of Forestry and Environment, 43400 Serdang, Selangor, Malaysia.
| |
Collapse
|
2
|
Singh P, St Clair JB, Lind BM, Cronn R, Wilhelmi NP, Feau N, Lu M, Vidakovic DO, Hamelin RC, Shaw DC, Aitken SN, Yeaman S. Genetic architecture of disease resistance and tolerance in Douglas-fir trees. THE NEW PHYTOLOGIST 2024; 243:705-719. [PMID: 38803110 DOI: 10.1111/nph.19797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/18/2024] [Indexed: 05/29/2024]
Abstract
Understanding the genetic basis of how plants defend against pathogens is important to monitor and maintain resilient tree populations. Swiss needle cast (SNC) and Rhabdocline needle cast (RNC) epidemics are responsible for major damage of forest ecosystems in North America. Here we investigate the genetic architecture of tolerance and resistance to needle cast diseases in Douglas-fir (Pseudotsuga menziesii) caused by two fungal pathogens: SNC caused by Nothophaeocryptopus gaeumannii, and RNC caused by Rhabdocline pseudotsugae. We performed case-control genome-wide association analyses and found disease resistance and tolerance in Douglas-fir to be polygenic and under strong selection. We show that stomatal regulation as well as ethylene and jasmonic acid pathways are important for resisting SNC infection, and secondary metabolite pathways play a role in tolerating SNC once the plant is infected. We identify a major transcriptional regulator of plant defense, ERF1, as the top candidate for RNC resistance. Our findings shed light on the highly polygenic architectures underlying fungal disease resistance and tolerance and have important implications for forestry and conservation as the climate changes.
Collapse
Affiliation(s)
- Pooja Singh
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
- Aquatic Ecology & Evolution Division, Institute of Ecology and Evolution, University of Bern, Bern, CH-3012, Switzerland
- Department of Fish Ecology & Evolution, Swiss Federal Institute of Aquatic Science and Technology (EAWAG), Kastanienbaum, CH-6047, Switzerland
| | - J Bradley St Clair
- USDA Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR, 97331, USA
| | - Brandon M Lind
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T1Z4, BC, Canada
| | - Richard Cronn
- USDA Forest Service, Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR, 97331, USA
| | - Nicholas P Wilhelmi
- Forest Health Protection, USDA Forest Service, Arizona Zone, Flagstaff, AZ, 86001, USA
| | - Nicolas Feau
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T1Z4, BC, Canada
| | - Mengmeng Lu
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Dragana Obreht Vidakovic
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T1Z4, BC, Canada
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T1Z4, BC, Canada
| | - David C Shaw
- Department of Forest Engineering, Resources and Management, Oregon State University, Corvallis, OR, 97331, USA
| | - Sally N Aitken
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, V6T1Z4, BC, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| |
Collapse
|
3
|
Amezrou R, Ducasse A, Compain J, Lapalu N, Pitarch A, Dupont L, Confais J, Goyeau H, Kema GHJ, Croll D, Amselem J, Sanchez-Vallet A, Marcel TC. Quantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing. Nat Commun 2024; 15:1933. [PMID: 38431601 PMCID: PMC10908820 DOI: 10.1038/s41467-024-46191-1] [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: 02/14/2024] [Indexed: 03/05/2024] Open
Abstract
Knowledge of genetic determinism and evolutionary dynamics mediating host-pathogen interactions is essential to manage fungal plant diseases. Studies on the genetic architecture of fungal pathogenicity often focus on large-effect effector genes triggering strong, qualitative resistance. It is not clear how this translates to predominately quantitative interactions. Here, we use the Zymoseptoria tritici-wheat model to elucidate the genetic architecture of quantitative pathogenicity and mechanisms mediating host adaptation. With a multi-host genome-wide association study, we identify 19 high-confidence candidate genes associated with quantitative pathogenicity. Analysis of genetic diversity reveals that sequence polymorphism is the main evolutionary process mediating differences in quantitative pathogenicity, a process that is likely facilitated by genetic recombination and transposable element dynamics. Finally, we use functional approaches to confirm the role of an effector-like gene and a methyltransferase in phenotypic variation. This study highlights the complex genetic architecture of quantitative pathogenicity, extensive diversifying selection and plausible mechanisms facilitating pathogen adaptation.
Collapse
Affiliation(s)
- Reda Amezrou
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France.
| | - Aurélie Ducasse
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | - Jérôme Compain
- Université Paris-Saclay, INRAE, UR URGI, Versailles, France
| | - Nicolas Lapalu
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
- Université Paris-Saclay, INRAE, UR URGI, Versailles, France
| | - Anais Pitarch
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | - Laetitia Dupont
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | - Johann Confais
- Université Paris-Saclay, INRAE, UR BIOGER, Palaiseau, France
| | | | - Gert H J Kema
- Plant Research International B.V., Wageningen, The Netherlands
| | - Daniel Croll
- Department of Ecology and Evolution, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Joëlle Amselem
- Université Paris-Saclay, INRAE, UR URGI, Versailles, France
| | | | | |
Collapse
|
4
|
Treindl AD, Stapley J, Croll D, Leuchtmann A. Two-speed genomes of Epichloe fungal pathogens show contrasting signatures of selection between species and across populations. Mol Ecol 2024; 33:e17242. [PMID: 38084851 DOI: 10.1111/mec.17242] [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: 02/08/2023] [Revised: 11/23/2023] [Accepted: 11/30/2023] [Indexed: 12/19/2023]
Abstract
Antagonistic selection between pathogens and their hosts can drive rapid evolutionary change and leave distinct molecular footprints of past and ongoing selection in the genomes of the interacting species. Despite an increasing availability of tools able to identify signatures of selection, the genetic mechanisms underlying coevolutionary interactions and the specific genes involved are still poorly understood, especially in heterogeneous natural environments. We searched the genomes of two species of Epichloe plant pathogen for evidence of recent selection. The Epichloe genus includes highly host-specific species that can sterilize their grass hosts. We performed selection scans using genome-wide SNP data from seven natural populations of two co-occurring Epichloe sibling species specialized on different hosts. We found evidence of recent (and ongoing) selective sweeps across the genome in both species. However, selective sweeps were more abundant in the species with a larger effective population size. Sweep regions often overlapped with highly polymorphic AT-rich regions supporting the role of these genome compartments in adaptive evolution. Although most loci under selection were specific to individual populations, we could also identify several candidate genes targeted by selection in sweep regions shared among populations. The genes encoded small secreted proteins typical of fungal effectors and cell wall-degrading enzymes. By investigating the genomic signatures of selection across multiple populations and species, this study contributes to our understanding of complex adaptive processes in natural plant pathogen systems.
Collapse
Affiliation(s)
- Artemis D Treindl
- Plant Ecological Genetics Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- Biodiversity and Conservation Biology, Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Jessica Stapley
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Adrian Leuchtmann
- Plant Ecological Genetics Group, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
5
|
Rad SH, Ebrahimi L, Croll D. Virulence Associations and Global Context of AvrStb6 Genetic Diversity in Iranian Populations of Zymoseptoria tritici. PHYTOPATHOLOGY 2023; 113:1924-1933. [PMID: 37261424 DOI: 10.1094/phyto-09-22-0348-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Managing pathogen damage in wheat production is important for sustaining yields. Fungal plant pathogen genomes encode many small secreted proteins acting as effectors that play key roles in the successful colonization of host tissue and triggering host defenses. AvrStb6 is the first described Zymoseptoria tritici avirulence effector, which triggers Stb6-mediated immunity in the wheat host in a gene-for-gene manner. Evasion of major resistance factors such as Stb6 challenges deployment decisions on wheat cultivars. In this study, we analyzed the evolution of the AvrStb6 effector in Iranian isolates of Z. tritici. In total, 78 isolates were isolated and purified from 30 infected wheat specimens collected from the East Azerbaijan and Ardabil provinces of Iran. The pathogenicity of all isolates was evaluated on the susceptible wheat cultivar 'Tajan'. A subset of 40 isolates were also tested for pathogenicity on the resistant cultivar 'Shafir' carrying Stb6. Genetic diversity at the AvrStb6 locus was analyzed for 14 isolates covering the breadth of the observed disease severity. The AvrStb6 sequence variation was high, with virulent isolates carrying highly diverse AvrStb6 haplotypes. In an analysis including more than 1,000 additional AvrStb6 sequences from a global set of isolates, we found that virulent isolates carried AvrStb6 haplotypes either clustering with known virulent haplotypes on different continents or constituting previously unknown haplotypes. Furthermore, we found that AvrStb6 variants from avirulent isolates clustered with known avirulent genotypes from Europe. Our study highlights the relevance of AvrStb6 for Z. tritici virulence and the exceptional global diversity patterns of this effector.
Collapse
Affiliation(s)
- Sepideh Hatami Rad
- Department of Entomology and Plant Pathology, College of Agricultural Technology, University College of Agriculture and Natural Resources, University of Tehran, Tehran 33916-53755, Iran
| | - Leila Ebrahimi
- Department of Entomology and Plant Pathology, College of Agricultural Technology, University College of Agriculture and Natural Resources, University of Tehran, Tehran 33916-53755, Iran
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchatel, CH-2000 Neuchatel, Switzerland
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Chen H, King R, Smith D, Bayon C, Ashfield T, Torriani S, Kanyuka K, Hammond-Kosack K, Bieri S, Rudd J. Combined pangenomics and transcriptomics reveals core and redundant virulence processes in a rapidly evolving fungal plant pathogen. BMC Biol 2023; 21:24. [PMID: 36747219 PMCID: PMC9903594 DOI: 10.1186/s12915-023-01520-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 01/19/2023] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Studying genomic variation in rapidly evolving pathogens potentially enables identification of genes supporting their "core biology", being present, functional and expressed by all strains or "flexible biology", varying between strains. Genes supporting flexible biology may be considered to be "accessory", whilst the "core" gene set is likely to be important for common features of a pathogen species biology, including virulence on all host genotypes. The wheat-pathogenic fungus Zymoseptoria tritici represents one of the most rapidly evolving threats to global food security and was the focus of this study. RESULTS We constructed a pangenome of 18 European field isolates, with 12 also subjected to RNAseq transcription profiling during infection. Combining this data, we predicted a "core" gene set comprising 9807 sequences which were (1) present in all isolates, (2) lacking inactivating polymorphisms and (3) expressed by all isolates. A large accessory genome, consisting of 45% of the total genes, was also defined. We classified genetic and genomic polymorphism at both chromosomal and individual gene scales. Proteins required for essential functions including virulence had lower-than average sequence variability amongst core genes. Both core and accessory genomes encoded many small, secreted candidate effector proteins that likely interact with plant immunity. Viral vector-mediated transient in planta overexpression of 88 candidates failed to identify any which induced leaf necrosis characteristic of disease. However, functional complementation of a non-pathogenic deletion mutant lacking five core genes demonstrated that full virulence was restored by re-introduction of the single gene exhibiting least sequence polymorphism and highest expression. CONCLUSIONS These data support the combined use of pangenomics and transcriptomics for defining genes which represent core, and potentially exploitable, weaknesses in rapidly evolving pathogens.
Collapse
Affiliation(s)
- Hongxin Chen
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, Herts UK
- Present address: School of Agriculture, Shenzhen Campus of Sun Yat-sen University, Guangming District, Shenzhen, Guangdong People’s Republic of China
| | - Robert King
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, Herts UK
| | - Dan Smith
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, Herts UK
| | - Carlos Bayon
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, Herts UK
| | - Tom Ashfield
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, Herts UK
- Crop Health and Protection (CHaP), Rothamsted Research, Harpenden, Herts UK
| | - Stefano Torriani
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Kostya Kanyuka
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, Herts UK
- Present address: National Institute for Agricultural Botany (NIAB), 93 Lawrence Weaver Road, Cambridge, UK
| | - Kim Hammond-Kosack
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, Herts UK
| | - Stephane Bieri
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Jason Rudd
- Department of Protecting Crops and the Environment, Rothamsted Research, Harpenden, Herts UK
| |
Collapse
|
8
|
Bracalini M, Benigno A, Aglietti C, Panzavolta T, Moricca S. Thousand Cankers Disease in Walnut Trees in Europe: Current Status and Management. Pathogens 2023; 12:pathogens12020164. [PMID: 36839436 PMCID: PMC9959596 DOI: 10.3390/pathogens12020164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/28/2022] [Accepted: 01/17/2023] [Indexed: 01/22/2023] Open
Abstract
Thousand cankers disease (TCD) is a new deadly disease in walnut trees (Juglans spp.), which is plaguing commercial plantations, natural groves, and ornamental black walnut trees (Juglans nigra) in their native and invasion areas in the US and, more recently, in artificial plantations and amenity trees in the newly-invaded areas in Europe (Italy). This insect/fungus complex arises from the intense trophic activity of the bark beetle vector Pityophthorus juglandis in the phloem of Juglans spp. and the subsequent development of multiple Geosmithia morbida cankers around beetles' entry/exit holes. After an analysis of the main biological and ecological traits of both members of this insect/fungus complex, this review explores the options available for TCD prevention and management. Special focus is given to those diagnostic tools developed for disease detection, surveillance, and monitoring, as well as to existing phytosanitary regulations, protocols, and measures that comply with TCD eradication and containment. Only integrated disease management can effectively curtail the pervasive spread of TCD, thus limiting the damage to natural ecosystems, plantations, and ornamental walnuts.
Collapse
|
9
|
Bazzicalupo A. Local adaptation in fungi. FEMS Microbiol Rev 2022; 46:6604384. [PMID: 35675293 DOI: 10.1093/femsre/fuac026] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 01/09/2023] Open
Abstract
In this review, I explore the pervasive but underappreciated role of local adaptation in fungi. It has been difficult historically to study local adaptation in fungi because of the limited understanding of fungal species and their traits, but new hope has been offered with technological advances in sequencing. The filamentous nature of fungi invalidates some assumptions made in evolution because of their ability to exist as multinucleate entities with genetically different nuclei sharing the same cytoplasm. Many insights on local adaptation have come from studying fungi, and much of the empirical evidence gathered about local adaptation in the context of host-pathogen interactions comes from studying fungal virulence genes, drug resistance, and environmental adaptation. Together, these insights paint a picture of the variety of processes involved in fungal local adaptation and their connections to the unusual cell biology of Fungi (multinucleate, filamentous habit), but there is much that remains unknown, with major gaps in our knowledge of fungal species, their phenotypes, and the ways by which they adapt to local conditions.
Collapse
Affiliation(s)
- Anna Bazzicalupo
- Department of Zoology, University of British Columbia, 4200 - 6270 University Blvd., Vancouver V6T 1Z4, Canada
| |
Collapse
|
10
|
Chaisiri C, Liu X, Lin Y, Luo C. Diaporthe citri: A Fungal Pathogen Causing Melanose Disease. PLANTS (BASEL, SWITZERLAND) 2022; 11:1600. [PMID: 35736750 PMCID: PMC9227384 DOI: 10.3390/plants11121600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/25/2022] [Accepted: 06/12/2022] [Indexed: 11/16/2022]
Abstract
Citrus melanose is a fungal disease caused by Diaporthe citri F.A. Wolf. It is found in various citrus-growing locations across the world. The host range of D. citri is limited to plants of the Citrus genus. The most economically important hosts are Citrus reticulata (mandarin), C. sinensis (sweet orange), C. grandis or C. maxima (pumelo), and C. paradisi (grapefruit). In the life cycle of D. citri throughout the citrus growing season, pycnidia can be seen in abundance on dead branches, especially after rain, with conidia appearing as slimy masses discharged from the dead twigs. Raindrops can transmit conidia to leaves, twigs, and fruits, resulting in disease dispersion throughout small distances. Persistent rains and warm climatic conditions generally favor disease onset and development. The melanose disease causes a decline in fruit quality, which lowers the value of fruits during marketing and exportation. High rainfall areas should avoid planting susceptible varieties. In this article, information about the disease symptoms, history, geographic distribution, epidemiology, impact, and integrated management practices, as well as the pathogen morphology and identification, was reviewed and discussed.
Collapse
Affiliation(s)
- Chingchai Chaisiri
- Key Lab of Horticultural Plant Biology, Ministry of Education, Wuhan 430070, China; (C.C.); (X.L.)
- Hubei Key Lab of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China;
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangyu Liu
- Key Lab of Horticultural Plant Biology, Ministry of Education, Wuhan 430070, China; (C.C.); (X.L.)
- Hubei Key Lab of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China;
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Lin
- Hubei Key Lab of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China;
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chaoxi Luo
- Key Lab of Horticultural Plant Biology, Ministry of Education, Wuhan 430070, China; (C.C.); (X.L.)
- Hubei Key Lab of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China;
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
11
|
Bolin LG, Lau JA. Linking genetic diversity and species diversity through plant–soil feedback. Ecology 2022; 103:e3692. [DOI: 10.1002/ecy.3692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/14/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Lana G. Bolin
- Department of Biology Indiana University Jordan Hall, 1001 E. 3rd St Bloomington IN USA
| | - Jennifer A. Lau
- Department of Biology Indiana University Jordan Hall, 1001 E. 3rd St Bloomington IN USA
- Environmental Resilience Institute Indiana University Bloomington IN USA
| |
Collapse
|
12
|
Stalder L, Oggenfuss U, Mohd‐Assaad N, Croll D. The population genetics of adaptation through copy‐number variation in a fungal plant pathogen. Mol Ecol 2022; 32:2443-2460. [PMID: 35313056 DOI: 10.1111/mec.16435] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 11/28/2022]
Abstract
Microbial pathogens can adapt rapidly to changing environments such as the application of pesticides or host resistance. Copy number variations (CNVs) are a major source of adaptive genetic variation for recent adaptation. Here, we analyse how a major fungal pathogen of barley, Rhynchosporium commune, has adapted to the host environment and fungicide applications. We screen the genomes of 125 isolates sampled across a worldwide set of populations and identify a total of 7,879 gene duplications and 116 gene deletions. Most gene duplications result from segmental chromosomal duplications. Although CNVs are generally under negative selection, we find that genes affected by CNVs are enriched in functions related to host exploitation (i.e., effectors and cell-wall-degrading enzymes). We perform genome-wide association studies (GWAS) and identify a large segmental duplication of CYP51A that has contributed to the emergence of azole resistance and a duplication encompassing an effector gene affecting virulence. We show that the adaptive CNVs were probably created by recently active transposable element families. Moreover, we find that specific transposable element families are important drivers of recent gene CNV. Finally, we use a genome-wide single nucleotide polymorphism data set to replicate the GWAS and contrast it with the CNV-focused analysis. Together, our findings show how extensive segmental duplications create the raw material for recent adaptation in global populations of a fungal pathogen.
Collapse
Affiliation(s)
- Luzia Stalder
- Laboratory of Evolutionary Genetics Institute of Biology University of Neuchâtel 2000 Neuchâtel Switzerland
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics Institute of Biology University of Neuchâtel 2000 Neuchâtel Switzerland
| | - Norfarhan Mohd‐Assaad
- Plant Pathology Institute of Integrative Biology ETH, Zurich 8092 Zurich Switzerland
- Department of Applied Physics Faculty of Science and Technology Universiti Kebangsaan Malaysia 43600 Bangi Selangor Malaysia
| | - Daniel Croll
- Laboratory of Evolutionary Genetics Institute of Biology University of Neuchâtel 2000 Neuchâtel Switzerland
| |
Collapse
|
13
|
Fabre F, Burie J, Ducrot A, Lion S, Richard Q, Djidjou‐Demasse R. An epi-evolutionary model for predicting the adaptation of spore-producing pathogens to quantitative resistance in heterogeneous environments. Evol Appl 2022; 15:95-110. [PMID: 35126650 PMCID: PMC8792485 DOI: 10.1111/eva.13328] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 11/28/2022] Open
Abstract
We have modeled the evolutionary epidemiology of spore-producing plant pathogens in heterogeneous environments sown with several cultivars carrying quantitative resistances. The model explicitly tracks the infection-age structure and genetic composition of the pathogen population. Each strain is characterized by pathogenicity traits determining its infection efficiency and a time-varying sporulation curve taking into account lesion aging. We first derived a general expression of the basic reproduction number R 0 for fungal pathogens in heterogeneous environments. We show that the evolutionary attractors of the model coincide with local maxima of R 0 only if the infection efficiency is the same on all host types. We then studied the contribution of three basic resistance characteristics (the pathogenicity trait targeted, resistance effectiveness, and adaptation cost), in interaction with the deployment strategy (proportion of fields sown with a resistant cultivar), to (i) pathogen diversification at equilibrium and (ii) the shaping of transient dynamics from evolutionary and epidemiological perspectives. We show that quantitative resistance affecting only the sporulation curve will always lead to a monomorphic population, whereas dimorphism (i.e., pathogen diversification) can occur if resistance alters infection efficiency, notably with high adaptation costs and proportions of the resistant cultivar. Accordingly, the choice of the quantitative resistance genes operated by plant breeders is a driver of pathogen diversification. From an evolutionary perspective, the time to emergence of the evolutionary attractor best adapted to the resistant cultivar tends to be shorter when resistance affects infection efficiency than when it affects sporulation. Conversely, from an epidemiological perspective, epidemiological control is always greater when the resistance affects infection efficiency. This highlights the difficulty of defining deployment strategies for quantitative resistance simultaneously maximizing epidemiological and evolutionary outcomes.
Collapse
Affiliation(s)
- Frédéric Fabre
- INRAEBordeaux Sciences AgroISVVSAVEVillenave d’OrnonFrance
| | | | | | - Sébastien Lion
- CEFECNRSUniv. MontpellierEPHEIRDUniv. Montpellier 3 Paul‐ValéryMontpellierFrance
| | | | | |
Collapse
|
14
|
Anand G, Rajeshkumar KC. Challenges and Threats Posed by Plant Pathogenic Fungi on Agricultural Productivity and Economy. Fungal Biol 2022. [DOI: 10.1007/978-981-16-8877-5_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
15
|
Eck JL, Barrès B, Soubeyrand S, Sirén J, Numminen E, Laine AL. Strain Diversity and Spatial Distribution Are Linked to Epidemic Dynamics in Host Populations. Am Nat 2022; 199:59-74. [DOI: 10.1086/717179] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
16
|
Castillo AI, Tsai CW, Su CC, Weng LW, Lin YC, Cho ST, Almeida RPP, Kuo CH. Genetic differentiation of Xylella fastidiosa following the introduction into Taiwan. Microb Genom 2021; 7:000727. [PMID: 34898423 PMCID: PMC8767338 DOI: 10.1099/mgen.0.000727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 10/22/2021] [Indexed: 12/15/2022] Open
Abstract
The economically important plant pathogen Xylella fastidiosa has been reported in multiple regions of the globe during the last two decades, threatening a growing list of plants. Particularly, X. fastidiosa subspecies fastidiosa causes Pierce's disease (PD) of grapevines, which is a problem in the USA, Spain, and Taiwan. In this work, we studied PD-causing subsp. fastidiosa populations and compared the genome sequences of 33 isolates found in Central Taiwan with 171 isolates from the USA and two from Spain. Phylogenetic relationships, haplotype networks, and genetic diversity analyses confirmed that subsp. fastidiosa was recently introduced into Taiwan from the Southeast USA (i.e. the PD-I lineage). Recent core-genome recombination events were detected among introduced subsp. fastidiosa isolates in Taiwan and contributed to the development of genetic diversity. The genetic diversity observed includes contributions through recombination from unknown donors, suggesting that higher genetic diversity exists in the region. Nevertheless, no recombination event was detected between X. fastidiosa subsp. fastidiosa and the endemic sister species Xylella taiwanensis, which is the causative agent of pear leaf scorch disease. In summary, this study improved our understanding of the genetic diversity of an important plant pathogenic bacterium after its invasion to a new region.
Collapse
Affiliation(s)
- Andreina I. Castillo
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Chi-Wei Tsai
- Department of Entomology, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Chiou-Chu Su
- Division of Pesticide Application, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Taichung 413, Taiwan, ROC
| | - Ling-Wei Weng
- Department of Entomology, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Yu-Chen Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Rodrigo P. P. Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan, ROC
| |
Collapse
|
17
|
Influence of H 2O 2-Induced Oxidative Stress on In Vitro Growth and Moniliformin and Fumonisins Accumulation by Fusarium proliferatum and Fusarium subglutinans. Toxins (Basel) 2021; 13:toxins13090653. [PMID: 34564657 PMCID: PMC8473447 DOI: 10.3390/toxins13090653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/07/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
Fusarium proliferatum and Fusarium subglutinans are common pathogens of maize which are known to produce mycotoxins, including moniliformin (MON) and fumonisins (FBs). Fungal secondary metabolism and response to oxidative stress are interlaced, where hydrogen peroxide (H2O2) plays a pivotal role in the modulation of mycotoxin production. The objective of this study is to examine the effect of H2O2-induced oxidative stress on fungal growth, as well as MON and FBs production, in different isolates of these fungi. When these isolates were cultured in the presence of 1, 2, 5, and 10 mM H2O2, the fungal biomass of F. subglutinans isolates showed a strong sensitivity to increasing oxidative conditions (27–58% reduction), whereas F. proliferatum isolates were not affected or even slightly improved (45% increase). H2O2 treatment at the lower concentration of 1 mM caused an almost total disappearance of MON and a strong reduction of FBs content in the two fungal species and isolates tested. The catalase activity, surveyed due to its crucial role as an H2O2 scavenger, showed no significant changes at 1 mM H2O2 treatment, thus indicating a lack of correlation with MON and FB changes. H2O2 treatment was also able to reduce MON and FB content in certified maize material, and the same behavior was observed in the presence and absence of these fungi, highlighting a direct effect of H2O2 on the stability of these mycotoxins. Taken together, these data provide insights into the role of H2O2 which, when increased under stress conditions, could affect the vegetative response and mycotoxin production (and degradation) of these fungi.
Collapse
|
18
|
Abundant Genetic Diversity and Extensive Differentiation among Geographic Populations of the Citrus Pathogen Diaporthe citri in Southern China. J Fungi (Basel) 2021; 7:jof7090749. [PMID: 34575787 PMCID: PMC8468327 DOI: 10.3390/jof7090749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/02/2021] [Accepted: 09/09/2021] [Indexed: 11/29/2022] Open
Abstract
The fungal pathogen Diaporthe citri is a major cause of diseases in citrus. One common disease is melanose, responsible for large economic losses to the citrus fruit industry. However, very little is known about the epidemiology and genetic structure of D. citri. In this study, we analyzed 339 isolates from leaves and fruits with melanose symptoms from five provinces in southern China at 14 polymorphic simple sequence repeat (SSR) loci and the mating type idiomorphs. The genetic variations were analyzed at three levels with separate samples: among provinces, among orchards within one county, and among trees within one orchard. The five provincial populations from Fujian, Zhejiang, Jiangxi, Hunan, and Guizhou were significantly differentiated, while limited differences were found among orchards from the same county or among trees from the same orchard. STRUCTURE analysis detected two genetic clusters in the total sample, with different provincial subpopulations showing different frequencies of isolates in these two clusters. Mantel analysis showed significant positive correlation between genetic and geographic distances, consistent with geographic separation as a significant barrier to gene flow in D. citri in China. High levels of genetic diversity were found within individual subpopulations at all three spatial scales of analyses. Interestingly, most subpopulations at all three spatial scales had the two mating types in similar frequencies and with alleles at the 14 SSR loci not significantly different from linkage equilibrium. Indeed, strains with different mating types and different multilocus genotypes were frequently isolated from the same leaves and fruits. The results indicate that sexual reproduction plays an important role in natural populations of D. citri in southern China and that its ascospores likely represent an important contributor to citrus disease.
Collapse
|
19
|
Zhong Z, McDonald BA, Palma-Guerrero J. Tolerance to oxidative stress is associated with both oxidative stress response and inherent growth in a fungal wheat pathogen. Genetics 2021; 217:6029569. [PMID: 33724407 DOI: 10.1093/genetics/iyaa022] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 11/23/2020] [Indexed: 01/25/2023] Open
Abstract
Reactive oxygen species are toxic byproducts of aerobic respiration that are also important in mediating a diversity of cellular functions. Reactive oxygen species form an important component of plant defenses to inhibit microbial pathogens during pathogen-plant interactions. Tolerance to oxidative stress is likely to make a significant contribution to the viability and pathogenicity of plant pathogens, but the complex network of oxidative stress responses hinders identification of the genes contributing to this trait. Here, we employed a forward genetic approach to investigate the genetic architecture of oxidative stress tolerance in the fungal wheat pathogen Zymoseptoria tritici. We used quantitative trait locus (QTL) mapping of growth and melanization under axenic conditions in two cross-populations to identify genomic regions associated with tolerance to oxidative stress. We found that QTLs associated with growth under oxidative stress as well as inherent growth can affect oxidative stress tolerance, and we identified two uncharacterized genes in a major QTL associated with this trait. Our data suggest that melanization does not affect tolerance to oxidative stress, which differs from what was found for animal pathogens. This study provides a whole-genome perspective on the genetic basis of oxidative stress tolerance in a plant pathogen.
Collapse
Affiliation(s)
- Ziming Zhong
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, 8092 Zürich, Switzerland
| | - Bruce A McDonald
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, 8092 Zürich, Switzerland
| | - Javier Palma-Guerrero
- Plant Pathology Group, Institute of Integrative Biology, ETH Zurich, 8092 Zürich, Switzerland.,Department of Biointeractions and Crop Protection, Rothamsted Research, AL5 2JQ Harpenden, UK
| |
Collapse
|
20
|
Zhang J, Shen N, Li C, Xiang X, Liu G, Gui Y, Patev S, Hibbett DS, Barry K, Andreopoulos W, Lipzen A, Riley R, He G, Yan M, Grigoriev IV, Shan Kwan H, Kit Cheung M, Bian Y, Xiao Y. Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes. J Adv Res 2021; 38:91-106. [PMID: 35572413 PMCID: PMC9091725 DOI: 10.1016/j.jare.2021.09.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/17/2021] [Accepted: 09/19/2021] [Indexed: 02/08/2023] Open
Abstract
We detected three subgroups of L. edodes with robust phenotypic differentiation. The three subgroups were diverged 36,871 generations ago. L. edodes cultivars in China might originate from the vicinity of Northeast China. We dissected the genetic basis of adaptive evolution in L. edodes. Genes related to fruiting body development are involved in adaptive evolution.
Introduction Mushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype and adaptation in mushroom-forming fungi. Objectives This study aimed to (1) uncover the population structure and demographic history of Lentinula edodes, (2) dissect the genetic basis of adaptive evolution in L. edodes, and (3) determine if genes related to fruiting body development are involved in adaptive evolution. Methods We analyzed genomes and fruiting body-related traits (FBRTs) in 133 L. edodes strains and conducted RNA-seq analysis of fruiting body development in the YS69 strain. Combined methods of genomic scan for divergence, genome-wide association studies (GWAS), and RNA-seq were used to dissect the genetic basis of adaptive evolution. Results We detected three distinct subgroups of L. edodes via single nucleotide polymorphisms, which showed robust phenotypic and temperature response differentiation and correlation with geographical distribution. Demographic history inference suggests that the subgroups diverged 36,871 generations ago. Moreover, L. edodes cultivars in China may have originated from the vicinity of Northeast China. A total of 942 genes were found to be related to genetic divergence by genomic scan, and 719 genes were identified to be candidates underlying FBRTs by GWAS. Integrating results of genomic scan and GWAS, 80 genes were detected to be related to phenotypic differentiation. A total of 364 genes related to fruiting body development were involved in genetic divergence and phenotypic differentiation. Conclusion Adaptation to the local environment, especially temperature, triggered genetic divergence and phenotypic differentiation of L. edodes. A general model for genetic divergence and phenotypic differentiation during adaptive evolution in L. edodes, which involves in signal perception and transduction, transcriptional regulation, and fruiting body morphogenesis, was also integrated here.
Collapse
|
21
|
Pereira D, Oggenfuss U, McDonald BA, Croll D. Population genomics of transposable element activation in the highly repressive genome of an agricultural pathogen. Microb Genom 2021; 7:000540. [PMID: 34424154 PMCID: PMC8549362 DOI: 10.1099/mgen.0.000540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/03/2021] [Indexed: 12/13/2022] Open
Abstract
The activity of transposable elements (TEs) can be an important driver of genetic diversity with TE-mediated mutations having a wide range of fitness consequences. To avoid deleterious effects of TE activity, some fungi have evolved highly sophisticated genomic defences to reduce TE proliferation across the genome. Repeat-induced point mutation (RIP) is a fungal-specific TE defence mechanism efficiently targeting duplicated sequences. The rapid accumulation of RIPs is expected to deactivate TEs over the course of a few generations. The evolutionary dynamics of TEs at the population level in a species with highly repressive genome defences is poorly understood. Here, we analyse 366 whole-genome sequences of Parastagonospora nodorum, a fungal pathogen of wheat with efficient RIP. A global population genomics analysis revealed high levels of genetic diversity and signs of frequent sexual recombination. Contrary to expectations for a species with RIP, we identified recent TE activity in multiple populations. The TE composition and copy numbers showed little divergence among global populations regardless of the demographic history. Miniature inverted-repeat transposable elements (MITEs) and terminal repeat retrotransposons in miniature (TRIMs) were largely underlying recent intra-species TE expansions. We inferred RIP footprints in individual TE families and found that recently active, high-copy TEs have possibly evaded genomic defences. We find no evidence that recent positive selection acted on TE-mediated mutations rather that purifying selection maintained new TE insertions at low insertion frequencies in populations. Our findings highlight the complex evolutionary equilibria established by the joint action of TE activity, selection and genomic repression.
Collapse
Affiliation(s)
- Danilo Pereira
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
- Present address: Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, D-24306 Plön, Germany
| | - Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Bruce A. McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| |
Collapse
|
22
|
Wang JT, Shen JP, Zhang LM, Singh BK, Delgado-Baquerizo M, Hu HW, Han LL, Wei WX, Fang YT, He JZ. Generalist Taxa Shape Fungal Community Structure in Cropping Ecosystems. Front Microbiol 2021; 12:678290. [PMID: 34305842 PMCID: PMC8299105 DOI: 10.3389/fmicb.2021.678290] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 06/17/2021] [Indexed: 12/05/2022] Open
Abstract
Fungi regulate nutrient cycling, decomposition, symbiosis, and pathogenicity in cropland soils. However, the relative importance of generalist and specialist taxa in structuring soil fungal community remains largely unresolved. We hypothesized that generalist fungi, which are adaptable to various environmental conditions, could potentially dominate the community and become the basis for fungal coexisting networks in cropping systems. In this study, we identified the generalist and habitat specialist fungi in cropland soils across a 2,200 kms environmental gradient, including three bioclimatic regions (subtropical, warm temperate, and temperate). A few fungal taxa in our database were classified as generalist taxa (~1%). These generalists accounted for >35% of the relative abundance of all fungal populations, and most of them are Ascomycota and potentially pathotrophic. Compared to the specialist taxa (5–17% of all phylotypes in three regions), generalists had a higher degree of connectivity and were often identified as hub within the network. Structural equation modeling provided further evidence that after accounting for spatial and climatic/edaphic factors, generalists had larger contributions to the fungal coexistence pattern than habitat specialists. Taken together, our study provided evidence that generalist taxa are crucial components for fungal community structure. The knowledge of generalists can provide important implication for understanding the ecological preference of fungal groups in cropland systems.
Collapse
Affiliation(s)
- Jun-Tao Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Ju-Pei Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Li-Mei Zhang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia.,Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Manuel Delgado-Baquerizo
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, United States
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.,Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
| | - Li-Li Han
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Wen-Xue Wei
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, China
| | - Yun-Ting Fang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, China
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia.,Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
| |
Collapse
|
23
|
Chen JY, Zhang DD, Huang JQ, Li R, Wang D, Song J, Puri KD, Yang L, Kong ZQ, Tong BZ, Li JJ, Huang YS, Simko I, Klosterman SJ, Dai XF, Subbarao KV. Dynamics of Verticillium dahliae race 1 population under managed agricultural ecosystems. BMC Biol 2021; 19:131. [PMID: 34172070 PMCID: PMC8235872 DOI: 10.1186/s12915-021-01061-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/01/2021] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Plant pathogens and their hosts undergo adaptive changes in managed agricultural ecosystems, by overcoming host resistance, but the underlying genetic adaptations are difficult to determine in natural settings. Verticillium dahliae is a fungal pathogen that causes Verticillium wilt on many economically important crops including lettuce. We assessed the dynamics of changes in the V. dahliae genome under selection in a long-term field experiment. RESULTS In this study, a field was fumigated before the Verticillium dahliae race 1 strain (VdLs.16) was introduced. A derivative 145-strain population was collected over a 6-year period from this field in which a seggregating population of lettuce derived from Vr1/vr1 parents were evaluated. We de novo sequenced the parental genome of VdLs.16 strain and resequenced the derivative strains to analyze the genetic variations that accumulate over time in the field cropped with lettuce. Population genomics analyses identified 2769 single-nucleotide polymorphisms (SNPs) and 750 insertion/deletions (In-Dels) in the 145 isolates compared with the parental genome. Sequence divergence was identified in the coding sequence regions of 378 genes and in the putative promoter regions of 604 genes. Five-hundred and nine SNPs/In-Dels were identified as fixed. The SNPs and In-Dels were significantly enriched in the transposon-rich, gene-sparse regions, and in those genes with functional roles in signaling and transcriptional regulation. CONCLUSIONS Under the managed ecosystem continuously cropped to lettuce, the local adaptation of V. dahliae evolves at a whole genome scale to accumulate SNPs/In-Dels nonrandomly in hypervariable regions that encode components of signal transduction and transcriptional regulation.
Collapse
Affiliation(s)
- Jie-Yin Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dan-Dan Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Ran Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dan Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Krishna D Puri
- Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA, USA
| | - Lin Yang
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Zhi-Qiang Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Jun-Jiao Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Ivan Simko
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA, USA
| | - Steven J Klosterman
- United States Department of Agriculture, Agricultural Research Service, Crop Improvement and Protection Research Unit, Salinas, CA, USA.
| | - Xiao-Feng Dai
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Krishna V Subbarao
- Department of Plant Pathology, University of California, Davis, c/o U.S. Agricultural Research Station, Salinas, CA, USA.
| |
Collapse
|
24
|
Skrede I, Murat C, Hess J, Maurice S, Sønstebø JH, Kohler A, Barry-Etienne D, Eastwood D, Högberg N, Martin F, Kauserud H. Contrasting demographic histories revealed in two invasive populations of the dry rot fungus Serpula lacrymans. Mol Ecol 2021; 30:2772-2789. [PMID: 33955084 DOI: 10.1111/mec.15934] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/21/2022]
Abstract
Globalization and international trade have impacted organisms around the world leading to a considerable number of species establishing in new geographic areas. Many organisms have taken advantage of human-made environments, including buildings. One such species is the dry rot fungus Serpula lacrymans, which is the most aggressive wood-decay fungus in indoor environments in temperate regions. Using population genomic analyses of 36 full genome sequenced isolates, we demonstrated that European and Japanese isolates are highly divergent and the populations split 3000-19,000 generations ago, probably predating human influence. Approximately 250 generations ago, the European population went through a tight bottleneck, probably corresponding to the fungus colonization of the built environment in Europe. The demographic history of these populations, probably lead to low adaptive potential. Only two loci under selection were identified using a Fst outlier approach, and selective sweep analyses identified three loci with extended haplotype homozygosity. The selective sweep analyses found signals in genes possibly related to decay of various substrates in Japan and in genes involved DNA replication and protein modification in Europe. Our results suggest that the dry rot fungus independently established in indoor environments in Europe and Japan and that invasive species can potentially establish large populations in new habitats based on a few colonizing individuals.
Collapse
Affiliation(s)
- Inger Skrede
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Claude Murat
- INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE-GrandEst Lorraine, Université de Lorraine, Champenoux, France
| | - Jaqueline Hess
- Department of Biosciences, University of Oslo, Oslo, Norway.,University of Vienna, Vienna, Austria
| | - Sundy Maurice
- Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Annegret Kohler
- INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE-GrandEst Lorraine, Université de Lorraine, Champenoux, France
| | | | - Dan Eastwood
- Department of Biosciences, University of Swansea, Swansea, UK
| | - Nils Högberg
- Department of Forest Mycology and Plant Pathology, Swedish Agricultural University, Uppsala, Sweden
| | - Francis Martin
- INRAE, UMR Interactions Arbres/Microorganismes, Centre INRAE-GrandEst Lorraine, Université de Lorraine, Champenoux, France.,Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Institute of Microbiology, Beijing Forestry University, Beijing, China
| | | |
Collapse
|
25
|
Dutta A, Hartmann FE, Francisco CS, McDonald BA, Croll D. Mapping the adaptive landscape of a major agricultural pathogen reveals evolutionary constraints across heterogeneous environments. THE ISME JOURNAL 2021; 15:1402-1419. [PMID: 33452474 PMCID: PMC8115182 DOI: 10.1038/s41396-020-00859-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/17/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023]
Abstract
The adaptive potential of pathogens in novel or heterogeneous environments underpins the risk of disease epidemics. Antagonistic pleiotropy or differential resource allocation among life-history traits can constrain pathogen adaptation. However, we lack understanding of how the genetic architecture of individual traits can generate trade-offs. Here, we report a large-scale study based on 145 global strains of the fungal wheat pathogen Zymoseptoria tritici from four continents. We measured 50 life-history traits, including virulence and reproduction on 12 different wheat hosts and growth responses to several abiotic stressors. To elucidate the genetic basis of adaptation, we used genome-wide association mapping coupled with genetic correlation analyses. We show that most traits are governed by polygenic architectures and are highly heritable suggesting that adaptation proceeds mainly through allele frequency shifts at many loci. We identified negative genetic correlations among traits related to host colonization and survival in stressful environments. Such genetic constraints indicate that pleiotropic effects could limit the pathogen's ability to cause host damage. In contrast, adaptation to abiotic stress factors was likely facilitated by synergistic pleiotropy. Our study illustrates how comprehensive mapping of life-history trait architectures across diverse environments allows to predict evolutionary trajectories of pathogens confronted with environmental perturbations.
Collapse
Affiliation(s)
- Anik Dutta
- grid.5801.c0000 0001 2156 2780Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Fanny E. Hartmann
- grid.5801.c0000 0001 2156 2780Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland ,grid.417885.70000 0001 2185 8223Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, 91400 Orsay, France
| | - Carolina Sardinha Francisco
- grid.5801.c0000 0001 2156 2780Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland ,Present Address: Environmental Genomics Group, Botanical Institute, CAU Kiel, Germany
| | - Bruce A. McDonald
- grid.5801.c0000 0001 2156 2780Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- grid.10711.360000 0001 2297 7718Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| |
Collapse
|
26
|
Hamann E, Denney D, Day S, Lombardi E, Jameel MI, MacTavish R, Anderson JT. Review: Plant eco-evolutionary responses to climate change: Emerging directions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 304:110737. [PMID: 33568289 DOI: 10.1016/j.plantsci.2020.110737] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/23/2020] [Accepted: 10/25/2020] [Indexed: 05/14/2023]
Abstract
Contemporary climate change is exposing plant populations to novel combinations of temperatures, drought stress, [CO2] and other abiotic and biotic conditions. These changes are rapidly disrupting the evolutionary dynamics of plants. Despite the multifactorial nature of climate change, most studies typically manipulate only one climatic factor. In this opinion piece, we explore how climate change factors interact with each other and with biotic pressures to alter evolutionary processes. We evaluate the ramifications of climate change across life history stages,and examine how mating system variation influences population persistence under rapid environmental change. Furthermore, we discuss how spatial and temporal mismatches between plants and their mutualists and antagonists could affect adaptive responses to climate change. For example, plant-virus interactions vary from highly pathogenic to mildly facilitative, and are partly mediated by temperature, moisture availability and [CO2]. Will host plants exposed to novel, stressful abiotic conditions be more susceptible to viral pathogens? Finally, we propose novel experimental approaches that could illuminate how plants will cope with unprecedented global change, such as resurrection studies combined with experimental evolution, genomics or epigenetics.
Collapse
Affiliation(s)
- Elena Hamann
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Derek Denney
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Samantha Day
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Elizabeth Lombardi
- Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14850, USA
| | - M Inam Jameel
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Rachel MacTavish
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA 30602, USA
| | - Jill T Anderson
- Department of Genetics and Odum School of Ecology, University of Georgia, Athens, GA 30602, USA.
| |
Collapse
|
27
|
Dutta A, Croll D, McDonald BA, Barrett LG. Maintenance of variation in virulence and reproduction in populations of an agricultural plant pathogen. Evol Appl 2021; 14:335-347. [PMID: 33664780 PMCID: PMC7896723 DOI: 10.1111/eva.13117] [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: 04/15/2020] [Revised: 07/04/2020] [Accepted: 08/13/2020] [Indexed: 11/27/2022] Open
Abstract
Genetic diversity within pathogen populations is critically important for predicting pathogen evolution, disease outcomes and prevalence. However, we lack a good understanding of the processes maintaining genetic variation and constraints on pathogen life-history evolution. Here, we analysed interactions between 12 wheat host genotypes and 145 strains of Zymoseptoria tritici from five global populations to investigate the evolution and maintenance of variation in pathogen virulence and reproduction. We found a strong positive correlation between virulence (amount of leaf necrosis) and reproduction (pycnidia density within lesions), with substantial variation in both traits maintained within populations. On average, highly virulent isolates exhibited higher reproduction, which might increase transmission potential in agricultural fields planted to homogeneous hosts at a high density. We further showed that pathogen strains with a narrow host range (i.e. specialists) for reproduction were on average less virulent, and those with a broader host range (i.e. generalists) were on average less fecund on a given specific host. These costs associated with adaptation to different host genotypes might constrain the emergence of generalists by disrupting the directional evolution of virulence and fecundity. We conclude that selection favouring pathogen strains that are virulent across diverse hosts, coupled with selection that maximizes fecundity on specific hosts, may explain the maintenance of these pathogenicity traits within and among populations.
Collapse
Affiliation(s)
- Anik Dutta
- Plant PathologyInstitute of Integrative BiologyETH ZurichZurichSwitzerland
| | - Daniel Croll
- Laboratory of Evolutionary GeneticsInstitute of BiologyUniversity of NeuchâtelNeuchâtelSwitzerland
| | - Bruce A. McDonald
- Plant PathologyInstitute of Integrative BiologyETH ZurichZurichSwitzerland
| | | |
Collapse
|
28
|
Singh NK, Dutta A, Puccetti G, Croll D. Tackling microbial threats in agriculture with integrative imaging and computational approaches. Comput Struct Biotechnol J 2020; 19:372-383. [PMID: 33489007 PMCID: PMC7787954 DOI: 10.1016/j.csbj.2020.12.018] [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: 09/01/2020] [Revised: 12/08/2020] [Accepted: 12/13/2020] [Indexed: 11/29/2022] Open
Abstract
Pathogens and pests are one of the major threats to agricultural productivity worldwide. For decades, targeted resistance breeding was used to create crop cultivars that resist pathogens and environmental stress while retaining yields. The often decade-long process of crossing, selection, and field trials to create a new cultivar is challenged by the rapid rise of pathogens overcoming resistance. Similarly, antimicrobial compounds can rapidly lose efficacy due to resistance evolution. Here, we review three major areas where computational, imaging and experimental approaches are revolutionizing the management of pathogen damage on crops. Recognizing and scoring plant diseases have dramatically improved through high-throughput imaging techniques applicable both under well-controlled greenhouse conditions and directly in the field. However, computer vision of complex disease phenotypes will require significant improvements. In parallel, experimental setups similar to high-throughput drug discovery screens make it possible to screen thousands of pathogen strains for variation in resistance and other relevant phenotypic traits. Confocal microscopy and fluorescence can capture rich phenotypic information across pathogen genotypes. Through genome-wide association mapping approaches, phenotypic data helps to unravel the genetic architecture of stress- and virulence-related traits accelerating resistance breeding. Finally, joint, large-scale screenings of trait variation in crops and pathogens can yield fundamental insights into how pathogens face trade-offs in the adaptation to resistant crop varieties. We discuss how future implementations of such innovative approaches in breeding and pathogen screening can lead to more durable disease control.
Collapse
Affiliation(s)
- Nikhil Kumar Singh
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| | - Anik Dutta
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, CH-8092 Zurich, Switzerland
| | - Guido Puccetti
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
- Syngenta Crop Protection AG, CH-4332 Stein, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, CH-2000 Neuchâtel, Switzerland
| |
Collapse
|
29
|
Pereira D, McDonald BA, Croll D. The Genetic Architecture of Emerging Fungicide Resistance in Populations of a Global Wheat Pathogen. Genome Biol Evol 2020; 12:2231-2244. [PMID: 32986802 PMCID: PMC7846115 DOI: 10.1093/gbe/evaa203] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/22/2020] [Indexed: 12/22/2022] Open
Abstract
Containing fungal diseases often depends on the application of fungicidal compounds. Fungicides can rapidly lose effectiveness due to the rise of resistant individuals in populations. However, the lack of knowledge about resistance mutations beyond known target genes challenges investigations into pathways to resistance. We used whole-genome sequencing data and association mapping to reveal the multilocus genetic architecture of fungicide resistance in a global panel of 159 isolates of Parastagonospora nodorum, an important fungal pathogen of wheat. We found significant differences in azole resistance among global field populations. The populations evolved distinctive combinations of resistance alleles which can interact when co-occurring in the same genetic background. We identified 34 significantly associated single nucleotide polymorphisms located in close proximity to genes associated with fungicide resistance in other fungi, including a major facilitator superfamily transporter. Using fungal colony growth rates and melanin production at different temperatures as fitness proxies, we found no evidence that resistance was constrained by genetic trade-offs. Our study demonstrates how genome-wide association studies of a global collection of pathogen strains can recapitulate the emergence of fungicide resistance. The distinct complement of resistance mutations found among populations illustrates how the evolutionary trajectory of fungicide adaptation can be complex and challenging to predict.
Collapse
Affiliation(s)
- Danilo Pereira
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| |
Collapse
|
30
|
Crandall SG, Gold KM, Jiménez-Gasco MDM, Filgueiras CC, Willett DS. A multi-omics approach to solving problems in plant disease ecology. PLoS One 2020; 15:e0237975. [PMID: 32960892 PMCID: PMC7508392 DOI: 10.1371/journal.pone.0237975] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/04/2020] [Indexed: 12/11/2022] Open
Abstract
The swift rise of omics-approaches allows for investigating microbial diversity and plant-microbe interactions across diverse ecological communities and spatio-temporal scales. The environment, however, is rapidly changing. The introduction of invasive species and the effects of climate change have particular impact on emerging plant diseases and managing current epidemics. It is critical, therefore, to take a holistic approach to understand how and why pathogenesis occurs in order to effectively manage for diseases given the synergies of changing environmental conditions. A multi-omics approach allows for a detailed picture of plant-microbial interactions and can ultimately allow us to build predictive models for how microbes and plants will respond to stress under environmental change. This article is designed as a primer for those interested in integrating -omic approaches into their plant disease research. We review -omics technologies salient to pathology including metabolomics, genomics, metagenomics, volatilomics, and spectranomics, and present cases where multi-omics have been successfully used for plant disease ecology. We then discuss additional limitations and pitfalls to be wary of prior to conducting an integrated research project as well as provide information about promising future directions.
Collapse
Affiliation(s)
- Sharifa G. Crandall
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, United States of America
| | - Kaitlin M. Gold
- Plant Pathology & Plant Microbe Biology Section, Cornell AgriTech, Cornell University, Geneva, NY, United States of America
| | - María del Mar Jiménez-Gasco
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, United States of America
| | - Camila C. Filgueiras
- Applied Chemical Ecology Technology, Cornell AgriTech, Cornell University, Geneva, NY, United States of America
| | - Denis S. Willett
- Applied Chemical Ecology Technology, Cornell AgriTech, Cornell University, Geneva, NY, United States of America
| |
Collapse
|
31
|
Ebert D, Fields PD. Host-parasite co-evolution and its genomic signature. Nat Rev Genet 2020; 21:754-768. [PMID: 32860017 DOI: 10.1038/s41576-020-0269-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2020] [Indexed: 01/14/2023]
Abstract
Studies in diverse biological systems have indicated that host-parasite co-evolution is responsible for the extraordinary genetic diversity seen in some genomic regions, such as major histocompatibility (MHC) genes in jawed vertebrates and resistance genes in plants. This diversity is believed to evolve under balancing selection on hosts by parasites. However, the mechanisms that link the genomic signatures in these regions to the underlying co-evolutionary process are only slowly emerging. We still lack a clear picture of the co-evolutionary concepts and of the genetic basis of the co-evolving phenotypic traits in the interacting antagonists. Emerging genomic tools that provide new options for identifying underlying genes will contribute to a fuller understanding of the co-evolutionary process.
Collapse
Affiliation(s)
- Dieter Ebert
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland. .,Wissenschaftskolleg zu Berlin, Berlin, Germany.
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| |
Collapse
|
32
|
Fones HN, Bebber DP, Chaloner TM, Kay WT, Steinberg G, Gurr SJ. Threats to global food security from emerging fungal and oomycete crop pathogens. ACTA ACUST UNITED AC 2020; 1:332-342. [PMID: 37128085 DOI: 10.1038/s43016-020-0075-0] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 04/09/2020] [Indexed: 11/09/2022]
Abstract
Emerging fungal and oomycete pathogens infect staple calorie crops and economically important commodity crops, thereby posing a significant risk to global food security. Our current agricultural systems - with emphasis on intensive monoculture practices - and globalized markets drive the emergence and spread of new pathogens and problematic traits, such as fungicide resistance. Climate change further promotes the emergence of pathogens on new crops and in new places. Here we review the factors affecting the introduction and spread of pathogens and current disease control strategies, illustrating these with the historic example of the Irish potato famine and contemporary examples of soybean rust, wheat blast and blotch, banana wilt and cassava root rot. Our Review looks to the future, summarizing what we see as the main challenges and knowledge gaps, and highlighting the direction that research must take to face the challenge of emerging crop pathogens.
Collapse
|
33
|
Fungal Evolution in Anthropogenic Environments: Botrytis cinerea Populations Infecting Small Fruit Hosts in the Pacific Northwest Rapidly Adapt to Human-Induced Selection Pressures. Appl Environ Microbiol 2020; 86:AEM.02908-19. [PMID: 32086310 DOI: 10.1128/aem.02908-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 02/13/2020] [Indexed: 12/21/2022] Open
Abstract
Many fungal pathogens have short generation times, large population sizes, and mixed reproductive systems, providing high potential to adapt to heterogeneous environments of agroecosystems. Such adaptation complicates disease management and threatens food production. A better understanding of pathogen population biology in such environments is important to reveal key aspects of adaptive divergence processes to allow improved disease management. Here, we studied how evolutionary forces shape population structure of Botrytis cinerea, the causal agent of gray mold, in the Pacific Northwest agroecosystems. Populations of B. cinerea from adjacent fields of small fruit hosts were characterized by combining neutral markers (microsatellites) with markers that directly respond to human-induced selection pressures (fungicide resistance). Populations were diverse, without evidence for recombination and association of pathogen genotype with host. Populations were highly localized with limited migration even among adjacent fields within a farm. A fungicide resistance marker revealed strong selection on population structure due to fungicide use. We found no association of resistance allele with genetic background, suggesting de novo development of fungicide resistance and frequent extinction/recolonization events by different genotypes rather than the spread of resistance alleles among fields via migration of a dominant genotype. Overall our results showed that in agroecosystems, B. cinerea populations respond strongly to selection by fungicide use with greater effect on population structure compared to adaptation to host plant species. This knowledge will be used to improve disease management by developing strategies that limit pathogen local adaptation to fungicides and other human-induced selection pressures present in Pacific Northwest agroecosystems and elsewhere.IMPORTANCE Agroecosystems represent an efficient model for studying fungal adaptation and evolution in anthropogenic environments. In this work, we studied what evolutionary forces shape populations of one of the most important fungal plant pathogens, B. cinerea, in small fruit agroecosystems of the Pacific Northwest. We hypothesized that host, geographic, and anthropogenic factors of agroecosystems structure B. cinerea populations. By combining neutral markers with markers that directly respond to human-induced selection pressures, we show that pathogen populations are highly localized and that selection pressure caused by fungicide use can have a greater effect on population structure than adaptation to host. Our results give a better understanding of population biology and evolution of this important plant pathogen in heterogeneous environments but also provide a practical framework for the development of efficient management strategies by limiting pathogen adaptation to fungicides and other human-induced selection pressures present in agroecosystems of the Pacific Northwest and elsewhere.
Collapse
|
34
|
Dumartinet T, Abadie C, Bonnot F, Carreel F, Roussel V, Habas R, Martinez RT, Perez‐Vicente L, Carlier J. Pattern of local adaptation to quantitative host resistance in a major pathogen of a perennial crop. Evol Appl 2020; 13:824-836. [PMID: 32211070 PMCID: PMC7086059 DOI: 10.1111/eva.12904] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/10/2019] [Accepted: 11/22/2019] [Indexed: 12/05/2022] Open
Abstract
Understanding the mechanisms involved in pathogen adaptation to quantitative resistance in plants has a key role to play in establishing durable strategies for resistance deployment, especially in perennial crops. The erosion of quantitative resistance has been recently suspected in Cuba and the Dominican Republic for a major fungal pathogen of such a crop: Pseudocercospora fijiensis, causing black leaf streak disease on banana. This study set out to test whether such erosion has resulted from an adaptation of P. fijiensis populations, and to determine whether or not the adaptation is local. Almost 600 P. fijiensis isolates from Cuba and the Dominican Republic were sampled using a paired-population sampling design on resistant and susceptible banana varieties. A low genetic structure of the P. fijiensis populations was detected in each country using 16 microsatellite markers. Cross-inoculation experiments using isolates from susceptible and resistant cultivars were carried out, measuring a quantitative trait (the diseased leaf area) related to pathogen fitness on three varieties. A further analysis based on those data suggested the existence of a local pattern of adaptation to resistant cultivars in both of the study countries, due to the existence of specific (or genotype by genotype) host-pathogen interactions. However, neither cost nor benefit effects for adapted populations were found on the widely used "Cavendish" banana group. These results highlight the need to study specific host-pathogen interactions and pathogen adaptation on a wide range of quantitative resistance phenotypes in banana, in order to develop durable strategies for resistance deployment.
Collapse
Affiliation(s)
- Thomas Dumartinet
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | - Catherine Abadie
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
- CIRADUMR BGPICapesterre‐Belle‐EauFrance
| | - François Bonnot
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | - Françoise Carreel
- UMR AGAPUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | - Véronique Roussel
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | - Rémy Habas
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| | | | | | - Jean Carlier
- UMR BGPIUniv MontpellierINRACIRADMontpellier SupAgroMontpellierFrance
| |
Collapse
|
35
|
Vanhove M, Sicard A, Ezennia J, Leviten N, Almeida RPP. Population structure and adaptation of a bacterial pathogen in California grapevines. Environ Microbiol 2020; 22:2625-2638. [PMID: 32114707 DOI: 10.1111/1462-2920.14965] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 01/03/2020] [Accepted: 02/26/2020] [Indexed: 12/30/2022]
Abstract
Xylella fastidiosa subsp. fastidiosa causes Pierce's disease of grapevine (PD) and has been present in California for over a century. A singly introduced genotype spread across the state causing large outbreaks and damaging the grapevine industry. This study presents 122 X. fastidiosa subsp. fastidiosa genomes from symptomatic grapevines, and explores pathogen genetic diversity associated with PD in California. A total of 5218 single-nucleotide polymorphisms (SNPs) were found in the dataset. Strong population genetic structure was found; isolates split into five genetic clusters divided into two lineages. The core/soft-core genome constituted 41.2% of the total genome, emphasizing the high genetic variability of X. fastidiosa genomes. An ecological niche model was performed to estimate the environmental niche of the pathogen within California and to identify key climatic factors involved in dispersal. A landscape genomic approach was undertaken aiming to link local adaptation to climatic factors. A total of 18 non-synonymous polymorphisms found to be under selective pressures were correlated with at least one environmental variable highlighting the role of temperature, precipitation and elevation on X. fastidiosa adaptation to grapevines in California. Finally, the contribution to virulence of three of the genes under positive selective pressure and of one recombinant gene was studied by reverse genetics.
Collapse
Affiliation(s)
- Mathieu Vanhove
- Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley, CA, 94720
| | - Anne Sicard
- Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley, CA, 94720
| | - Jeffery Ezennia
- Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley, CA, 94720
| | - Nina Leviten
- Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley, CA, 94720
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California-Berkeley, Berkeley, CA, 94720
| |
Collapse
|
36
|
Geographic and genetic variation in susceptibility of Butomus umbellatus to foliar fungal pathogens. Biol Invasions 2020. [DOI: 10.1007/s10530-019-02109-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
37
|
White PS, Choi A, Pandey R, Menezes A, Penley M, Gibson AK, de Roode J, Morran L. Host heterogeneity mitigates virulence evolution. Biol Lett 2020; 16:20190744. [PMID: 31992149 PMCID: PMC7013476 DOI: 10.1098/rsbl.2019.0744] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/19/2019] [Indexed: 01/21/2023] Open
Abstract
Parasites often infect genetically diverse host populations, and the evolutionary trajectories of parasite populations may be shaped by levels of host heterogeneity. Mixed genotype host populations, compared to homogeneous host populations, can reduce parasite prevalence and potentially reduce rates of parasite adaptation due to trade-offs associated with adapting to specific host genotypes. Here, we used experimental evolution to select for increased virulence in populations of the bacterial parasite Serratia marcescens exposed to either heterogeneous or homogeneous populations of Caenorhabditis elegans. We found that parasites exposed to heterogeneous host populations evolved significantly less virulence than parasites exposed to homogeneous host populations over several hundred bacterial generations. Thus, host heterogeneity impeded parasite adaptation to host populations. While we detected trade-offs in virulence evolution, parasite adaptation to two specific host genotypes also resulted in modestly increased virulence against the reciprocal host genotypes. These results suggest that parasite adaptation to heterogeneous host populations may be impeded by both trade-offs and a reduction in the efficacy of selection as different host genotypes exert different selective pressures on a parasite population.
Collapse
Affiliation(s)
- P. Signe White
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
- Population Biology, Ecology, and Evolution Graduate Program, Laney Graduate School, Emory University, Atlanta, GA 30322, USA
| | - Angela Choi
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
| | - Rishika Pandey
- Department of Genetics, Franklin College of Arts and Sciences, University of Georgia, Athens, GA 30602, USA
| | - Arthur Menezes
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
| | - McKenna Penley
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
| | - Amanda K. Gibson
- Department of Biology, College and Graduate School of Arts and Sciences, University of Virginia, Charlottesville, VA 22904, USA
| | - Jacobus de Roode
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
| | - Levi Morran
- Department of Biology, College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA
| |
Collapse
|
38
|
Zhang X, Liu B, Zou F, Shen D, Yin Z, Wang R, He F, Wang Y, Tyler BM, Fan W, Qian W, Dou D. Whole Genome Re-sequencing Reveals Natural Variation and Adaptive Evolution of Phytophthora sojae. Front Microbiol 2019; 10:2792. [PMID: 31849921 PMCID: PMC6895562 DOI: 10.3389/fmicb.2019.02792] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/18/2019] [Indexed: 12/23/2022] Open
Abstract
Due to the monocultural basis of agricultural crops, mutated plant microbes with increased pathogenicity can easily spread in the field and lead to serious yield losses. As a major threat to a wide range of crop plants, oomycete pathogens continuously undergo adaptive evolution to overcome plant defense barriers. However, the genetic basis of their evolution at the molecular level remains largely unknown. Here, we investigated the nature variation and the population genomics of the soybean pathogen Phytophthora sojae by high-throughput genome re-sequencing. Genomic variation analysis revealed uneven “two-speed” evolutionary pattern with genes in gene-sparse regions (GSRs) showing higher rates of structural polymorphisms and positive selection. GSRs are enriched in effector genes and transposase-related genes. Our results also suggested that the NADH oxidase and MIP transporter gene families undergo rapid and diversifying selection. Furthermore, we demonstrated that P. sojae isolates possess varying numbers of RxLR effectors with diverse sequences, totaling 471 members. Among them, 42 core RxLR effectors are assumed to be important for infection. Finally, we observed that Avr genes exhibit abundant sequence variation in P. sojae isolates. Several novel variants lead to the evading of host resistance, including a complete deletion in Avr3c and amino acid mutations in Avr1a. Taken together, our results provide an adaptive landscape of P. sojae at single-nucleotide resolution, as well as resources for further resistance breeding and disease prevention against this important plant pathogen.
Collapse
Affiliation(s)
- Xiong Zhang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Bo Liu
- Agricultural Genomic Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Fen Zou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Zhiyuan Yin
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Rongbo Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Feng He
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Brett M Tyler
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, United States
| | - Wei Fan
- Agricultural Genomic Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Wanqiang Qian
- Agricultural Genomic Institute, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Daolong Dou
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.,Department of Plant Pathology, China Agricultural University, Beijing, China
| |
Collapse
|
39
|
Cavicchioli R, Ripple WJ, Timmis KN, Azam F, Bakken LR, Baylis M, Behrenfeld MJ, Boetius A, Boyd PW, Classen AT, Crowther TW, Danovaro R, Foreman CM, Huisman J, Hutchins DA, Jansson JK, Karl DM, Koskella B, Mark Welch DB, Martiny JBH, Moran MA, Orphan VJ, Reay DS, Remais JV, Rich VI, Singh BK, Stein LY, Stewart FJ, Sullivan MB, van Oppen MJH, Weaver SC, Webb EA, Webster NS. Scientists' warning to humanity: microorganisms and climate change. Nat Rev Microbiol 2019; 17:569-586. [PMID: 31213707 PMCID: PMC7136171 DOI: 10.1038/s41579-019-0222-5] [Citation(s) in RCA: 673] [Impact Index Per Article: 134.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2019] [Indexed: 11/27/2022]
Abstract
In the Anthropocene, in which we now live, climate change is impacting most life on Earth. Microorganisms support the existence of all higher trophic life forms. To understand how humans and other life forms on Earth (including those we are yet to discover) can withstand anthropogenic climate change, it is vital to incorporate knowledge of the microbial 'unseen majority'. We must learn not just how microorganisms affect climate change (including production and consumption of greenhouse gases) but also how they will be affected by climate change and other human activities. This Consensus Statement documents the central role and global importance of microorganisms in climate change biology. It also puts humanity on notice that the impact of climate change will depend heavily on responses of microorganisms, which are essential for achieving an environmentally sustainable future.
Collapse
Affiliation(s)
- Ricardo Cavicchioli
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia.
| | - William J Ripple
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, USA
| | - Kenneth N Timmis
- Institute of Microbiology, Technical University Braunschweig, Braunschweig, Germany
| | - Farooq Azam
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Lars R Bakken
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Matthew Baylis
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Michael J Behrenfeld
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Antje Boetius
- Alfred Wegener Institute, Helmholtz Center for Marine and Polar Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Philip W Boyd
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, Australia
| | - Aimée T Classen
- Rubenstein School of Environment and Natural Resources, and The Gund Institute for Environment, University of Vermont, Burlington, VT, USA
| | | | - Roberto Danovaro
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
- Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Christine M Foreman
- Center for Biofilm Engineering, and Chemical and Biological Engineering Department, Montana State University, Bozeman, MT, USA
| | - Jef Huisman
- Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - David A Hutchins
- Department of Biological Sciences, Marine and Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Janet K Jansson
- Biological Sciences Division, Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, USA
| | - David M Karl
- Daniel K. Inouye Center for Microbial Oceanography: Research and Education, School of Ocean and Earth Science & Technology, University of Hawaii at Manoa, Honolulu, HI, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | | | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA, USA
| | - Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Victoria J Orphan
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA
| | - David S Reay
- School of Geosciences, University of Edinburgh, Edinburgh, UK
| | - Justin V Remais
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Virginia I Rich
- Microbiology Department, and the Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, USA
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, and Global Centre for Land-Based Innovation, Western Sydney University, Penrith, NSW, Australia
| | - Lisa Y Stein
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Frank J Stewart
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Matthew B Sullivan
- Department of Microbiology, and Department of Civil, Environmental and Geodetic Engineering, and the Byrd Polar and Climate Research Center, The Ohio State University, Columbus, OH, USA
| | - Madeleine J H van Oppen
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
- Australian Institute of Marine Science, Townsville, QLD, Australia
| | - Scott C Weaver
- Department of Microbiology and Immunology, and Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Eric A Webb
- Department of Biological Sciences, Marine and Environmental Biology Section, University of Southern California, Los Angeles, CA, USA
| | - Nicole S Webster
- Australian Institute of Marine Science, Townsville, QLD, Australia
- Australian Centre for Ecogenomics, University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
40
|
Hartmann FE, Rodríguez de la Vega RC, Carpentier F, Gladieux P, Cornille A, Hood ME, Giraud T. Understanding Adaptation, Coevolution, Host Specialization, and Mating System in Castrating Anther-Smut Fungi by Combining Population and Comparative Genomics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:431-457. [PMID: 31337277 DOI: 10.1146/annurev-phyto-082718-095947] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Anther-smut fungi provide a powerful system to study host-pathogen specialization and coevolution, with hundreds of Microbotryum species specialized on diverse Caryophyllaceae plants, castrating their hosts through manipulation of the hosts' reproductive organs to facilitate disease transmission. Microbotryum fungi have exceptional genomic characteristics, including dimorphic mating-type chromosomes, that make this genus anexcellent model for studying the evolution of mating systems and their influence on population genetics structure and adaptive potential. Important insights into adaptation, coevolution, host specialization, and mating system evolution have been gained using anther-smut fungi, with new insights made possible by the recent advent of genomic approaches. We illustrate with Microbotryum case studies how using a combination of comparative genomics, population genomics, and transcriptomics approaches enables the integration of different evolutionary perspectives across different timescales. We also highlight current challenges and suggest future studies that will contribute to advancing our understanding of the mechanisms underlying adaptive processes in populations of fungal pathogens.
Collapse
Affiliation(s)
- Fanny E Hartmann
- Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France;
| | | | - Fantin Carpentier
- Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France;
| | - Pierre Gladieux
- UMR BGPI, Univ. Montpellier, INRA, CIRAD, Montpellier SupAgro, 34398 Montpellier, France
| | - Amandine Cornille
- Génétique Quantitative et Evolution-Le Moulon, INRA; Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91198 Gif-sur-Yvette, France
| | - Michael E Hood
- Biology Department, Amherst College, Amherst, Massachusetts 01002-5000, USA
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, 91400 Orsay, France;
| |
Collapse
|
41
|
Tian L, Chang C, Ma L, Nasir F, Zhang J, Li W, Tran LSP, Tian C. Comparative study of the mycorrhizal root transcriptomes of wild and cultivated rice in response to the pathogen Magnaporthe oryzae. RICE (NEW YORK, N.Y.) 2019; 12:35. [PMID: 31076886 PMCID: PMC6510786 DOI: 10.1186/s12284-019-0287-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/09/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Rice, which serves as a staple food for more than half of the world's population, is very susceptible to the pathogenic fungus, Magnaporthe oryzae. However, common wild rice (Oryza rufipogon), which is the ancestor of Asian cultivated rice (O. sativa), has significant potential as a genetic source of resistance to M. oryzae. Recent studies have shown that the domestication of rice has altered its relationship to symbiotic arbuscular mycorrhizae. A comparative response of wild and domestic rice inhabited by mycorrhizae to infection by M. oryzae has not been documented. RESULTS In the current study, roots of wild and cultivated rice colonized with the arbuscular mycorrhizal (AM) fungus (AMF) Rhizoglomus intraradices were used to compare the transcriptomic responses of the two species to infection by M. oryzae. Phenotypic analysis indicated that the colonization of wild and cultivated rice with R. intraradices improved the resistance of both genotypes to M. oryzae. Wild AM rice, however, was more resistant to M. oryzae than the cultivated AM rice, as well as nonmycorrhizal roots of wild rice. Transcriptome analysis indicated that the mechanisms regulating the responses of wild and cultivated AM rice to M. oryzae invasion were significantly different. The expression of a greater number of genes was changed in wild AM rice than in cultivated AM rice in response to the pathogen. Both wild and cultivated AM rice exhibited a shared response to M. oryzae which included genes related to the auxin and salicylic acid pathways; all of these play important roles in pathogenesis-related protein synthesis. In wild AM rice, secondary metabolic and biotic stress-related analyses indicated that the jasmonic acid synthesis-related α-linolenic acid pathway, the phenolic and terpenoid pathways, as well as the phenolic and terpenoid syntheses-related mevalonate (MVA) pathway were more affected by the pathogen. Genes related to these pathways were more significantly enriched in wild AM rice than in cultivated AM rice in response to M. oryzae. On the other hand, genes associated with the 'brassinosteroid biosynthesis' were more enriched in cultivated AM rice. CONCLUSIONS The AMF R. intraradices-colonized rice plants exhibited greater resistance to M. oryzae than non-AMF-colonized plants. The findings of the current study demonstrate the potential effects of crop domestication on the benefits received by the host via root colonization with AMF(s), and provide new information on the underlying molecular mechanisms. In addition, results of this study can also help develop guidelines for the applications of AMF(s) when planting rice.
Collapse
Affiliation(s)
- Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102 China
| | - Chunling Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Lina Ma
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102 China
- School of Life Sciences, Northeast Normal University, Changchun City, Jilin China
| | - Jianfeng Zhang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102 China
- College of Life Science, Jilin Agricultural University, Changchun, Jilin China
| | - Weiqiang Li
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
| | - Lam-Son Phan Tran
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045 Japan
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, 550000 Vietnam
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102 China
| |
Collapse
|
42
|
Evidence of within-species specialization by soil microbes and the implications for plant community diversity. Proc Natl Acad Sci U S A 2019; 116:7371-7376. [PMID: 30842279 DOI: 10.1073/pnas.1810767116] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Microbes are thought to maintain diversity in plant communities by specializing on particular species, but it is not known whether microbes that specialize within species (i.e., on genotypes) affect diversity or dynamics in plant communities. Here we show that soil microbes can specialize at the within-population level in a wild plant species, and that such specialization could promote species diversity and seed dispersal in plant communities. In a shadehouse experiment in Panama, we found that seedlings of the native tree species, Virola surinamensis (Myristicaceae), had reduced performance in the soil microbial community of their maternal tree compared with in the soil microbial community of a nonmaternal tree from the same population. Performance differences were unrelated to soil nutrients or to colonization by mycorrhizal fungi, suggesting that highly specialized pathogens were the mechanism reducing seedling performance in maternal soils. We then constructed a simulation model to explore the ecological and evolutionary consequences of genotype-specific pathogens in multispecies plant communities. Model results indicated that genotype-specific pathogens promote plant species coexistence-albeit less strongly than species-specific pathogens-and are most effective at maintaining species richness when genetic diversity is relatively low. Simulations also revealed that genotype-specific pathogens select for increased seed dispersal relative to species-specific pathogens, potentially helping to create seed dispersal landscapes that allow pathogens to more effectively promote diversity. Combined, our results reveal that soil microbes can specialize within wild plant populations, affecting seedling performance near conspecific adults and influencing plant community dynamics on ecological and evolutionary time scales.
Collapse
|
43
|
Giraud T, Koskella B, Laine AL. Introduction: microbial local adaptation: insights from natural populations, genomics and experimental evolution. Mol Ecol 2018; 26:1703-1710. [PMID: 28409900 DOI: 10.1111/mec.14091] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 02/14/2017] [Accepted: 03/02/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Tatiana Giraud
- Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Anna-Liisa Laine
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Viikinkaari 1, 00014, Helsinki, Finland
| |
Collapse
|
44
|
Krishnan P, Meile L, Plissonneau C, Ma X, Hartmann FE, Croll D, McDonald BA, Sánchez-Vallet A. Transposable element insertions shape gene regulation and melanin production in a fungal pathogen of wheat. BMC Biol 2018; 16:78. [PMID: 30012138 PMCID: PMC6047131 DOI: 10.1186/s12915-018-0543-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 06/20/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Fungal plant pathogens pose major threats to crop yield and sustainable food production if they are highly adapted to their host and the local environment. Variation in gene expression contributes to phenotypic diversity within fungal species and affects adaptation. However, very few cases of adaptive regulatory changes have been reported in fungi and the underlying mechanisms remain largely unexplored. Fungal pathogen genomes are highly plastic and harbor numerous insertions of transposable elements, which can potentially contribute to gene expression regulation. In this work, we elucidated how transposable elements contribute to variation in melanin accumulation, a quantitative trait in fungi that affects survival under stressful conditions. RESULTS We demonstrated that differential transcriptional regulation of the gene encoding the transcription factor Zmr1, which controls expression of the genes in the melanin biosynthetic gene cluster, is responsible for variation in melanin accumulation in the fungal plant pathogen Zymoseptoria tritici. We show that differences in melanin levels between two strains of Z. tritici are due to two levels of transcriptional regulation: (1) variation in the promoter sequence of Zmr1 and (2) an insertion of transposable elements upstream of the Zmr1 promoter. Remarkably, independent insertions of transposable elements upstream of Zmr1 occurred in 9% of Z. tritici strains from around the world and negatively regulated Zmr1 expression, contributing to variation in melanin accumulation. CONCLUSIONS Our studies identified two levels of transcriptional control that regulate the synthesis of melanin. We propose that these regulatory mechanisms evolved to balance the fitness costs associated with melanin production against its positive contribution to survival in stressful environments.
Collapse
Affiliation(s)
- Parvathy Krishnan
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Lukas Meile
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Clémence Plissonneau
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Xin Ma
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris Saclay, Orsay, France
| | - Daniel Croll
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | | |
Collapse
|
45
|
Evidence for local adaptation and pleiotropic effects associated with melanization in a plant pathogenic fungus. Fungal Genet Biol 2018; 115:33-40. [DOI: 10.1016/j.fgb.2018.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 03/28/2018] [Accepted: 04/02/2018] [Indexed: 11/19/2022]
|
46
|
Hartmann FE, McDonald BA, Croll D. Genome-wide evidence for divergent selection between populations of a major agricultural pathogen. Mol Ecol 2018; 27:2725-2741. [PMID: 29729657 PMCID: PMC6032900 DOI: 10.1111/mec.14711] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 04/05/2018] [Accepted: 04/17/2018] [Indexed: 12/30/2022]
Abstract
The genetic and environmental homogeneity in agricultural ecosystems is thought to impose strong and uniform selection pressures. However, the impact of this selection on plant pathogen genomes remains largely unknown. We aimed to identify the proportion of the genome and the specific gene functions under positive selection in populations of the fungal wheat pathogen Zymoseptoria tritici. First, we performed genome scans in four field populations that were sampled from different continents and on distinct wheat cultivars to test which genomic regions are under recent selection. Based on extended haplotype homozygosity and composite likelihood ratio tests, we identified 384 and 81 selective sweeps affecting 4% and 0.5% of the 35 Mb core genome, respectively. We found differences both in the number and the position of selective sweeps across the genome between populations. Using a XtX‐based outlier detection approach, we identified 51 extremely divergent genomic regions between the allopatric populations, suggesting that divergent selection led to locally adapted pathogen populations. We performed an outlier detection analysis between two sympatric populations infecting two different wheat cultivars to identify evidence for host‐driven selection. Selective sweep regions harboured genes that are likely to play a role in successfully establishing host infections. We also identified secondary metabolite gene clusters and an enrichment in genes encoding transporter and protein localization functions. The latter gene functions mediate responses to environmental stress, including interactions with the host. The distinct gene functions under selection indicate that both local host genotypes and abiotic factors contributed to local adaptation.
Collapse
Affiliation(s)
- Fanny E Hartmann
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland.,Ecologie Systématique Evolution, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-Saclay, Orsay, France
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| |
Collapse
|
47
|
Mohd-Assaad N, McDonald BA, Croll D. Genome-Wide Detection of Genes Under Positive Selection in Worldwide Populations of the Barley Scald Pathogen. Genome Biol Evol 2018; 10:1315-1332. [PMID: 29722810 PMCID: PMC5972619 DOI: 10.1093/gbe/evy087] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2018] [Indexed: 12/29/2022] Open
Abstract
Coevolution between hosts and pathogens generates strong selection pressures to maintain resistance and infectivity, respectively. Genomes of plant pathogens often encode major effect loci for the ability to successfully infect specific host genotypes. Hence, spatial heterogeneity in host genotypes coupled with abiotic factors could lead to locally adapted pathogen populations. However, the genetic basis of local adaptation is poorly understood. Rhynchosporium commune, the pathogen causing barley scald disease, interacts at least partially in a gene-for-gene manner with its host. We analyzed global field populations of 125 R. commune isolates to identify candidate genes for local adaptation. Whole genome sequencing data showed that the pathogen is subdivided into three genetic clusters associated with distinct geographic and climatic regions. Using haplotype-based selection scans applied independently to each genetic cluster, we found strong evidence for selective sweeps throughout the genome. Comparisons of loci under selection among clusters revealed little overlap, suggesting that ecological differences associated with each cluster led to variable selection regimes. The strongest signals of selection were found predominantly in the two clusters composed of isolates from Central Europe and Ethiopia. The strongest selective sweep regions encoded protein functions related to biotic and abiotic stress responses. Selective sweep regions were enriched in genes encoding functions in cellular localization, protein transport activity, and DNA damage responses. In contrast to the prevailing view that a small number of gene-for-gene interactions govern plant pathogen evolution, our analyses suggest that the evolutionary trajectory is largely determined by spatially heterogeneous biotic and abiotic selection pressures.
Collapse
Affiliation(s)
- Norfarhan Mohd-Assaad
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, Bangi, Selangor, Malaysia
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH Zurich, Zurich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Switzerland
| |
Collapse
|