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Rogério F, Van Oosterhout C, Ciampi-Guillardi M, Correr FH, Hosaka GK, Cros-Arteil S, Rodrigues Alves Margarido G, Massola Júnior NS, Gladieux P. Means, motive and opportunity for biological invasions: Genetic introgression in a fungal pathogen. Mol Ecol 2023; 32:2428-2442. [PMID: 35076152 DOI: 10.1111/mec.16366] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 11/28/2022]
Abstract
Invasions by fungal plant pathogens pose a significant threat to the health of agricultural ecosystems. Despite limited standing genetic variation, many invasive fungal species can adapt and spread rapidly, resulting in significant losses to crop yields. Here, we report on the population genomics of Colletotrichum truncatum, a polyphagous pathogen that can infect more than 460 plant species, and an invasive pathogen of soybean in Brazil. We study the whole-genome sequences of 18 isolates representing 10 fields from two major regions of soybean production. We show that Brazilian C. truncatum is subdivided into three phylogenetically distinct lineages that exchange genetic variation through hybridization. Introgression affects 2%-30% of the nucleotides of genomes and varies widely between the lineages. We find that introgressed regions comprise secreted protein-encoding genes, suggesting possible co-evolutionary targets for selection in those regions. We highlight the inherent vulnerability of genetically uniform crops in the agro-ecological environment, particularly when faced with pathogens that can take full advantage of the opportunities offered by an increasingly globalized world. Finally, we discuss "the means, motive and opportunity" of fungal pathogens and how they can become invasive species of crops. We call for more population genomic studies because such analyses can help identify geographical areas and pathogens that pose a risk, thereby helping to inform control strategies to better protect crops in the future.
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Affiliation(s)
- Flávia Rogério
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
- Institute for Agribiotechnology Research (CIALE), University of Salamanca, Salamanca, Spain
| | | | - Maisa Ciampi-Guillardi
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
| | | | | | | | | | - Nelson S Massola Júnior
- Department of Plant Pathology and Nematology, University of São Paulo, Piracicaba, SP, Brazil
| | - Pierre Gladieux
- UMR PHIM, University of Montpellier, INRAE, CIRAD, Montpellier, France
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Alkemade JA, Baroncelli R, Messmer MM, Hohmann P. Attack of the clones: Population genetics reveals clonality of Colletotrichum lupini, the causal agent of lupin anthracnose. MOLECULAR PLANT PATHOLOGY 2023; 24:616-627. [PMID: 37078402 DOI: 10.1111/mpp.13332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/08/2023] [Accepted: 03/17/2023] [Indexed: 05/03/2023]
Abstract
Colletotrichum lupini, the causative agent of lupin anthracnose, affects lupin cultivation worldwide. Understanding its population structure and evolutionary potential is crucial to design successful disease management strategies. The objective of this study was to employ population genetics to investigate the diversity, evolutionary dynamics, and molecular basis of the interaction of this notorious lupin pathogen with its host. A collection of globally representative C. lupini isolates was genotyped through triple digest restriction site-associated DNA sequencing, resulting in a data set of unparalleled resolution. Phylogenetic and structural analysis could distinguish four independent lineages (I-IV). The strong population structure and high overall standardized index of association (r̅d ) indicates that C. lupini reproduces clonally. Different morphologies and virulence patterns on white lupin (Lupinus albus) and Andean lupin (Lupinus mutabilis) were observed between and within clonal lineages. Isolates belonging to lineage II were shown to have a minichromosome that was also partly present in lineage III and IV, but not in lineage I isolates. Variation in the presence of this minichromosome could imply a role in host-pathogen interaction. All four lineages were present in the South American Andes region, which is suggested to be the centre of origin of this species. Only members of lineage II have been found outside South America since the 1990s, indicating it as the current pandemic population. As a seedborne pathogen, C. lupini has mainly spread through infected but symptomless seeds, stressing the importance of phytosanitary measures to prevent future outbreaks of strains that are yet confined to South America.
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Affiliation(s)
- Joris A Alkemade
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
- Centre for Studies on Bioinspired Agro-Enviromental Technology, Università di Napoli Federico II, Portici, 80055, Italy
| | - Monika M Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
- Bonaplanta, BioCrops Innovations SL, Manresa, Spain
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Melese AS, Makinde OD, Obsu LL. Mathematical modelling and analysis of coffee berry disease dynamics on a coffee farm. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:7349-7373. [PMID: 35730310 DOI: 10.3934/mbe.2022347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This paper focuses on a mathematical model for coffee berry disease infestation dynamics. This model considers coffee berry and vector populations with the interaction of fungal pathogens. In order to gain an insight into the global dynamics of coffee berry disease transmission and eradication on any given coffee farm, the assumption of logistic growth with a carrying capacity reflects the fact that the amount of coffee plants depends on the limited size of the coffee farm. First, we show that all solutions of the chosen model are bounded and non-negative with positive initial data in a feasible region. Subsequently, endemic and disease-free equilibrium points are calculated. The basic reproduction number with respect to the coffee berry disease-free equilibrium point is derived using a next generation matrix approach. Furthermore, the local stability of the equilibria is established based on the Jacobian matrix and Routh Hurwitz criteria. The global stability of the equilibria is also proved by using the Lyapunov function. Moreover, bifurcation analysis is proved by the center manifold theory. The sensitivity indices for the basic reproduction number with respect to the main parameters are determined. Finally, the numerical simulations show the agreement with the analytical results of the model analysis.
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Affiliation(s)
- Abdisa Shiferaw Melese
- Department of Applied Mathematics, Adama Science and Technology University, Adama, Ethiopia
| | | | - Legesse Lemecha Obsu
- Department of Applied Mathematics, Adama Science and Technology University, Adama, Ethiopia
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Castillo AI, Tsai CW, Su CC, Weng LW, Lin YC, Cho ST, Almeida RPP, Kuo CH. Genetic differentiation of Xylella fastidiosa following the introduction into Taiwan. Microb Genom 2021; 7. [PMID: 34898423 PMCID: PMC8767338 DOI: 10.1099/mgen.0.000727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The economically important plant pathogen Xylella fastidiosa has been reported in multiple regions of the globe during the last two decades, threatening a growing list of plants. Particularly, X. fastidiosa subspecies fastidiosa causes Pierce’s disease (PD) of grapevines, which is a problem in the USA, Spain, and Taiwan. In this work, we studied PD-causing subsp. fastidiosa populations and compared the genome sequences of 33 isolates found in Central Taiwan with 171 isolates from the USA and two from Spain. Phylogenetic relationships, haplotype networks, and genetic diversity analyses confirmed that subsp. fastidiosa was recently introduced into Taiwan from the Southeast USA (i.e. the PD-I lineage). Recent core-genome recombination events were detected among introduced subsp. fastidiosa isolates in Taiwan and contributed to the development of genetic diversity. The genetic diversity observed includes contributions through recombination from unknown donors, suggesting that higher genetic diversity exists in the region. Nevertheless, no recombination event was detected between X. fastidiosa subsp. fastidiosa and the endemic sister species Xylella taiwanensis, which is the causative agent of pear leaf scorch disease. In summary, this study improved our understanding of the genetic diversity of an important plant pathogenic bacterium after its invasion to a new region.
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Affiliation(s)
- Andreina I Castillo
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Chi-Wei Tsai
- Department of Entomology, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Chiou-Chu Su
- Division of Pesticide Application, Taiwan Agricultural Chemicals and Toxic Substances Research Institute, Taichung 413, Taiwan, ROC
| | - Ling-Wei Weng
- Department of Entomology, National Taiwan University, Taipei 106, Taiwan, ROC
| | - Yu-Chen Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Shu-Ting Cho
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan, ROC
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Chih-Horng Kuo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan, ROC
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Cabral A, Azinheira HG, Talhinhas P, Batista D, Ramos AP, Silva MDC, Oliveira H, Várzea V. Pathological, Morphological, Cytogenomic, Biochemical and Molecular Data Support the Distinction between Colletotrichum cigarro comb. et stat. nov. and Colletotrichum kahawae. PLANTS (BASEL, SWITZERLAND) 2020; 9:E502. [PMID: 32295225 PMCID: PMC7238176 DOI: 10.3390/plants9040502] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/10/2020] [Accepted: 04/12/2020] [Indexed: 12/20/2022]
Abstract
The genus Colletotrichum has witnessed tremendous variations over the years in the number of species recognized, ranging from 11 to several hundreds. Host-specific fungal species, once the rule, are now the exception, with polyphagous behavior regarded as normal in this genus. The species Colletotrichum kahawae was created to accommodate the pathogens that have the unique ability to infect green developing coffee berries causing the devastating Coffee Berry Disease in Africa, but its close phylogenetic relationship to a polyphagous group of fungi in the C. gloeosporioides species complex led some researchers to regard these pathogens as members of a wider species. In this work we combine pathological, morphological, cytogenomic, biochemical, and molecular data of a comprehensive set of phylogenetically-related isolates to show that the Coffee Berry Disease pathogen forms a separate species, C. kahawae, and also to assign the closely related fungi, previously in C. kahawae subsp. cigarro, to a new species, C. cigarro comb. et stat. nov. This taxonomic clarification provides an opportunity to link phylogeny and functional biology, and additionally enables a much-needed tool for plant pathology and agronomy, associating exclusively C. kahawae to the Coffee Berry Disease pathogen.
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Affiliation(s)
- Ana Cabral
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
| | - Helena G. Azinheira
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
| | - Pedro Talhinhas
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
| | - Dora Batista
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Ana Paula Ramos
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Laboratório de Patologia Vegetal “Veríssimo de Almeida”, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal
| | - Maria do Céu Silva
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
| | - Helena Oliveira
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
| | - Vítor Várzea
- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, 1349-017 Lisbon, Portugal; (A.C.); (H.G.A.); (D.B.); (A.P.R.); (M.d.C.S.); (H.O.); (V.V.)
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2780-505 Oeiras, Portugal
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Fungal species boundaries in the genomics era. Fungal Genet Biol 2019; 131:103249. [PMID: 31279976 DOI: 10.1016/j.fgb.2019.103249] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 05/21/2019] [Accepted: 06/28/2019] [Indexed: 12/30/2022]
Abstract
Genomic data has opened new possibilities to understand how organisms change over time, and could enable the discovery of previously undescribed species. Although taxonomy used to be based on phenotypes, molecular data has frequently revealed that morphological traits are insufficient to describe biodiversity. Genomics holds the promise of revealing even more genetic discontinuities, but the parameters on how to describe species from genomic data remain unclear. Fungi have been a successful case in which the use of molecular markers has uncovered the existence of genetic boundaries where no crosses are possible. In this minireview, we highlight recent advances, propose a set of standards to use genomic sequences to uncover species boundaries, point out potential pitfalls, and present possible future research directions.
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Vieira A, Silva DN, Várzea V, Paulo OS, Batista D. Genome-Wide Signatures of Selection in Colletotrichum kahawae Reveal Candidate Genes Potentially Involved in Pathogenicity and Aggressiveness. Front Microbiol 2019; 10:1374. [PMID: 31275287 PMCID: PMC6593080 DOI: 10.3389/fmicb.2019.01374] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 06/03/2019] [Indexed: 12/26/2022] Open
Abstract
Plants and their pathogens are engaged in continuous evolutionary battles, with pathogens evolving to circumvent plant defense mechanisms and plants responding through enhanced protection to prevent or mitigate damage induced by pathogen attack. Managed ecosystems are composed of genetically identical populations of crop plants with few changes from year to year. These environments are highly conducive to the emergence and dissemination of pathogens and they exert selective pressure for both qualitative virulence factors responsible for fungal pathogenicity, and quantitative traits linked to pathogen fitness, such as aggressiveness. In this study, we used a comparative genome-wide approach to investigate the genomic basis underlying the pathogenicity and aggressiveness of the fungal coffee pathogen Colletotrichum kahawae infecting green coffee berries. The pathogenicity was investigated by comparing genomic variation between C. kahawae and its non-pathogenic sibling species, while the aggressiveness was studied by a genome-wide association approach with groups of isolates with different phenotypic profiles. High genetic differentiation was observed between C. kahawae and the most closely related species with 5,560 diagnostic SNPs identified, in which a significant enrichment of non-synonymous mutations was detected. Functional annotation of these non-synonymous mutations revealed a significant enrichment mainly in two gene ontology categories, “oxidation–reduction process” and “integral component of membrane.” Finally, the annotation of several genes potentially under-selection revealed that C. kahawae’s pathogenicity may be a complex biological process, in which important biological functions, such as, detoxification and transport, regulation of host and pathogen gene expression, and signaling are involved. On the other hand, the genome-wide association analyses for aggressiveness were able to identify 10 SNPs and 15 SNPs of small effect in single and multi-association analysis, respectively, from which 7 were common, giving in total 18 SNPs potentially associated. The annotation of these genomic regions allowed the identification of four candidate genes encoding F-box domain-containing, nitrosoguanidine resistance, Fungal specific transcription factor domain-containing and C6 transcription factor that could be associated with aggressiveness. This study shed light, for the first time, on the genetic mechanisms of C. kahawae host specialization.
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Affiliation(s)
- Ana Vieira
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal.,Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.,Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Diogo Nuno Silva
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal.,Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.,Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Vitor Várzea
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal.,Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Octávio Salgueiro Paulo
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Dora Batista
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal.,Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.,Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
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