51
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Ahmad S, Wei X, Sheng Z, Hu P, Tang S. CRISPR/Cas9 for development of disease resistance in plants: recent progress, limitations and future prospects. Brief Funct Genomics 2020; 19:26-39. [DOI: 10.1093/bfgp/elz041] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Abstract
Several plant pathogens severely affect crop yield and quality, thereby threatening global food security. In order to cope with this challenge, genetic improvement of plant disease resistance is required for sustainable agricultural production, for which conventional breeding is unlikely to do enough. Luckily, genome editing systems that particularly clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) has revolutionized crop improvement by enabling robust and precise targeted genome modifications. It paves the way towards new methods for genetic improvement of plant disease resistance and accelerates resistance breeding. In this review, the challenges, limitations and prospects for conventional breeding and the applications of CRISPR/Cas9 system for the development of transgene-free disease-resistant crops are discussed.
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52
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Corredor‐Moreno P, Saunders DGO. Expecting the unexpected: factors influencing the emergence of fungal and oomycete plant pathogens. THE NEW PHYTOLOGIST 2020; 225:118-125. [PMID: 31225901 PMCID: PMC6916378 DOI: 10.1111/nph.16007] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 06/06/2019] [Indexed: 05/12/2023]
Abstract
In recent years, the number of emergent plant pathogens (EPPs) has grown substantially, threatening agroecosystem stability and native biodiversity. Contributing factors include, among others, shifts in biogeography, with EPP spread facilitated by the global unification of monocultures in modern agriculture, high volumes of trade in plants and plant products and an increase in sexual recombination within pathogen populations. The unpredictable nature of EPPs as they move into new territories is a situation that has led to sudden and widespread epidemics. Understanding the underlying causes of pathogen emergence is key to managing the impact of EPPs. Here, we review some factors specifically influencing the emergence of oomycete and fungal EPPs, including new introductions through anthropogenic movement, natural dispersal and weather events, as well as genetic factors linked to shifts in host range.
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53
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Thierry M, Gladieux P, Fournier E, Tharreau D, Ioos R. A Genomic Approach to Develop a New qPCR Test Enabling Detection of the Pyricularia oryzae Lineage Causing Wheat Blast. PLANT DISEASE 2020; 104:60-70. [PMID: 31647693 DOI: 10.1094/pdis-04-19-0685-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rapid detection is key to managing emerging diseases because it allows their spread around the world to be monitored and limited. The first major wheat blast epidemics were reported in 1985 in the Brazilian state of Paraná. Following this outbreak, the disease quickly spread to neighboring regions and countries and, in 2016, the first report of wheat blast disease outside South America was released. This Asian outbreak was due to the trade of infected South American seed, demonstrating the importance of detection tests in order to avoid importing contaminated biological material into regions free from the pathogen. Genomic analysis has revealed that one particular lineage within the fungal species Pyricularia oryzae is associated with this disease: the Triticum lineage. A comparison of 81 Pyricularia genomes highlighted polymorphisms specific to the Triticum lineage, and this study developed a real-time PCR test targeting one of these polymorphisms. The test's performance was then evaluated in order to measure its analytical specificity, analytical sensitivity, and robustness. The C17 quantitative PCR test detected isolates belonging to the Triticum lineage with high sensitivity, down to 13 plasmid copies or 1 pg of genomic DNA per reaction tube. The blast-based approach developed here to study P. oryzae can be transposed to other emerging diseases.
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Affiliation(s)
- Maud Thierry
- UMR BGPI, Montpellier University, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR BGPI, F-34398 Montpellier, France
- ANSES Plant Health Laboratory, Mycology Unit, Domaine de Pixérécourt, Bâtiment E, F-54220 Malzéville, France
| | - Pierre Gladieux
- UMR BGPI, Montpellier University, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Elisabeth Fournier
- UMR BGPI, Montpellier University, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Didier Tharreau
- UMR BGPI, Montpellier University, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
- CIRAD, UMR BGPI, F-34398 Montpellier, France
| | - Renaud Ioos
- ANSES Plant Health Laboratory, Mycology Unit, Domaine de Pixérécourt, Bâtiment E, F-54220 Malzéville, France
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54
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Gong L, Liu Y, Xiong Y, Li T, Yin C, Zhao J, Yu J, Yin Q, Gupta VK, Jiang Y, Duan X. New insights into the evolution of host specificity of three Penicillium species and the pathogenicity of P. Italicum involving the infection of Valencia orange ( Citrus sinensis). Virulence 2020; 11:748-768. [PMID: 32525727 PMCID: PMC7549954 DOI: 10.1080/21505594.2020.1773038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Blue and green molds, the common phenotypes of post-harvest diseases in fruits, are mainly caused by Penicillium fungal species, including P. italicum, P. digitatum, and P. expansum. We sequenced and assembled the genome of a P. italicum strain, which contains 31,034,623 bp with 361 scaffolds and 627 contigs. The mechanisms underlying the evolution of host specificity among the analyzed Penicillium species were associated with the expansion of protein families, genome restructuring, horizontal gene transfer, and positive selection pressure. A dual-transcriptome analysis following the infection of Valencia orange (Citrus sinensis) by P. italicum resulted in the annotation of 9,307 P. italicum genes and 24,591 Valencia orange genes. The pathogenicity of P. italicum may be due to the activation of effectors, including 51 small secreted cysteine-rich proteins, 110 carbohydrate-active enzymes, and 12 G protein-coupled receptors. Additionally, 211 metabolites related to the interactions between P. italicum and Valencia orange were identified by gas chromatography-time of flight mass spectrography, three of which were further confirmed by ultra-high performance liquid chromatography triple quadrupole mass spectrometry. A metabolomics analysis indicated that P. italicum pathogenicity is associated with the sphingolipid and salicylic acid signaling pathways. Moreover, a correlation analysis between the metabolite contents and gene expression levels suggested that P. italicum induces carbohydrate metabolism in Valencia orange fruits as part of its infection strategy. This study provides useful information regarding the genomic determinants that drive the evolution of host specificity in Penicillium species and clarifies the host-plant specificity during the infection of Valencia orange by P. italicum. IMPORTANCE P. italicum GL_Gan1, a local strain in Guangzhou, China, was sequenced. Comparison of the genome of P. italicum GL_Gan1 with other pathogenic Penicillium species, P. digitatum and P. expansum, revealed that the expansion of protein families, genome restructuring, HGT, and positive selection pressure were related to the host range expansion of the analyzed Penicillium species. Moreover, gene gains or losses might be associated with the speciation of these Penicillium species. In addition, the molecular basis of host-plant specificity during the infection of Valencia orange (Citrus sinensis) by P. italicum was also elucidated by transcriptomic and metabolomics analysis. The data presented herein may be useful for further elucidating the molecular basis of the evolution of host specificity of Penicillium species and for illustrating the host-plant specificity during the infection of Valencia orange by P. italicum.
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Affiliation(s)
- Liang Gong
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences , Guangzhou, China.,Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture , Guangzhou, China
| | - Yongfeng Liu
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen , Shenzhen, China
| | - Yehui Xiong
- Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University , Beijing, China
| | - Taotao Li
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences , Guangzhou, China.,Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture , Guangzhou, China
| | - Chunxiao Yin
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences , Guangzhou, China.,Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture , Guangzhou, China
| | - Juanni Zhao
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen , Shenzhen, China
| | - Jialin Yu
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen , Shenzhen, China
| | - Qi Yin
- BGI PathoGenesis Pharmaceutical Technology Co., Ltd, BGI-Shenzhen , Shenzhen, China
| | - Vijai Kumar Gupta
- Department of Chemistry and Biotechnology, ERA Chair of Green Chemistry, School of Science, Tallinn University of Technology , Tallinn, Estonia
| | - Yueming Jiang
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences , Guangzhou, China.,Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture , Guangzhou, China
| | - Xuewu Duan
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences , Guangzhou, China.,Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences , Guangzhou, China.,Key Laboratory of Post-Harvest Handling of Fruits, Ministry of Agriculture , Guangzhou, China
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55
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Sarrocco S, Mauro A, Battilani P. Use of Competitive Filamentous Fungi as an Alternative Approach for Mycotoxin Risk Reduction in Staple Cereals: State of Art and Future Perspectives. Toxins (Basel) 2019; 11:E701. [PMID: 31810316 PMCID: PMC6950288 DOI: 10.3390/toxins11120701] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 12/23/2022] Open
Abstract
Among plant fungal diseases, those affecting cereals represent a huge problem in terms of food security and safety. Cereals, such as maize and wheat, are very often targets of mycotoxigenic fungi. The limited availability of chemical plant protection products and physical methods to control mycotoxigenic fungi and to reduce food and feed mycotoxin contamination fosters alternative approaches, such as the use of beneficial fungi as an active ingredient of biological control products. Competitive interactions, including both exploitation and interference competition, between pathogenic and beneficial fungi, are generally recognized as mechanisms to control plant pathogens populations and to manage plant diseases. In the present review, two examples concerning the use of competitive beneficial filamentous fungi for the management of cereal diseases are discussed. The authors retrace the history of the well-established use of non-aflatoxigenic isolates of Aspergillus flavus to prevent aflatoxin contamination in maize and give an overview of the potential use of competitive beneficial filamentous fungi to manage Fusarium Head Blight on wheat and mitigate fusaria toxin contamination. Although important steps have been made towards the development of microorganisms as active ingredients of plant protection products, a reasoned revision of the registration rules is needed to significantly reduce the chemical based plant protection products in agriculture.
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Affiliation(s)
- Sabrina Sarrocco
- Department of Agriculture, Food and Environment, University of Pisa, 56124 Pisa, Italy;
| | - Antonio Mauro
- International Institute of Tropical Agriculture, P.O. Box 34441 Dar es Salaam, Tanzania;
| | - Paola Battilani
- Department of Sustainable Crop Production, Università Cattolica del Sacro Cuore, 29122 Piacenza, Italy
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56
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Okamoto KW, Amarasekare P, Post DM, Vasseur DA, Turner PE. The interplay between host community structure and pathogen life‐history constraints in driving the evolution of host‐range shifts. Funct Ecol 2019. [DOI: 10.1111/1365-2435.13467] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Kenichi W. Okamoto
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
- Department of Biology University of St. Thomas St. Paul MN USA
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
| | - Priyanga Amarasekare
- Department of Ecology and Evolutionary Biology University of California Los Angeles CA USA
| | - David M. Post
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
| | - David A. Vasseur
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology Yale University New Haven CT USA
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57
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Jain A, Sarsaiya S, Wu Q, Lu Y, Shi J. A review of plant leaf fungal diseases and its environment speciation. Bioengineered 2019; 10:409-424. [PMID: 31502497 PMCID: PMC6779379 DOI: 10.1080/21655979.2019.1649520] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/20/2019] [Accepted: 07/24/2019] [Indexed: 11/08/2022] Open
Abstract
There is increasing difficulty in identifying new plant leaf diseases as a result of environmental change. There is a need to identify the factors influencing the emergence and the increasing incidences of these diseases. Here, we present emerging fungal plant leaf diseases and describe their environmental speciation. We considered the factors controlling for local adaptation associated with environmental speciation. We determined that the advent of emergent fungal leaf diseases is closely connected to environmental speciation. Fungal pathogens targeting the leaves may adversely affect the entire plant body. To mitigate the injury caused by these pathogens, it is necessary to be able to detect and identify them early in the infection process. In this way, their distribution, virulence, incidence, and severity could be attenuated.
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Affiliation(s)
- Archana Jain
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Surendra Sarsaiya
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
- Bioresource Institute for Healthy Utilization, Zunyi Medical University, Zunyi, Guizhou, China
| | - Qin Wu
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Yuanfu Lu
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
| | - Jingshan Shi
- Key Laboratory of Basic Pharmacology and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi, Guizhou, China
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58
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Mercier A, Carpentier F, Duplaix C, Auger A, Pradier JM, Viaud M, Gladieux P, Walker AS. The polyphagous plant pathogenic fungus Botrytis cinerea encompasses host-specialized and generalist populations. Environ Microbiol 2019; 21:4808-4821. [PMID: 31608584 DOI: 10.1111/1462-2920.14829] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 10/08/2019] [Accepted: 10/08/2019] [Indexed: 12/01/2022]
Abstract
The host plant is often the main variable explaining population structure in fungal plant pathogens, because specialization contributes to reduce gene flow between populations associated with different hosts. Previous population genetic analysis revealed that French populations of the grey mould pathogen Botrytis cinerea were structured by hosts tomato and grapevine, suggesting host specialization in this highly polyphagous pathogen. However, these findings raised questions about the magnitude of this specialization and the possibility of specialization to other hosts. Here we report specialization of B. cinerea populations to tomato and grapevine hosts but not to other tested plants. Population genetic analysis revealed two pathogen clusters associated with tomato and grapevine, while the other clusters co-occurred on hydrangea, strawberry and bramble. Measurements of quantitative pathogenicity were consistent with host specialization of populations found on tomato, and to a lesser extent, populations found on grapevine. Pathogen populations from hydrangea and strawberry appeared to be generalist, while populations from bramble may be weakly specialized. Our results suggest that the polyphagous B. cinerea is more accurately described as a collection of generalist and specialist individuals in populations. This work opens new perspectives for grey mould management, while suggesting spatial optimization of crop organization within agricultural landscapes.
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Affiliation(s)
- Alex Mercier
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France.,Université Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Florence Carpentier
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France.,UR MaIAGE, INRA, Université Paris-Saclay, Jouy-en-Josas, France
| | - Clémentine Duplaix
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Annie Auger
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Jean-Marc Pradier
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Muriel Viaud
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Pierre Gladieux
- UMR BGPI, INRA, CIRAD, Montpellier Supagro, Université de Montpellier, Montpellier, France
| | - Anne-Sophie Walker
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
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59
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Bakovic V, Schuler H, Schebeck M, Feder JL, Stauffer C, Ragland GJ. Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi. Mol Ecol 2019; 28:4648-4666. [PMID: 31495015 PMCID: PMC6899720 DOI: 10.1111/mec.15239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022]
Abstract
Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host‐related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants, Prunus spp. (cherries) and Lonicera spp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci between Prunus and Lonicera flies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher FST values between host plants than others. They also showed high levels of linkage disequilibrium within and between Prunus and Lonicera flies, supporting host‐related selection and reduced gene flow. Our findings support the existence of sympatric host races in R. cerasi embedded within broader patterns of geographic variation in the fly, similar to the related apple maggot, Rhagoletis pomonella, in North America.
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Affiliation(s)
- Vid Bakovic
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.,Department of Biology, IFM, University of Linköping, Linköping, Sweden
| | - Hannes Schuler
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Martin Schebeck
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Christian Stauffer
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Gregory J Ragland
- Department of Integrative Biology, University of Colorado-Denver, Denver, CO, USA
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60
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Hýsek J, Vavera R, Růžek P. Cultivation Intensity in Combination with Other Ecological Factors as Limiting Ones for the Abundance of Phytopathogenic Fungi on Wheat. MICROBIAL ECOLOGY 2019; 78:565-574. [PMID: 30895363 DOI: 10.1007/s00248-019-01337-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/28/2019] [Indexed: 06/09/2023]
Abstract
In field and laboratory experiments during 2014-2017, we investigated the influence of lower and higher cultivation intensity of wheat and ecological factors (weather-temperature and rainfalls, year) on the occurrence of phytopathogenic fungi on the leaves of winter wheat. The prevailing fungi in those years were Mycosphaerella graminicola (Fuckel) J. Schrott and Pyrenophora tritici-repentis (Died.) Drechsler. Using cluster analysis, we statistically evaluated interrelationships of known factors on the abundance of the fungi on leaf surfaces. Our results showed strongest correlation with Mycosphaerella graminicola and Pyrenophora tritici-repentis abundance to be with lower cultivation intensity and year done by the temperature and the rainfalls. The two pathogens-Puccinia tritici Oerst and Hymenula cerealis Ellis & Everh. occurred only very sparsely in some years and had little positive or negative correlation with named factors. The semi-early and semi-late winter wheat varieties Matchball, Annie, Fakir, and Tobak were used for our experiments. Higher cultivation intensity had protective effect against leaf phytopathogenic fungi.
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Affiliation(s)
- Josef Hýsek
- Crop Research Institute (CRI), Ruzyně, Prague 6, Czech Republic.
| | - Radek Vavera
- Crop Research Institute (CRI), Ruzyně, Prague 6, Czech Republic
| | - Pavel Růžek
- Crop Research Institute (CRI), Ruzyně, Prague 6, Czech Republic
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61
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Bonneaud C, Weinert LA, Kuijper B. Understanding the emergence of bacterial pathogens in novel hosts. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180328. [PMID: 31401968 PMCID: PMC6711297 DOI: 10.1098/rstb.2018.0328] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2019] [Indexed: 01/03/2023] Open
Abstract
Our understanding of the ecological and evolutionary context of novel infections is largely based on viral diseases, even though bacterial pathogens may display key differences in the processes underlying their emergence. For instance, host-shift speciation, in which the jump of a pathogen into a novel host species is followed by the specialization on that host and the loss of infectivity of previous host(s), is commonly observed in viruses, but less often in bacteria. Here, we suggest that the extent to which pathogens evolve host generalism or specialism following a jump into a novel host will depend on their level of adaptation to dealing with different environments, their rates of molecular evolution and their ability to recombine. We then explore these hypotheses using a formal model and show that the high levels of phenotypic plasticity, low rates of evolution and the ability to recombine typical of bacterial pathogens should reduce their propensity to specialize on novel hosts. Novel bacterial infections may therefore be more likely to result in transient spillovers or increased host ranges than in host shifts. Finally, consistent with our predictions, we show that, in two unusual cases of contemporary bacterial host shifts, the bacterial pathogens both have small genomes and rapid rates of substitution. Further tests are required across a greater number of emerging pathogens to assess the validity of our hypotheses. This article is part of the theme issue 'Dynamic and integrative approaches to understanding pathogen spillover'.
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Affiliation(s)
- Camille Bonneaud
- Centre for Ecology and Conservation, University of Exeter, Penryn TR10 9FE, UK
| | - Lucy A. Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Bram Kuijper
- Centre for Ecology and Conservation, University of Exeter, Penryn TR10 9FE, UK
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62
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Genome-Wide Association Mapping of Anthracnose ( Colletotrichum sublineolum) Resistance in NPGS Ethiopian Sorghum Germplasm. G3-GENES GENOMES GENETICS 2019; 9:2879-2885. [PMID: 31289022 PMCID: PMC6723129 DOI: 10.1534/g3.119.400350] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The National Plant Germplasm System (NPGS) Ethiopian sorghum [Sorghum bicolor (L.) Moench] collection of the United States is an important genetic resource for sorghum improvement. Anthracnose (Colletotrichum sublineolum) is one of the most harmful fungal diseases in humid sorghum production regions. Although multiple resistance sources have been identified in temperate-adapted germplasm in the Sorghum Association Panel (SAP), these resistance loci explain a limited portion of the total variation, and sources of resistance from tropical germplasm are not available for breeding programs at temperate regions. Using a core set of 335 previously genotyped NPGS Ethiopian accessions, we identified 169 accessions resistant to anthracnose. To identify resistance loci, we merged the genotypic and anthracnose response data for both NPGS Ethiopian germplasm and the SAP and performed genome-wide association scans using 219,037 single nucleotide polymorphisms and 617 accessions. The integrated data set enabled the detection of a locus on chromosome 9 present in the SAP at a low frequency. The locus explains a limited portion of the observed phenotypic variation (r2 = 0.31), suggesting the presence of other resistance loci. The locus in chromosome 9 was constituted by three R genes clustered within a 47-kb region. The presence of multiple sources of resistance in NPGS Ethiopian germplasm and SAP requires the inclusion of other resistance response evaluation that could revealed others low frequency resistance alleles in the panel.
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63
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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: 13] [Impact Index Per Article: 2.6] [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.
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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;
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Treindl AD, Leuchtmann A. Assortative mating in sympatric ascomycete fungi revealed by experimental fertilizations. Fungal Biol 2019; 123:676-686. [PMID: 31416587 DOI: 10.1016/j.funbio.2019.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/14/2019] [Accepted: 06/03/2019] [Indexed: 11/19/2022]
Abstract
Mate recognition mechanisms resulting in assortative mating constitute an effective reproductive barrier that may promote sexual isolation and speciation. While such mechanisms are widely documented for animals and plants, they remain poorly studied in fungi. We used two interfertile species of Epichloë (Clavicipitaceae, Ascomycota), E. typhina and E. clarkii, which are host-specific endophytes of two sympatrically occurring grasses. The life cycle of these obligatory outcrossing fungi entails dispersal of gametes by a fly vector among external fungal structures (stromata). To test for assortative mating, we mimicked the natural fertilization process by applying mixtures of spermatia from both species and examined their reproductive success. Our trials revealed that fertilization is non-random and preferentially takes place between conspecific mating partners, which is indicative of assortative mating. Additionally, the viability of hybrid and non-hybrid ascospore offspring was assessed. Germination rates were lower in E. clarkii than in E. typhina and were reduced in ascospore progeny from treatments with high proportions of heterospecific spermatia. The preferential mating between conspecific genotypes and reduced hybrid viability represent important reproductive barriers that have not been documented before in Epichloë. Insights from fungal systems will deepen our understanding of the evolutionary mechanisms leading to reproductive isolation and speciation.
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Affiliation(s)
- Artemis D Treindl
- Plant Ecological Genetics, Institute of Integrative Biology, ETH Zurich, Zürich, Switzerland
| | - Adrian Leuchtmann
- Plant Ecological Genetics, Institute of Integrative Biology, ETH Zurich, Zürich, Switzerland.
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66
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Hood ME, Antonovics J, Wolf M, Stern ZL, Giraud T, Abbate JL. Sympatry and interference of divergent Microbotryum pathogen species. Ecol Evol 2019; 9:5457-5467. [PMID: 31110694 PMCID: PMC6509394 DOI: 10.1002/ece3.5140] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/05/2019] [Accepted: 03/15/2019] [Indexed: 01/18/2023] Open
Abstract
The impact of infectious diseases in natural ecosystems is strongly influenced by the degree of pathogen specialization and by the local assemblies of potential host species. This study investigated anther-smut disease, caused by fungi in the genus Microbotryum, among natural populations of plants in the Caryophyllaceae. A broad geographic survey focused on sites of the disease on multiple host species in sympatry. Analysis of molecular identities for the pathogens revealed that sympatric disease was most often due to co-occurrence of distinct, host-specific anther-smut fungi, rather than localized cross-species disease transmission. Flowers from sympatric populations showed that the Microbotryum spores were frequently moved between host species. Experimental inoculations to simulate cross-species exposure to the pathogens in these plant communities showed that the anther-smut pathogen was less able to cause disease on its regular host when following exposure of the plants to incompatible pathogens from another host species. These results indicate that multi-host/multi-pathogen communities are common in this system and they involve a previously hidden mechanism of interference between Microbotryum fungi, which likely affects both pathogen and host distributions.
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Affiliation(s)
| | - Janis Antonovics
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginia
| | - Monroe Wolf
- Department of BiologyAmherst CollegeAmherstMassachusetts
| | | | - Tatiana Giraud
- Ecologie Systematique et Evolution, Univ. Paris‐Sud, CNRS, AgroParisTechUniversité Paris SaclayOrsayFrance
| | - Jessica L. Abbate
- Department of BiologyUniversity of VirginiaCharlottesvilleVirginia
- INRA ‐ UMR 1062 CBGP (INRA, IRD, CIRAD, Montpellier SupAgro)Montferrier‐sur‐LezFrance
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67
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Bush SE, Villa SM, Altuna JC, Johnson KP, Shapiro MD, Clayton DH. Host defense triggers rapid adaptive radiation in experimentally evolving parasites. Evol Lett 2019; 3:120-128. [PMID: 31007943 PMCID: PMC6457392 DOI: 10.1002/evl3.104] [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: 10/18/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 01/12/2023] Open
Abstract
Adaptive radiation occurs when the members of a single lineage evolve different adaptive forms in response to selection imposed by competitors or predators. Iconic examples include Darwin's finches, Caribbean anoles, and Hawaiian silverswords, all of which live on islands. Although adaptive radiation is thought to be an important generator of biodiversity, most studies concern groups that have already diversified. Here, we take the opposite approach. We experimentally triggered diversification in the descendants of a single population of host-specific parasites confined to different host "islands." We show rapid adaptive divergence of experimentally evolving feather lice in response to preening, which is a bird's main defense against ectoparasites. We demonstrate that host defense exerts strong phenotypic selection for crypsis in lice transferred to different colored rock pigeons (Columba livia). During four years of experimental evolution (∼60 generations), the lice evolved heritable differences in color. Strikingly, the observed color differences spanned the range of phenotypes found among congeneric lice adapted to other species of birds. To our knowledge, this is the first real-time demonstration that microevolution is fast enough to simulate millions of years of macroevolutionary change. Our results further indicate that host-mediated selection triggers rapid divergence in the adaptive radiation of parasites, which are among the most diverse organisms on Earth.
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Affiliation(s)
- Sarah E. Bush
- School of Biological SciencesUniversity of UtahSalt Lake CityUtah84112
| | - Scott M. Villa
- School of Biological SciencesUniversity of UtahSalt Lake CityUtah84112
| | - Juan C. Altuna
- School of Biological SciencesUniversity of UtahSalt Lake CityUtah84112
| | - Kevin P. Johnson
- Illinois Natural History Survey, Prairie Research InstituteUniversity of Illinois at Urbana‐ChampaignChampaignIllinois61820
| | | | - Dale H. Clayton
- School of Biological SciencesUniversity of UtahSalt Lake CityUtah84112
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68
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Potter KM, Escanferla ME, Jetton RM, Man G, Crane BS. Prioritizing the conservation needs of United States tree species: Evaluating vulnerability to forest insect and disease threats. Glob Ecol Conserv 2019. [DOI: 10.1016/j.gecco.2019.e00622] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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69
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Gladieux P. What makes a specialized endophyte special? Mol Ecol 2019; 27:3037-3039. [PMID: 30133874 DOI: 10.1111/mec.14775] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 06/08/2018] [Indexed: 02/05/2023]
Abstract
Fungal plant symbionts can be highly specialized on a limited range of host genotypes and species. Understanding the genetic basis of this specialization, the mechanisms governing its establishment and the relationship between specialization and speciation is a major challenge for evolutionary biologists (Timms & Read, ). A deeper knowledge of evolutionary plant-microbe interactions could be exploited to improve agricultural management, by bringing fungal biodiversity and fungal biomass under greater and more durable human control. Previous studies on pathogens have shown that effectors, that is, small secreted proteins that modulate plant physiology to favour host colonization, play a key role in infection of novel hosts (e.g., Inoue et al., ) or in host specialization (e.g., Liao et al. ()). Like pathogens, endophytes also manipulate the physiology of their hosts and colonize novel hosts to which they specialize (Hardoim et al., ). These biological characteristics of endophytes raise the question of similarities in the protein arsenal contributing to the specialization of pathogens and endophytes. In this issue of Molecular Ecology, Schirrmann et al. () used a combination of divergence genome scans and tests for positive selection to investigate the genetic basis of specialization of two subspecies of the symbiont Epichloë typhina occurring on two different grass hosts. Their analyses suggest a key role of effectors as determinants of host specialization. This study paves the way towards the comparative analysis of the genomics of speciation among plant symbionts.
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Affiliation(s)
- Pierre Gladieux
- UMR BGPI, INRA, CIRAD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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70
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Dale AL, Feau N, Everhart SE, Dhillon B, Wong B, Sheppard J, Bilodeau GJ, Brar A, Tabima JF, Shen D, Brasier CM, Tyler BM, Grünwald NJ, Hamelin RC. Mitotic Recombination and Rapid Genome Evolution in the Invasive Forest Pathogen Phytophthora ramorum. mBio 2019; 10:e02452-18. [PMID: 30862749 PMCID: PMC6414701 DOI: 10.1128/mbio.02452-18] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/29/2019] [Indexed: 12/21/2022] Open
Abstract
Invasive alien species often have reduced genetic diversity and must adapt to new environments. Given the success of many invasions, this is sometimes called the genetic paradox of invasion. Phytophthora ramorum is invasive, limited to asexual reproduction within four lineages, and presumed clonal. It is responsible for sudden oak death in the United States, sudden larch death in Europe, and ramorum blight in North America and Europe. We sequenced the genomes of 107 isolates to determine how this pathogen can overcome the invasion paradox. Mitotic recombination (MR) associated with transposons and low gene density has generated runs of homozygosity (ROH) affecting 2,698 genes, resulting in novel genotypic diversity within the lineages. One ROH enriched in effectors was fixed in the NA1 lineage. An independent ROH affected the same scaffold in the EU1 lineage, suggesting an MR hot spot and a selection target. Differences in host infection between EU1 isolates with and without the ROH suggest that they may differ in aggressiveness. Non-core regions (not shared by all lineages) had signatures of accelerated evolution and were enriched in putative pathogenicity genes and transposons. There was a striking pattern of gene loss, including all effectors, in the non-core EU2 genome. Positive selection was observed in 8.0% of RxLR and 18.8% of Crinkler effector genes compared with 0.9% of the core eukaryotic gene set. We conclude that the P. ramorum lineages are diverging via a rapidly evolving non-core genome and that the invasive asexual lineages are not clonal, but display genotypic diversity caused by MR.IMPORTANCE Alien species are often successful invaders in new environments, despite the introduction of a few isolates with a reduced genetic pool. This is called the genetic paradox of invasion. We found two mechanisms by which the invasive forest pathogen causing sudden oak and sudden larch death can evolve. Extensive mitotic recombination producing runs of homozygosity generates genotypic diversity even in the absence of sexual reproduction, and rapid turnover of genes in the non-core, or nonessential portion of genome not shared by all isolates, allows pathogenicity genes to evolve rapidly or be eliminated while retaining essential genes. Mitotic recombination events occur in genomic hot spots, resulting in similar ROH patterns in different isolates or groups; one ROH, independently generated in two different groups, was enriched in pathogenicity genes and may be a target for selection. This provides important insights into the evolution of invasive alien pathogens and their potential for adaptation and future persistence.
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Affiliation(s)
- Angela L Dale
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- GC-New Construction Materials, FPInnovations, Vancouver, British Columbia, Canada
| | - Nicolas Feau
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sydney E Everhart
- Department of Plant Pathology, University of Nebraska, Lincoln, Nebraska, USA
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Braham Dhillon
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Barbara Wong
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Faculté de Foresterie et Géomatique, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
| | - Julie Sheppard
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Guillaume J Bilodeau
- Ottawa Plant Laboratory, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Avneet Brar
- Ottawa Plant Laboratory, Canadian Food Inspection Agency, Ottawa, Ontario, Canada
| | - Javier F Tabima
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
| | - Danyu Shen
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Clive M Brasier
- Forest Research, Alice Holt Lodge, Farnham, Surrey, United Kingdom
| | - Brett M Tyler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, USA
| | - Niklaus J Grünwald
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, USA
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, Oregon, USA
| | - Richard C Hamelin
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
- Faculté de Foresterie et Géomatique, Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec, Quebec, Canada
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71
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Tang H, Hood ME, Ren Z, Li H, Zhao Y, Wolfe LM, Li D, Wang H. Specificity and seasonal prevalence of anther smut disease
Microbotryum
on sympatric Himalayan
Silene
species. J Evol Biol 2019; 32:451-462. [DOI: 10.1111/jeb.13427] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/03/2019] [Accepted: 02/05/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Hui Tang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of Sciences Kunming Yunnan China
- Kunming College of Life ScienceUniversity of Chinese Academy of Sciences Kunming Yunnan China
| | | | - Zong‐Xin Ren
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of Sciences Kunming Yunnan China
| | - Hai‐Dong Li
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of Sciences Kunming Yunnan China
| | - Yan‐Hui Zhao
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of Sciences Kunming Yunnan China
| | - Lorne M. Wolfe
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of Sciences Kunming Yunnan China
| | - De‐Zhu Li
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of Sciences Kunming Yunnan China
- Kunming College of Life ScienceUniversity of Chinese Academy of Sciences Kunming Yunnan China
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of Sciences Kunming Yunnan China
| | - Hong Wang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of Sciences Kunming Yunnan China
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72
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Leal I, Bergeron MJ, Feau N, Tsui CKM, Foord B, Pellow K, Hamelin RC, Sturrock RN. Cryptic Speciation in Western North America and Eastern Eurasia of the Pathogens Responsible for Laminated Root Rot. PHYTOPATHOLOGY 2019; 109:456-468. [PMID: 30145938 DOI: 10.1094/phyto-12-17-0399-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Coniferiporia sulphurascens is a facultative fungal pathogen that causes laminated root rot (LRR) in commercially important coniferous species worldwide. This fungus spreads primarily by way of vegetative mycelium transferring at points of contact between infected and healthy roots. Successful intervention to control LRR requires a better understanding of the population structure and genetic variability of C. sulphurascens. In this study, we investigated the population genetic structure and origin of C. sulphurascens populations in western North America and eastern Eurasia collected from multiple coniferous hosts. By analyzing the small and large mitochondrial ribosomal RNA subunit genes combined with six nuclear loci (internal transcribed spacer region, actin, RNA polymerase II largest subunit, RNA polymerase II second-largest subunit, laccase-like multicopper oxidase, and translation elongation factor 1-α), we observed that none of the alleles among the loci were shared between North American (NA) and Eurasian C. sulphurascens populations. In total, 55 multilocus genotypes (MLGs) were retrieved in C. sulphurascens isolates occurring in these two continental regions. Of these, 41 MLGs were observed among 58 isolates collected from widespread locations in British Columbia (Canada) and the northwestern United States, while 14 MLGs were observed among 16 isolates sampled in Siberia and Japan. Our data showed that the levels of genetic differentiation between the NA and Eurasian populations are much greater than the populations from within each continental region; the two continental populations formed clearly divergent phylogenetic clades or lineages since they were separated approximately 7.5 million years ago. Moreover, the Eurasian population could be the source of the NA population. Our study indicates the existence of cryptic diversity in this pathogen species, and strongly suggests that the NA and Eurasian populations represent two lineages, which have progressively diverged from each other in allopatry.
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Affiliation(s)
- I Leal
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - M-J Bergeron
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - N Feau
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - C K M Tsui
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - B Foord
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - K Pellow
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - R C Hamelin
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
| | - R N Sturrock
- First, fifth, sixth, and eighth authors: Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada; second author: Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, 1055 rue du P.E.P.S., Québec, QC G1V 4C7 Canada; third and seventh authors: Department of Forest and Conservation Sciences, University of British Columbia, 3041-2424 Main Mall, Vancouver, BC V6T 1Z4 Canada; fourth author: Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar, and Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, Doha, Qatar; and seventh author: Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval/Pavillon Charles-Eugène Marchand, 1030 avenue de la Médecine, Québec, QC G1V 0A6 Canada
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Muñoz IV, Sarrocco S, Malfatti L, Baroncelli R, Vannacci G. CRISPR-Cas for Fungal Genome Editing: A New Tool for the Management of Plant Diseases. FRONTIERS IN PLANT SCIENCE 2019; 10:135. [PMID: 30828340 PMCID: PMC6384228 DOI: 10.3389/fpls.2019.00135] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 01/28/2019] [Indexed: 05/02/2023]
Affiliation(s)
- Isabel Vicente Muñoz
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Sabrina Sarrocco
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
- *Correspondence: Sabrina Sarrocco
| | - Luca Malfatti
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Riccardo Baroncelli
- Spanish-Portuguese Center for Agricultural Research (CIALE), Department of Microbiology and Genetics, University of Salamanca, Villamayor, Spain
| | - Giovanni Vannacci
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
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Desprez-Loustau ML, Massot M, Toïgo M, Fort T, Aday Kaya AG, Boberg J, Braun U, Capdevielle X, Cech T, Chandelier A, Christova P, Corcobado T, Dogmus T, Dutech C, Fabreguettes O, Faivre d'Arcier J, Gross A, Horta Jung M, Iturritxa E, Jung T, Junker C, Kiss L, Kostov K, Lehtijarvi A, Lyubenova A, Marçais B, Oliva J, Oskay F, Pastirčák M, Pastirčáková K, Piou D, Saint-Jean G, Sallafranque A, Slavov S, Stenlid J, Talgø V, Takamatsu S, Tack AJM. From leaf to continent: The multi-scale distribution of an invasive cryptic pathogen complex on oak. FUNGAL ECOL 2018. [DOI: 10.1016/j.funeco.2018.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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75
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Sumabat LG, Kemerait RC, Kim DK, Mehta YR, Brewer MT. Clonality and geographic structure of host-specialized populations of Corynespora cassiicola causing emerging target spot epidemics in the southeastern United States. PLoS One 2018; 13:e0205849. [PMID: 30321244 PMCID: PMC6188889 DOI: 10.1371/journal.pone.0205849] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/02/2018] [Indexed: 11/21/2022] Open
Abstract
Corynespora cassiicola is a destructive plant-pathogenic fungus causing widespread target spot epidemics, including outbreaks on cotton, soybean, and tomato in the southeastern United States. Previous studies revealed that populations from the three hosts are genetically distinct and host specialized. Although variation in aggressiveness to cotton and tomato were observed, no genetic diversity was detected within populations sampled from each of these hosts. We aimed to gain a better understanding of the emerging target spot epidemics by developing microsatellite markers for C. cassiicola to assess genetic variation, population structure, and to infer modes of reproduction and mechanisms of dispersal. Two hundred sixty-five isolates from cotton, soybean, tomato, and other host plants were genotyped with 13 microsatellite markers. Genotypic diversity revealed genetic variation within each of the populations collected from different hosts, with the population from cotton dominated by clonal genotypes and showing the least genetic diversity. In addition, C. cassiicola populations on different host species were genetically distinct and structured based on host species. No association between genetic and geographic distances was identified in the tomato populations, and the association in cotton populations was low. However, significant regional geographic structure was detected in the soybean populations of C. cassiicola. These results further support previous findings of introduced host specialized isolates or the evolution of more aggressive strains on each host. The lack of geographic structure suggests that the clones on cotton and tomato spread rapidly, or similar founder populations were established by human-mediated dispersal, and that dispersal is not limited. However, regional geographic structure of populations on soybean suggests limited dispersal among more established populations of C. cassiicola, or genetic differences in founder populations that colonized different geographic areas.
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Affiliation(s)
- Leilani G. Sumabat
- Department of Plant Pathology, University of Georgia, Athens, Georgia, United States of America
| | - Robert C. Kemerait
- Department of Plant Pathology, University of Georgia, Tifton, Georgia, United States of America
| | - Dong Kyun Kim
- Department of Plant Pathology, University of Georgia, Athens, Georgia, United States of America
| | | | - Marin T. Brewer
- Department of Plant Pathology, University of Georgia, Athens, Georgia, United States of America
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76
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Ye Z, Pan Y, Zhang Y, Cui H, Jin G, McHardy AC, Fan L, Yu X. Comparative whole-genome analysis reveals artificial selection effects on Ustilago esculenta genome. DNA Res 2018; 24:635-648. [PMID: 28992048 PMCID: PMC5726479 DOI: 10.1093/dnares/dsx031] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 07/06/2017] [Indexed: 12/31/2022] Open
Abstract
Ustilago esculenta, infects Zizania latifolia, and induced host stem swollen to be a popular vegetable called Jiaobai in China. It is the long-standing artificial selection that maximizes the occurrence of favourable Jiaobai, and thus maintaining the plant-fungi interaction and modulating the fungus evolving from plant pathogen to entophyte. In this study, whole genome of U. esculenta was sequenced and transcriptomes of the fungi and its host were analysed. The 20.2 Mb U. esculenta draft genome of 6,654 predicted genes including mating, primary metabolism, secreted proteins, shared a high similarity to related Smut fungi. But U. esculenta prefers RNA silencing not repeat-induced point in defence and has more introns per gene, indicating relatively slow evolution rate. The fungus also lacks some genes in amino acid biosynthesis pathway which were filled by up-regulated host genes and developed distinct amino acid response mechanism to balance the infection-resistance interaction. Besides, U. esculenta lost some surface sensors, important virulence factors and host range-related effectors to maintain the economic endophytic life. The elucidation of the U. esculenta genomic information as well as expression profiles can not only contribute to more comprehensive insights into the molecular mechanism underlying artificial selection but also into smut fungi-host interactions.
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Affiliation(s)
- Zihong Ye
- Department of Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou, China
| | - Yao Pan
- Department of Algorithmic Bioinformatics, Heinrich Heine University, Düsseldorf, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Yafen Zhang
- Department of Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou, China
| | - Haifeng Cui
- Department of Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou, China
| | - Gulei Jin
- Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, China
| | - Alice C McHardy
- Department of Algorithmic Bioinformatics, Heinrich Heine University, Düsseldorf, Germany.,Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Longjiang Fan
- Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, China
| | - Xiaoping Yu
- Department of Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, China Jiliang University, Hangzhou, China
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77
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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.
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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
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78
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Sumabat LG, Kemerait RC, Brewer MT. Phylogenetic Diversity and Host Specialization of Corynespora cassiicola Responsible for Emerging Target Spot Disease of Cotton and Other Crops in the Southeastern United States. PHYTOPATHOLOGY 2018; 108:892-901. [PMID: 29436985 DOI: 10.1094/phyto-12-17-0407-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Corynespora cassiicola is a ubiquitous fungus causing emerging plant diseases worldwide, including target spot of cotton, soybean, and tomato, which have rapidly increased in incidence and severity throughout the southeastern United States. The objectives of this study were to understand the causes for the emerging target spot epidemics in the United States by comparing phylogenetic relationships of isolates from cotton, tomato, soybean, and other crop plants and ornamental hosts, and through the determination of the host range of isolates from emerging populations. Fifty-three isolates were sampled from plants in the southeastern United States and 1,380 nucleotides from four nuclear loci were sequenced. Additionally, sequences of the same loci from 23 isolates representing each of the distinct lineages of C. cassiicola described from previous studies were included. Isolates clustered based on host of origin, regardless of the geographic location of sampling. There was no genetic diversity detected among isolates from cotton, which were genetically distinct from isolates from other host species. Furthermore, pathogenicity and virulence assays of 40 isolates from various hosts onto cotton, soybean, tomato, and cucumber showed that isolates from cotton were more aggressive to cotton than those from other hosts. Soybean and tomato were most susceptible to isolates that originated from the same host, providing evidence of host specialization. These results suggest that emerging target spot epidemics in the United States are caused by either the introduction of host-specific isolates or the evolution of more aggressive strains on each host.
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Affiliation(s)
- Leilani G Sumabat
- First and third authors: Department of Plant Pathology, University of Georgia, Athens 30602; and second author: Department of Plant Pathology, University of Georgia, Tifton 31793
| | - Robert C Kemerait
- First and third authors: Department of Plant Pathology, University of Georgia, Athens 30602; and second author: Department of Plant Pathology, University of Georgia, Tifton 31793
| | - Marin Talbot Brewer
- First and third authors: Department of Plant Pathology, University of Georgia, Athens 30602; and second author: Department of Plant Pathology, University of Georgia, Tifton 31793
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79
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Silva DN, Várzea V, Paulo OS, Batista D. Population genomic footprints of host adaptation, introgression and recombination in coffee leaf rust. MOLECULAR PLANT PATHOLOGY 2018; 19:1742-1753. [PMID: 29328532 PMCID: PMC6638104 DOI: 10.1111/mpp.12657] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 01/04/2018] [Accepted: 01/09/2018] [Indexed: 05/30/2023]
Abstract
Coffee leaf rust, caused by Hemileia vastatrix (Hv), represents the biggest threat to coffee production worldwide and ranks amongst the most serious fungal diseases in history. Despite a recent series of outbreaks and emergence of hypervirulent strains, the population evolutionary history and potential of this pathogen remain poorly understood. To address this issue, we used restriction site-associated DNA sequencing (RADseq) to generate ∼19 000 single nucleotide polymorphisms (SNPs) across a worldwide collection of 37 Hv samples. Contrary to the long-standing idea that Hv represents a genetically unstructured and cosmopolitan species, our results reveal the existence of a cryptic species complex with marked host tropism. Using phylogenetic and pathological data, we show that one of these lineages (C3) infects almost exclusively the most economically valuable coffee species (tetraploids that include Coffea arabica and interspecific hybrids), whereas the other lineages (C1 and C2) are severely maladapted to these hosts, but successfully infect diploid coffee species. Population dynamic analyses suggest that the C3 group may be a recent 'domesticated' lineage that emerged via host shift from diploid coffee hosts. We also found evidence of recombination occurring within this group, which could explain the high pace of pathotype emergence despite the low genetic variation. Moreover, genomic footprints of introgression between the C3 and C2 groups were discovered and raise the possibility that virulence factors may be quickly exchanged between groups with different pathogenic abilities. This work advances our understanding of the evolutionary strategies used by plant pathogens in agro-ecosystems with direct and far-reaching implications for disease control.
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Affiliation(s)
- Diogo Nuno Silva
- Departamento de Biologia Animal, Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG)Faculdade de Ciências, Universidade de LisboaLisboaPortugal
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC), Instituto Superior de AgronomiaUniversidade de LisboaOeirasPortugal
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
| | - Vítor Várzea
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC), Instituto Superior de AgronomiaUniversidade de LisboaOeirasPortugal
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
| | - Octávio Salgueiro Paulo
- Departamento de Biologia Animal, Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG)Faculdade de Ciências, Universidade de LisboaLisboaPortugal
| | - Dora Batista
- Departamento de Biologia Animal, Centre for Ecology, Evolution and Environmental Changes (cE3c), Computational Biology and Population Genomics Group (CoBiG)Faculdade de Ciências, Universidade de LisboaLisboaPortugal
- Centro de Investigação das Ferrugens do Cafeeiro (CIFC), Instituto Superior de AgronomiaUniversidade de LisboaOeirasPortugal
- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de AgronomiaUniversidade de LisboaLisboaPortugal
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80
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Lawrence DP, Holland LA, Nouri MT, Travadon R, Abramians A, Michailides TJ, Trouillas FP. Molecular phylogeny of Cytospora species associated with canker diseases of fruit and nut crops in California, with the descriptions of ten new species and one new combination. IMA Fungus 2018; 9:333-370. [PMID: 30622886 PMCID: PMC6317586 DOI: 10.5598/imafungus.2018.09.02.07] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 09/12/2018] [Indexed: 11/29/2022] Open
Abstract
Cytospora species are destructive canker and dieback pathogens of woody hosts in natural and agroecosystems around the world. In this genus, molecular identification has been limited due to the paucity of multi-locus sequence typing studies and the lack of sequence data from type specimens in public repositories, stalling robust phylogenetic reconstructions. In most cases a morphological species concept could not be applied due to the plasticity of characters and significant overlap of morphological features such as spore dimensions and fruiting body characters. In this study, we employed a molecular phylogenetic framework with the inclusion of four nuclear loci (ITS, translation elongation factor 1-alpha, actin, and beta-tubulin) to unveil the biodiversity and taxonomy of this understudied important genus of plant pathogens. Phylogenetic inferences based on 150 Californian isolates revealed 15 Cytospora species associated with branch and twig cankers and dieback of almond, apricot, cherry, cottonwood, olive, peach, pistachio, plum, pomegranate, and walnut trees in California. Of the 15 species recovered in this study, 10 are newly described and typified, in addition to one new combination. The pathogenic status of the newly described Cytospora species requires further investigation as most species were associated with severe dieback and decline of diverse and economically important fruit and nut crops in California.
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Affiliation(s)
- Daniel P Lawrence
- Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Leslie A Holland
- Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Mohamed T Nouri
- Department of Plant Pathology, University of California, Davis and Kearney Agricultural Research and Extension Centre, Parlier, CA 93648, USA
| | - Renaud Travadon
- Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Ara Abramians
- Department of Plant Pathology, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Themis J Michailides
- Department of Plant Pathology, University of California, Davis and Kearney Agricultural Research and Extension Centre, Parlier, CA 93648, USA
| | - Florent P Trouillas
- Department of Plant Pathology, University of California, Davis and Kearney Agricultural Research and Extension Centre, Parlier, CA 93648, USA
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81
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Schirrmann MK, Zoller S, Croll D, Stukenbrock EH, Leuchtmann A, Fior S. Genomewide signatures of selection in Epichloë reveal candidate genes for host specialization. Mol Ecol 2018; 27:3070-3086. [PMID: 29633410 DOI: 10.1111/mec.14585] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 02/21/2018] [Accepted: 02/23/2018] [Indexed: 12/31/2022]
Abstract
Host specialization is a key process in ecological divergence and speciation of plant-associated fungi. The underlying determinants of host specialization are generally poorly understood, especially in endophytes, which constitute one of the most abundant components of the plant microbiome. We addressed the genetic basis of host specialization in two sympatric subspecies of grass-endophytic fungi from the Epichloë typhina complex: subsp. typhina and clarkii. The life cycle of these fungi entails unrestricted dispersal of gametes and sexual reproduction before infection of a new host, implying that the host imposes a selective barrier on viability of the progeny. We aimed to detect genes under divergent selection between subspecies, experiencing restricted gene flow due to adaptation to different hosts. Using pooled whole-genome sequencing data, we combined FST and DXY population statistics in genome scans and detected 57 outlier genes showing strong differentiation between the two subspecies. Genomewide analyses of nucleotide diversity (π), Tajima's D and dN/dS ratios indicated that these genes have evolved under positive selection. Genes encoding secreted proteins were enriched among the genes showing evidence of positive selection, suggesting that molecular plant-fungus interactions are strong drivers of endophyte divergence. We focused on five genes encoding secreted proteins, which were further sequenced in 28 additional isolates collected across Europe to assess genetic variation in a larger sample size. Signature of positive selection in these isolates and putative identification of pathogenic function supports our findings that these genes represent strong candidates for host specialization determinants in Epichloë endophytes. Our results highlight the role of secreted proteins as key determinants of host specialization.
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Affiliation(s)
- Melanie K Schirrmann
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland.,Research Group Molecular Diagnostics, Genomics and Bioinformatics, Agroscope, Wädenswil, Switzerland
| | - Stefan Zoller
- Genetic Diversity Centre (GDC), ETH Zürich, Zürich, Switzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
| | - Eva H Stukenbrock
- Environmental Genomics, Christian-Albrechts University of Kiel, Kiel, Germany.,Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Adrian Leuchtmann
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland
| | - Simone Fior
- Institute of Integrative Biology (IBZ), ETH Zürich, Zürich, Switzerland
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82
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Benevenuto J, Teixeira-Silva NS, Kuramae EE, Croll D, Monteiro-Vitorello CB. Comparative Genomics of Smut Pathogens: Insights From Orphans and Positively Selected Genes Into Host Specialization. Front Microbiol 2018; 9:660. [PMID: 29681893 PMCID: PMC5897528 DOI: 10.3389/fmicb.2018.00660] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 03/21/2018] [Indexed: 12/20/2022] Open
Abstract
Host specialization is a key evolutionary process for the diversification and emergence of new pathogens. However, the molecular determinants of host range are poorly understood. Smut fungi are biotrophic pathogens that have distinct and narrow host ranges based on largely unknown genetic determinants. Hence, we aimed to expand comparative genomics analyses of smut fungi by including more species infecting different hosts and to define orphans and positively selected genes to gain further insights into the genetics basis of host specialization. We analyzed nine lineages of smut fungi isolated from eight crop and non-crop hosts: maize, barley, sugarcane, wheat, oats, Zizania latifolia (Manchurian rice), Echinochloa colona (a wild grass), and Persicaria sp. (a wild dicot plant). We assembled two new genomes: Ustilago hordei (strain Uhor01) isolated from oats and U. tritici (strain CBS 119.19) isolated from wheat. The smut genomes were of small sizes, ranging from 18.38 to 24.63 Mb. U. hordei species experienced genome expansions due to the proliferation of transposable elements and the amount of these elements varied among the two strains. Phylogenetic analysis confirmed that Ustilago is not a monophyletic genus and, furthermore, detected misclassification of the U. tritici specimen. The comparison between smut pathogens of crop and non-crop hosts did not reveal distinct signatures, suggesting that host domestication did not play a dominant role in shaping the evolution of smuts. We found that host specialization in smut fungi likely has a complex genetic basis: different functional categories were enriched in orphans and lineage-specific selected genes. The diversification and gain/loss of effector genes are probably the most important determinants of host specificity.
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Affiliation(s)
- Juliana Benevenuto
- Microbial Genetics Laboratory, Department of Genetics, University of São Paulo/Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
| | - Natalia S. Teixeira-Silva
- Microbial Genetics Laboratory, Department of Genetics, University of São Paulo/Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel (UNINE), Neuchâtel, Switzerland
| | - Claudia B. Monteiro-Vitorello
- Microbial Genetics Laboratory, Department of Genetics, University of São Paulo/Luiz de Queiroz College of Agriculture (USP/ESALQ), Piracicaba, Brazil
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83
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Abstract
The rice blast fungus Magnaporthe oryzae (syn., Pyricularia oryzae) is both a threat to global food security and a model for plant pathology. Molecular pathologists need an accurate understanding of the origins and line of descent of M. oryzae populations in order to identify the genetic and functional bases of pathogen adaptation and to guide the development of more effective control strategies. We used a whole-genome sequence analysis of samples from different times and places to infer details about the genetic makeup of M. oryzae from a global collection of isolates. Analyses of population structure identified six lineages within M. oryzae, including two pandemic on japonica and indica rice, respectively, and four lineages with more restricted distributions. Tip-dating calibration indicated that M. oryzae lineages separated about a millennium ago, long after the initial domestication of rice. The major lineage endemic to continental Southeast Asia displayed signatures of sexual recombination and evidence of DNA acquisition from multiple lineages. Tests for weak natural selection revealed that the pandemic spread of clonal lineages entailed an evolutionary “cost,” in terms of the accumulation of deleterious mutations. Our findings reveal the coexistence of multiple endemic and pandemic lineages with contrasting population and genetic characteristics within a widely distributed pathogen. The rice blast fungus Magnaporthe oryzae (syn., Pyricularia oryzae) is a textbook example of a rapidly adapting pathogen, and it is responsible for one of the most damaging diseases of rice. Improvements in our understanding of Magnaporthe oryzae’s diversity and evolution are required to guide the development of more effective control strategies. We used genome sequencing data for samples from around the world to infer the evolutionary history of M. oryzae. We found that M. oryzae diversified about 1,000 years ago, separating into six main lineages: two pandemic on japonica and indica rice, respectively, and four with more restricted distributions. We also found that a lineage endemic to continental Southeast Asia displayed signatures of sexual recombination and the acquisition of genetic material from multiple lineages. This work provides a population-level genomic framework for defining molecular markers for the control of rice blast and investigations of the molecular basis of differences in pathogenicity between M. oryzae lineages.
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84
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Phylogenetic study of indigenous grapevine leaf rust fungi in North America and biological identity of an invasive grapevine leaf rust fungus in Brazil. MYCOSCIENCE 2018. [DOI: 10.1016/j.myc.2017.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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85
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Fungal species and their boundaries matter – Definitions, mechanisms and practical implications. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2017.11.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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86
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Gladieux P, Condon B, Ravel S, Soanes D, Maciel JLN, Nhani A, Chen L, Terauchi R, Lebrun MH, Tharreau D, Mitchell T, Pedley KF, Valent B, Talbot NJ, Farman M, Fournier E. Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae. mBio 2018. [PMID: 29487238 DOI: 10.01210.01128/mbio] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multihost pathogen that infects multiple grasses and cereals, is responsible for the most damaging rice disease (rice blast), and is of growing concern due to the recent introduction of wheat blast to Bangladesh from South America. However, the genetic structure and evolutionary history of M. oryzae, including the possible existence of cryptic phylogenetic species, remain poorly defined. Here, we use whole-genome sequence information for 76 M. oryzae isolates sampled from 12 grass and cereal genera to infer the population structure of M. oryzae and to reassess the species status of wheat-infecting populations of the fungus. Species recognition based on genealogical concordance, using published data or extracting previously used loci from genome assemblies, failed to confirm a prior assignment of wheat blast isolates to a new species (Pyricularia graminis-tritici). Inference of population subdivisions revealed multiple divergent lineages within M. oryzae, each preferentially associated with one host genus, suggesting incipient speciation following host shift or host range expansion. Analyses of gene flow, taking into account the possibility of incomplete lineage sorting, revealed that genetic exchanges have contributed to the makeup of multiple lineages within M. oryzae These findings provide greater understanding of the ecoevolutionary factors that underlie the diversification of M. oryzae and highlight the practicality of genomic data for epidemiological surveillance in this important multihost pathogen.IMPORTANCE Infection of novel hosts is a major route for disease emergence by pathogenic microorganisms. Understanding the evolutionary history of multihost pathogens is therefore important to better predict the likely spread and emergence of new diseases. Magnaporthe oryzae is a multihost fungus that causes serious cereal diseases, including the devastating rice blast disease and wheat blast, a cause of growing concern due to its recent spread from South America to Asia. Using whole-genome analysis of 76 fungal strains from different hosts, we have documented the divergence of M. oryzae into numerous lineages, each infecting a limited number of host species. Our analyses provide evidence that interlineage gene flow has contributed to the genetic makeup of multiple M. oryzae lineages within the same species. Plant health surveillance is therefore warranted to safeguard against disease emergence in regions where multiple lineages of the fungus are in contact with one another.
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Affiliation(s)
- Pierre Gladieux
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Bradford Condon
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | - Sebastien Ravel
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Darren Soanes
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | | | | | - Li Chen
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | | | | | - Didier Tharreau
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Thomas Mitchell
- Department of Plant Pathology, Ohio State University, Columbus, Ohio, USA
| | - Kerry F Pedley
- USDA, Agricultural Research Service, FDWSRU, Ft. Detrick, Maryland, USA
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Nicholas J Talbot
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Mark Farman
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | - Elisabeth Fournier
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
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87
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Gladieux P, Condon B, Ravel S, Soanes D, Maciel JLN, Nhani A, Chen L, Terauchi R, Lebrun MH, Tharreau D, Mitchell T, Pedley KF, Valent B, Talbot NJ, Farman M, Fournier E. Gene Flow between Divergent Cereal- and Grass-Specific Lineages of the Rice Blast Fungus Magnaporthe oryzae. mBio 2018; 9:e01219-17. [PMID: 29487238 PMCID: PMC5829825 DOI: 10.1128/mbio.01219-17] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/20/2017] [Indexed: 11/25/2022] Open
Abstract
Delineating species and epidemic lineages in fungal plant pathogens is critical to our understanding of disease emergence and the structure of fungal biodiversity and also informs international regulatory decisions. Pyricularia oryzae (syn. Magnaporthe oryzae) is a multihost pathogen that infects multiple grasses and cereals, is responsible for the most damaging rice disease (rice blast), and is of growing concern due to the recent introduction of wheat blast to Bangladesh from South America. However, the genetic structure and evolutionary history of M. oryzae, including the possible existence of cryptic phylogenetic species, remain poorly defined. Here, we use whole-genome sequence information for 76 M. oryzae isolates sampled from 12 grass and cereal genera to infer the population structure of M. oryzae and to reassess the species status of wheat-infecting populations of the fungus. Species recognition based on genealogical concordance, using published data or extracting previously used loci from genome assemblies, failed to confirm a prior assignment of wheat blast isolates to a new species (Pyricularia graminis-tritici). Inference of population subdivisions revealed multiple divergent lineages within M. oryzae, each preferentially associated with one host genus, suggesting incipient speciation following host shift or host range expansion. Analyses of gene flow, taking into account the possibility of incomplete lineage sorting, revealed that genetic exchanges have contributed to the makeup of multiple lineages within M. oryzae These findings provide greater understanding of the ecoevolutionary factors that underlie the diversification of M. oryzae and highlight the practicality of genomic data for epidemiological surveillance in this important multihost pathogen.IMPORTANCE Infection of novel hosts is a major route for disease emergence by pathogenic microorganisms. Understanding the evolutionary history of multihost pathogens is therefore important to better predict the likely spread and emergence of new diseases. Magnaporthe oryzae is a multihost fungus that causes serious cereal diseases, including the devastating rice blast disease and wheat blast, a cause of growing concern due to its recent spread from South America to Asia. Using whole-genome analysis of 76 fungal strains from different hosts, we have documented the divergence of M. oryzae into numerous lineages, each infecting a limited number of host species. Our analyses provide evidence that interlineage gene flow has contributed to the genetic makeup of multiple M. oryzae lineages within the same species. Plant health surveillance is therefore warranted to safeguard against disease emergence in regions where multiple lineages of the fungus are in contact with one another.
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Affiliation(s)
- Pierre Gladieux
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Bradford Condon
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | - Sebastien Ravel
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Darren Soanes
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | | | | | - Li Chen
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | | | | | - Didier Tharreau
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
| | - Thomas Mitchell
- Department of Plant Pathology, Ohio State University, Columbus, Ohio, USA
| | - Kerry F Pedley
- USDA, Agricultural Research Service, FDWSRU, Ft. Detrick, Maryland, USA
| | - Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA
| | - Nicholas J Talbot
- College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Mark Farman
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | - Elisabeth Fournier
- UMR BGPI, Univ Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France
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Meng JW, He DC, Zhu W, Yang LN, Wu EJ, Xie JH, Shang LP, Zhan J. Human-Mediated Gene Flow Contributes to Metapopulation Genetic Structure of the Pathogenic Fungus Alternaria alternata from Potato. FRONTIERS IN PLANT SCIENCE 2018; 9:198. [PMID: 29497439 PMCID: PMC5818430 DOI: 10.3389/fpls.2018.00198] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 02/01/2018] [Indexed: 06/01/2023]
Abstract
Metapopulation structure generated by recurrent extinctions and recolonizations plays an important role in the evolution of species but is rarely considered in agricultural systems. In this study, generation and mechanism of metapopulation structure were investigated by microsatellite assaying 725 isolates of Alternaria alternata sampled from potato hosts at 16 locations across China. We found a single major cluster, no isolate-geography associations and no bottlenecks in the A. alternata isolates, suggesting a metapopulation genetic structure of the pathogen. We also found weak isolation-by-distance, lower among than within cropping region population differentiation, concordant moving directions of potato products and net gene flow and the highest gene diversity in the region with the most potato imports. These results indicate that in addition to natural dispersal, human-mediated gene flow also contributes to the generation and dynamics of the metapopulation genetic structure of A. alternata in China. Metapopulation structure increases the adaptive capacity of the plant pathogen as a result of enhanced genetic variation and reduced population fragmentation. Consequently, rigid quarantine regulations may be required to reduce population connectivity and the evolutionary potential of A. alternata and other pathogens with a similar population dynamics for a sustainable plant disease management.
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Affiliation(s)
- Jing-Wen Meng
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dun-Chun He
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wen Zhu
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li-Na Yang
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - E-Jiao Wu
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jia-Hui Xie
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Li-Ping Shang
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiasui Zhan
- Fujian Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
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89
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Molano EPL, Cabrera OG, Jose J, do Nascimento LC, Carazzolle MF, Teixeira PJPL, Alvarez JC, Tiburcio RA, Tokimatu Filho PM, de Lima GMA, Guido RVC, Corrêa TLR, Leme AFP, Mieczkowski P, Pereira GAG. Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC). BMC Genomics 2018; 19:58. [PMID: 29343217 PMCID: PMC5773145 DOI: 10.1186/s12864-018-4440-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/08/2018] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta is a necrotrophic fungus responsible for lethal wilt disease in cacao. The aim of this work is to analyze the genome of C. cacaofunesta through a comparative approach with genomes of other Sordariomycetes in order to better understand the molecular basis of pathogenicity in the Ceratocystis genus. RESULTS We present an analysis of the C. cacaofunesta genome focusing on secreted proteins that might constitute pathogenicity factors. Comparative genome analyses among five Ceratocystidaceae species and 23 other Sordariomycetes fungi showed a strong reduction in gene content of the Ceratocystis genus. However, some gene families displayed a remarkable expansion, in particular, the Phosphatidylinositol specific phospholipases-C (PI-PLC) family. Also, evolutionary rate calculations suggest that the evolution process of this family was guided by positive selection. Interestingly, among the 82 PI-PLCs genes identified in the C. cacaofunesta genome, 70 genes encoding extracellular PI-PLCs are grouped in eight small scaffolds surrounded by transposon fragments and scars that could be involved in the rapid evolution of the PI-PLC family. Experimental secretome using LC-MS/MS validated 24% (86 proteins) of the total predicted secretome (342 proteins), including four PI-PLCs and other important pathogenicity factors. CONCLUSION Analysis of the Ceratocystis cacaofunesta genome provides evidence that PI-PLCs may play a role in pathogenicity. Subsequent functional studies will be aimed at evaluating this hypothesis. The observed genetic arsenals, together with the analysis of the PI-PLC family shown in this work, reveal significant differences in the Ceratocystis genome compared to the classical vascular fungi, Verticillium and Fusarium. Altogether, our analyses provide new insights into the evolution and the molecular basis of plant pathogenicity.
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Affiliation(s)
- Eddy Patricia Lopez Molano
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Odalys García Cabrera
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Juliana Jose
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | | | - Marcelo Falsarella Carazzolle
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil.,Centro Nacional de Processamento de Alto Desempenho, Universidade Estadual de Campinas, Campinas, Brazil
| | - Paulo José Pereira Lima Teixeira
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil.,Present Address: Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Javier Correa Alvarez
- Departamento de Ciencias Biológicas, Escuela de Ciencias, Universidad EAFIT, Medellın, Colombia
| | - Ricardo Augusto Tiburcio
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Paulo Massanari Tokimatu Filho
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | - Gustavo Machado Alvares de Lima
- Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, Brazil
| | - Rafael Victório Carvalho Guido
- Centro de Biotecnologia Molecular Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, Brazil
| | - Thamy Lívia Ribeiro Corrêa
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil
| | | | - Piotr Mieczkowski
- High-Throughput Sequencing Facility, University of North Carolina, Chapel Hill, NC, USA
| | - Gonçalo Amarante Guimarães Pereira
- Genomic and Expression Laboratory, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, 13083-970, Brazil.
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90
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Lee DH, Roux J, Wingfield BD, Wingfield MJ. Non-Mendelian segregation influences the infection biology and genetic structure of the African tree pathogen Ceratocystis albifundus. Fungal Biol 2017; 122:222-230. [PMID: 29551196 DOI: 10.1016/j.funbio.2017.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 12/02/2017] [Accepted: 12/12/2017] [Indexed: 02/04/2023]
Abstract
The African fungal tree pathogen, Ceratocystis albifundus, undergoes uni-directional mating type switching, giving rise to either self-fertile or self-sterile progeny. Self-sterile isolates lack the MAT1-2-1 gene and have reduced fitness such as slower growth and reduced pathogenicity, relative to self-fertile isolates. While it has been hypothesized that there is a 1:1 ratio of self-fertile to self-sterile ascospore progeny in relatives of C. albifundus, some studies have reported a significant bias in this ratio. This could be due to the fact that either fewer self-sterile ascospores are produced or that self-sterile ascospores have low viability. We quantified the percentage of self-sterile and self-fertile ascospores from ascospore masses in C. albifundus using real-time PCR. Primers were designed to distinguish between spores that contained the MAT1-2-1 gene and those where this gene had been deleted. A significant bias towards the self-fertile mating type was observed in all single ascospore masses taken from sexual structures produced in haploid-selfed cultures. The same result was observed from a disease outbreak situation in an intensively managed field of cultivated native trees, and this was coupled with very low population diversity in the pathogen. This was in contrast to the results obtained from ascospore masses taken from the crosses performed under laboratory conditions or ascomata on native trees in a non-disease situation, where either self-fertile or self-sterile ascospores were dominant. The results suggest that reproductive strategies play a significant role in the infection biology and genetic structure of C. albifundus populations.
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Affiliation(s)
- Dong-Hyeon Lee
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Jolanda Roux
- Department of Plant and Soil Sciences, FABI, University of Pretoria, Pretoria, South Africa
| | - Brenda D Wingfield
- Department of Genetics, FABI, University of Pretoria, Pretoria, South Africa.
| | - Michael J Wingfield
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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91
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Sharma P, Sharma A, Sharma M, Bhalla N, Estrela P, Jain A, Thakur P, Thakur A. Nanomaterial Fungicides: In Vitro and In Vivo Antimycotic Activity of Cobalt and Nickel Nanoferrites on Phytopathogenic Fungi. GLOBAL CHALLENGES (HOBOKEN, NJ) 2017; 1:1700041. [PMID: 31565296 PMCID: PMC6607179 DOI: 10.1002/gch2.201700041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 10/04/2017] [Indexed: 05/15/2023]
Abstract
Recent advances in engineering lead to the fabrication of nanomaterials with unique properties targeted toward specific applications. The use of nanotechnology in agriculture, in particular for plant protection and production, is an under-explored area in the research community. Fungal diseases are one of the leading causes of crop destruction and, in this context, the antifungal effect of nanoparticles of cobalt and nickel ferrite against phytopathogenic fungi is reported here. As a proof of concept, it is also shown how such nanoparticles can be used as fungicides in plants. The developed cobalt and nickel ferrite nanoparticles (CoFe2O4 and NiFe2O4) are successfully tested for antimycotic activity against three plant-pathogenic fungi: Fusarium oxysporum, Colletotrichum gloeosporioides, and Dematophora necatrix. In addition, it is also observed that these ferrite nanoparticles reduce the incidence of Fusarium wilt in capsicum. The study suggests that nanoparticles of CoFe2O4 and NiFe2O4 can be used as an effective fungicide in plant disease management.
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Affiliation(s)
- Parul Sharma
- Nanotechnology WingInnovative Science Research SocietyShimlaHP171002India
| | - Adikshita Sharma
- Department of Plant PathologyDr. Y. S. Parmar University of Horticulture and ForestryNauni, SolanHP173230India
| | - Monica Sharma
- Department of Plant PathologyDr. Y. S. Parmar University of Horticulture and ForestryNauni, SolanHP173230India
| | - Nikhil Bhalla
- Department of Electronic and Electrical EngineeringUniversity of BathBathBA2 7AYUK
- Micro/Bio/Nanofluidics UnitOkinawa Institute of Science and Technology Graduate University (OIST)1919‐1 Tancha, OnnaKunigami District, Okinawa PrefectureOkinawa904‐0412Japan
| | - Pedro Estrela
- Department of Electronic and Electrical EngineeringUniversity of BathBathBA2 7AYUK
| | - Aditya Jain
- Institute of Energy EfficiencyUniversity of California Santa BarbaraSanta BarbaraCA93106‐9560USA
| | - Preeti Thakur
- Amity School of Applied SciencesAmity University GurgaonHaryana122413India
| | - Atul Thakur
- Amity Center of NanotechnologyAmity University GurgaonHaryana122413India
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92
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Delong W, Yongling W, Lanying W, Juntao F, Xing Z. Design, synthesis and evaluation of 3-arylidene azetidin-2-ones as potential antifungal agents against Alternaria solani Sorauer. Bioorg Med Chem 2017; 25:6661-6673. [PMID: 29137937 DOI: 10.1016/j.bmc.2017.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/26/2017] [Accepted: 11/02/2017] [Indexed: 12/29/2022]
Abstract
A new concise and facile method was explored to synthesize a collection of new 3-arylidene azetidin-2-ones, which could be regarded as the derivatives of the hybrid scaffold of bioactive natural cinnamamide and heterocycle azetidi-2-one. The structures of the synthesized compounds were characterized by 1H, 13C NMR, and MS; and their antifungal activity were evaluated against Alternaria solani Sorauer. These antifungal data were subjected to a quantitative structure-activity relationship (QSAR) analysis using Codessa software on the basis of the results from B3LYP/6-31G(d,p) quantum calculations. The best regressive model revealed that potentially more active compounds should have low dipole moments and QC-min (minimal net atomic charge for a C atom), and high QO-max (maximal net atomic charge for an O atom) and QN-min (minimal net atomic charge for an N atom). The most potent compound 7k could lead to intracellular accumulation of reactive oxygen species, dissipation of mitochondrial transmembrane potential, and an autophagy-like cell death process in A. solani Sorauer. Taken together, these results laid the foundation for further design of improved crop-protection agents based on this hybrid scaffold.
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Affiliation(s)
- Wang Delong
- Research & Development Center of Biorational Pesticide, Shaanxi Research Center of Biopesticide Engineering & Technology, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Yangling 712100, China
| | - Wu Yongling
- Research & Development Center of Biorational Pesticide, Shaanxi Research Center of Biopesticide Engineering & Technology, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Yangling 712100, China
| | - Wang Lanying
- Research & Development Center of Biorational Pesticide, Shaanxi Research Center of Biopesticide Engineering & Technology, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Yangling 712100, China; College of Environment and Plant Protection, Hainan University, Haikou, Hainan 570228, China
| | - Feng Juntao
- Research & Development Center of Biorational Pesticide, Shaanxi Research Center of Biopesticide Engineering & Technology, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Yangling 712100, China.
| | - Zhang Xing
- Research & Development Center of Biorational Pesticide, Shaanxi Research Center of Biopesticide Engineering & Technology, Key Laboratory of Plant Protection Resources and Pest Management of Ministry of Education, Northwest A&F University, Yangling 712100, China
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93
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Vincenot L, Popa F, Laso F, Donges K, Rexer KH, Kost G, Yang ZL, Nara K, Selosse MA. Out of Asia: Biogeography of fungal populations reveals Asian origin of diversification of the Laccaria amethystina complex, and two new species of violet Laccaria. Fungal Biol 2017; 121:939-955. [DOI: 10.1016/j.funbio.2017.08.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 07/28/2017] [Accepted: 08/09/2017] [Indexed: 12/13/2022]
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94
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Farrer RA, Fisher MC. Describing Genomic and Epigenomic Traits Underpinning Emerging Fungal Pathogens. ADVANCES IN GENETICS 2017; 100:73-140. [PMID: 29153405 DOI: 10.1016/bs.adgen.2017.09.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An unprecedented number of pathogenic fungi are emerging and causing disease in animals and plants, putting the resilience of wild and managed ecosystems in jeopardy. While the past decades have seen an increase in the number of pathogenic fungi, they have also seen the birth of new big data technologies and analytical approaches to tackle these emerging pathogens. We review how the linked fields of genomics and epigenomics are transforming our ability to address the challenge of emerging fungal pathogens. We explore the methodologies and bioinformatic toolkits that currently exist to rapidly analyze the genomes of unknown fungi, then discuss how these data can be used to address key questions that shed light on their epidemiology. We show how genomic approaches are leading a revolution into our understanding of emerging fungal diseases and speculate on future approaches that will transform our ability to tackle this increasingly important class of emerging pathogens.
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95
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Doña J, Sweet AD, Johnson KP, Serrano D, Mironov S, Jovani R. Cophylogenetic analyses reveal extensive host-shift speciation in a highly specialized and host-specific symbiont system. Mol Phylogenet Evol 2017; 115:190-196. [DOI: 10.1016/j.ympev.2017.08.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 01/21/2023]
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96
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Grünwald NJ, Everhart SE, Knaus BJ, Kamvar ZN. Best Practices for Population Genetic Analyses. PHYTOPATHOLOGY 2017; 107:1000-1010. [PMID: 28513284 DOI: 10.1094/phyto-12-16-0425-rvw] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Population genetic analysis is a powerful tool to understand how pathogens emerge and adapt. However, determining the genetic structure of populations requires complex knowledge on a range of subtle skills that are often not explicitly stated in book chapters or review articles on population genetics. What is a good sampling strategy? How many isolates should I sample? How do I include positive and negative controls in my molecular assays? What marker system should I use? This review will attempt to address many of these practical questions that are often not readily answered from reading books or reviews on the topic, but emerge from discussions with colleagues and from practical experience. A further complication for microbial or pathogen populations is the frequent observation of clonality or partial clonality. Clonality invariably makes analyses of population data difficult because many assumptions underlying the theory from which analysis methods were derived are often violated. This review provides practical guidance on how to navigate through the complex web of data analyses of pathogens that may violate typical population genetics assumptions. We also provide resources and examples for analysis in the R programming environment.
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Affiliation(s)
- N J Grünwald
- First and third authors: Horticultural Crop Research Unit, USDA-ARS, Corvallis, OR; and second and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis
| | - S E Everhart
- First and third authors: Horticultural Crop Research Unit, USDA-ARS, Corvallis, OR; and second and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis
| | - B J Knaus
- First and third authors: Horticultural Crop Research Unit, USDA-ARS, Corvallis, OR; and second and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis
| | - Z N Kamvar
- First and third authors: Horticultural Crop Research Unit, USDA-ARS, Corvallis, OR; and second and fourth authors: Department of Botany and Plant Pathology, Oregon State University, Corvallis
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98
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De Silva DD, Crous PW, Ades PK, Hyde KD, Taylor PW. Life styles of Colletotrichum species and implications for plant biosecurity. FUNGAL BIOL REV 2017. [DOI: 10.1016/j.fbr.2017.05.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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99
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Matsubayashi KW, Kohyama TI, Kobayashi N, Yamasaki S, Kuwajima M, Katakura H. Genetic divergence with ongoing gene flow is maintained by the use of different hosts in phytophagous ladybird beetles genus Henosepilachna. J Evol Biol 2017; 30:1110-1123. [PMID: 28306172 DOI: 10.1111/jeb.13071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/12/2017] [Indexed: 12/12/2022]
Abstract
Adaptation to different environments can promote population divergence via natural selection even in the presence of gene flow - a phenomenon that typically occurs during ecological speciation. To elucidate how natural selection promotes and maintains population divergence during speciation, we investigated the population genetic structure, degree of gene flow and heterogeneous genomic divergence in three closely related Japanese phytophagous ladybird beetles: Henosepilachna pustulosa, H. niponica and H. yasutomii. These species act as a generalist, a wild thistle (Cirsium spp.) specialist and a blue cohosh (Caulophyllum robustum) specialist, respectively, and their ranges differ accordingly. The two specialist species widely co-occur but are reproductively isolated solely due to their high specialization to a particular host plant. Genomewide amplified fragment-length polymorphism (AFLP) markers and mitochondrial cytochrome c oxidase subunit I (COI) gene sequences demonstrated obvious genomewide divergence associated with both geographic distance and ecological divergence. However, a hybridization assessment for both AFLP loci and the mitochondrial sequences revealed a certain degree of unidirectional gene flow between the two sympatric specialist species. Principal coordinates analysis (PCoA) based on all of the variable AFLP loci demonstrated that there are genetic similarities between populations from adjacent localities irrespective of the species (i.e. host range). However, a further comparative genome scan identified a few fractions of loci representing approximately 1% of all loci as different host-associated outliers. These results suggest that these three species had a complex origin, which could be obscured by current gene flow, and that ecological divergence can be maintained with only a small fraction of the genome is related to different host use even when there is a certain degree of gene flow between sympatric species pairs.
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Affiliation(s)
- K W Matsubayashi
- The Faculty of Arts and Science, Kyushu University, Fukuoka, Fukuoka, Japan
| | - T I Kohyama
- Faculty of Earth and Environmental Sciences, Hokkaido University, Sapporo, Hokkaido, Japan
| | - N Kobayashi
- Saitama Prefecture University, Koshigaya, Saitama, Japan
| | - S Yamasaki
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - M Kuwajima
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
| | - H Katakura
- Department of Natural History Sciences, Faculty of Science, Hokkaido University, Sapporo, Hokkaido, Japan
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Vanhove M, Beale MA, Rhodes J, Chanda D, Lakhi S, Kwenda G, Molloy S, Karunaharan N, Stone N, Harrison TS, Bicanic T, Fisher MC. Genomic epidemiology of Cryptococcus yeasts identifies adaptation to environmental niches underpinning infection across an African HIV/AIDS cohort. Mol Ecol 2017; 26:1991-2005. [PMID: 27862555 PMCID: PMC5412878 DOI: 10.1111/mec.13891] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 10/15/2016] [Accepted: 10/17/2016] [Indexed: 12/21/2022]
Abstract
Emerging infections caused by fungi have become a widely recognized global phenomenon and are causing an increasing burden of disease. Genomic techniques are providing new insights into the structure of fungal populations, revealing hitherto undescribed fine-scale adaptations to environments and hosts that govern their emergence as infections. Cryptococcal meningitis is a neglected tropical disease that is responsible for a large proportion of AIDS-related deaths across Africa; however, the ecological determinants that underlie a patient's risk of infection remain largely unexplored. Here, we use genome sequencing and ecological genomics to decipher the evolutionary ecology of the aetiological agents of cryptococcal meningitis, Cryptococcus neoformans and Cryptococcus gattii, across the central African country of Zambia. We show that the occurrence of these two pathogens is differentially associated with biotic (macroecological) and abiotic (physical) factors across two key African ecoregions, Central Miombo woodlands and Zambezi Mopane woodlands. We show that speciation of Cryptococcus has resulted in adaptation to occupy different ecological niches, with C. neoformans found to occupy Zambezi Mopane woodlands and C. gattii primarily recovered from Central Miombo woodlands. Genome sequencing shows that C. neoformans causes 95% of human infections in this region, of which over three-quarters belonged to the globalized lineage VNI. We show that VNI infections are largely associated with urbanized populations in Zambia. Conversely, the majority of C. neoformans isolates recovered in the environment belong to the genetically diverse African-endemic lineage VNB, and we show hitherto unmapped levels of genomic diversity within this lineage. Our results reveal the complex evolutionary ecology that underpins the reservoirs of infection for this, and likely other, deadly pathogenic fungi.
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MESH Headings
- Adaptation, Physiological/genetics
- Cryptococcus gattii/genetics
- Cryptococcus neoformans/genetics
- DNA Barcoding, Taxonomic
- DNA, Fungal/genetics
- DNA, Ribosomal Spacer/genetics
- Forests
- Genetics, Population
- Genome, Fungal
- Genomics
- Humans
- Meningitis, Cryptococcal/epidemiology
- Meningitis, Cryptococcal/microbiology
- Models, Biological
- Phylogeny
- Plant Bark/microbiology
- Polymorphism, Single Nucleotide
- Soil Microbiology
- Trees/microbiology
- Zambia
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Affiliation(s)
- Mathieu Vanhove
- Department of Infectious Disease Epidemiology, St Mary's Hospital, Imperial College London, London, W2 1PG, UK
| | - Mathew A Beale
- Department of Infectious Disease Epidemiology, St Mary's Hospital, Imperial College London, London, W2 1PG, UK
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
- Division of Infection & Immunity, University College London, Gower St, London WC1E 6BT, UK
| | - Johanna Rhodes
- Department of Infectious Disease Epidemiology, St Mary's Hospital, Imperial College London, London, W2 1PG, UK
| | - Duncan Chanda
- School of Medicine, University of Zambia, Nationalist Road, PO Box 50110, Lusaka, Zambia
| | - Shabir Lakhi
- School of Medicine, University of Zambia, Nationalist Road, PO Box 50110, Lusaka, Zambia
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, University of Zambia, PO Box 32379, Lusaka, Zambia
| | - Sile Molloy
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
| | - Natasha Karunaharan
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
| | - Neil Stone
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
| | - Thomas S Harrison
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
| | - Tihana Bicanic
- Institute of Infection and Immunity, St. George's University of London, Blackshaw Road, London SW17 0QT, UK
| | - Matthew C Fisher
- Department of Infectious Disease Epidemiology, St Mary's Hospital, Imperial College London, London, W2 1PG, UK
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