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Zong X, Lou Y, Xia M, Zhao K, Chen J, Huang J, Yang S, Wang L. Recombination and repeat-induced point mutation landscapes reveal trade-offs between the sexual and asexual cycles of Magnaporthe oryzae. J Genet Genomics 2024; 51:723-734. [PMID: 38490361 DOI: 10.1016/j.jgg.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 03/17/2024]
Abstract
The fungal disease caused by Magnaporthe oryzae is one of the most devastating diseases that endanger many crops worldwide. Evidence shows that sexual reproduction can be advantageous for fungal diseases as hybridization facilitates host-jumping. However, the pervasive clonal lineages of M. oryzae observed in natural fields contradict this expectation. A better understanding of the roles of recombination and the fungi-specific repeat-induced point mutation (RIP) in shaping its evolutionary trajectory is essential to bridge this knowledge gap. Here we systematically investigate the RIP and recombination landscapes in M. oryzae using a whole genome sequencing data from 252 population samples and 92 cross progenies. Our data reveal that the RIP can robustly capture the population history of M. oryzae, and we provide accurate estimations of the recombination and RIP rates across different M. oryzae clades. Significantly, our results highlight a parent-of-origin bias in both recombination and RIP rates, tightly associating with their sexual potential and variations of effector proteins. This bias suggests a critical trade-off between generating novel allelic combinations in the sexual cycle to facilitate host-jumping and stimulating transposon-associated diversification of effectors in the asexual cycle to facilitate host coevolution. These findings provide unique insights into understanding the evolution of blast fungus.
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Affiliation(s)
- Xifang Zong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Yaxin Lou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Mengshuang Xia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Kunyang Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Jingxuan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China
| | - Ju Huang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, Jiangsu 210000, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu 210000, China.
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu 210000, China.
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Kita K, Uchida M, Arie T, Teraoka T, Kaku H, Kanda Y, Mori M, Arazoe T, Kamakura T. The MAT1 locus is required for microconidia-mediated sexual fertility in the rice blast fungus. FEMS Microbiol Lett 2024; 371:fnae004. [PMID: 38305094 DOI: 10.1093/femsle/fnae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/22/2023] [Accepted: 01/31/2024] [Indexed: 02/03/2024] Open
Abstract
Rice blast fungus (Pyricularia oryzae) is a heterothallic ascomycete that causes the most destructive disease in cultivated rice worldwide. This fungus reproduces sexually and asexually, and its mating type is determined by the MAT1 locus, MAT1-1 or MAT1-2. Interestingly, most rice-infecting field isolates show a loss of female fertility, but the MAT1 locus is highly conserved in female-sterile isolates. In this study, we performed a functional analysis of MAT1 using the CRISPR/Cas9 system in female- and male-fertile isolates and female-sterile (male-fertile) isolates. Consistent with a previous report, MAT1 was essential for sexual reproduction but not for asexual reproduction. Meanwhile, deletion mutants of MAT1-1-1, MAT1-1-2, and MAT1-1-3 exhibited phenotypes different from those of other previously described isolates, suggesting that the function of MAT1-1 genes and/or their target genes in sexual reproduction differs among strains or isolates. The MAT1 genes, excluding MAT1-2-6, retained their functions even in female-sterile isolates, and deletion mutants lead to loss or reduction of male fertility. Although MAT1 deletion did not affect microconidia (spermatia) production, microconidia derived from the mutants could not induce perithecia formation. These results indicated that MAT1 is required for microconidia-mediated male fertility in addition to female fertility in P. oryzae .
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Affiliation(s)
- Kohtetsu Kita
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 2788510, Japan
| | - Momotaka Uchida
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 2788510, Japan
| | - Tsutomu Arie
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwai-cho, Fuchu, Tokyo 1830054, Japan
| | - Tohru Teraoka
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwai-cho, Fuchu, Tokyo 1830054, Japan
| | - Hisatoshi Kaku
- JICA Tsukuba Center, Japan International Coorporation Agency, 3-6 Koyadai, Tsukuba, Ibaraki 3050074, Japan
- Division of Plant Molecular Regulation Research, Institute of Agrobiological Sciences, NARO (NIAS), 2-1-2 Kan-nondai, Tsukuba, Ibaraki 3058602, Japan
| | - Yasukazu Kanda
- Division of Plant Molecular Regulation Research, Institute of Agrobiological Sciences, NARO (NIAS), 2-1-2 Kan-nondai, Tsukuba, Ibaraki 3058602, Japan
| | - Masaki Mori
- Division of Plant Molecular Regulation Research, Institute of Agrobiological Sciences, NARO (NIAS), 2-1-2 Kan-nondai, Tsukuba, Ibaraki 3058602, Japan
| | - Takayuki Arazoe
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 2788510, Japan
| | - Takashi Kamakura
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 2788510, Japan
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Uchida M, Konishi T, Fujigasaki A, Kita K, Arie T, Teraoka T, Kanda Y, Mori M, Arazoe T, Kamakura T. Dysfunctional Pro1 leads to female sterility in rice blast fungi. iScience 2023; 26:107020. [PMID: 37416480 PMCID: PMC10320130 DOI: 10.1016/j.isci.2023.107020] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/20/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Although sexual reproduction is widespread in eukaryotes, some fungal species can only reproduce asexually. In the rice blast fungus Pyricularia (Magnaporthe) oryzae, several isolates from the region of origin retain mating ability, but most isolates are female sterile. Therefore, female fertility may have been lost during its spread from the origin. Here, we show that functional mutations of Pro1, a global transcriptional regulator of mating-related genes in filamentous fungi, is one cause of loss of female fertility in this fungus. We identified the mutation of Pro1 by backcrossing analysis between female-fertile and female-sterile isolates. The dysfunctional Pro1 did not affect the infection processes but conidial release was increased. Furthermore, various mutations in Pro1 were detected in geographically distant P. oryzae, including pandemic isolates of wheat blast fungus. These results provide the first evidence that loss of female fertility may be advantageous to the life cycle of some plant pathogenic fungi.
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Affiliation(s)
- Momotaka Uchida
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Takahiro Konishi
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Ayaka Fujigasaki
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kohtetsu Kita
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Tsutomu Arie
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-0054, Japan
| | - Tohru Teraoka
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology (TUAT), 3-5-8 Saiwai-cho, Fuchu, Tokyo 183-0054, Japan
| | - Yasukazu Kanda
- Division of Plant Molecular Regulation Research, Institute of Agrobiological Sciences, NARO (NIAS), 2-1-2 Kan-nondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Masaki Mori
- Division of Plant Molecular Regulation Research, Institute of Agrobiological Sciences, NARO (NIAS), 2-1-2 Kan-nondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Takayuki Arazoe
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Takashi Kamakura
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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Thi Le L, Adreit H, Thi Ha L, Milazzo J, Lebrun M, Tharreau D, Hoi Pham X, Thanh Nguyen H, Fournier E, Thi Hoang G. Population structure of Pyricularia oryzae on rice in Vietnam reveals diversified populations with four pandemic and two endemic clusters. Fungal Genet Biol 2023; 166:103794. [PMID: 37003467 DOI: 10.1016/j.fgb.2023.103794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/25/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
We characterized the genetic structure of 609 strains of Pyricularia oryzae, the fungal pathogen causing rice blast disease, in three main regions in Vietnam using microsatellites (SSR) markers. From the 447 distinct multilocus genotypes identified, six genetic clusters were defined, all of them showing elevated genetic and genotypic diversities. Four of these clusters were related to rice-attacking lineages already described at the worldwide scale, whereas the two remaining clusters were endemic to Vietnam. Strains were unevenly distributed into the six clusters depending on their groups of rice variety (indica / japonica) or type of varieties (traditional / modern) of origin, but none of the clusters was specifically related to these two factors. The highest diversity of blast population was found in Northern mountainous area, and the lowest in Red River Delta in both term of genetic diversity and gene diversity. Hierarchical AMOVAs confirmed that all three factors considered (rice variety group, type of variety origin and geography) significantly contributed to the population structure of P. oryzae in Vietnam, with highest contribution from rice variety group. Mating types were unevenly distributed among clusters. Combined with results of female fertility and linkage disequilibirum, we hypothesized that clonal reproduction probably occurred in all clusters, but that sexual reproduction likely took place at least in some restricted areas in the Northern mountainous area for strains belonging to the cluster related to the previously described recombinant lineage (worldwide lineage 1). Our study pictures the genetic diversity, population structure and reproductive mode of the blast fungus in central and north Vietnam, and shows that the observed population structure is explained by several factors, the most important one being the variability of rice variety. All these new information might help for elaborating appropriate strategies to controlling the blast disease.
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Affiliation(s)
- Lieu Thi Le
- Agricultural Genetics Institute, VAAS, National Key Laboratory for Plant Cell Biotechnology, LMI RICE-2, Hanoi, Vietnam; University of Science and Technology of Hanoi, Hanoi, Vietnam
| | - Henri Adreit
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France; CIRAD, UMR PHIM, 34090 Montpellier, France
| | - Loan Thi Ha
- Agricultural Genetics Institute, VAAS, National Key Laboratory for Plant Cell Biotechnology, LMI RICE-2, Hanoi, Vietnam
| | - Joelle Milazzo
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France; CIRAD, UMR PHIM, 34090 Montpellier, France
| | - Michel Lebrun
- University of Science and Technology of Hanoi, Hanoi, Vietnam
| | - Didier Tharreau
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France; CIRAD, UMR PHIM, 34090 Montpellier, France
| | - Xuan Hoi Pham
- Agricultural Genetics Institute, VAAS, National Key Laboratory for Plant Cell Biotechnology, LMI RICE-2, Hanoi, Vietnam
| | - Hai Thanh Nguyen
- Vietnam National University of Agriculture, Faculty of Biotechnology, Faculty of Agronomy, Hanoi, Vietnam
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France.
| | - Giang Thi Hoang
- Agricultural Genetics Institute, VAAS, National Key Laboratory for Plant Cell Biotechnology, LMI RICE-2, Hanoi, Vietnam; Vietnam National University of Agriculture, Faculty of Biotechnology, Faculty of Agronomy, Hanoi, Vietnam.
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Lassagne A, Brun S, Malagnac F, Adreit H, Milazzo J, Fournier E, Tharreau D. Male fertility in Pyricularia oryzae: Microconidia are spermatia. Environ Microbiol 2022; 24:6365-6375. [PMID: 36165613 PMCID: PMC10092719 DOI: 10.1111/1462-2920.16226] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/25/2022] [Indexed: 01/12/2023]
Abstract
Sexual reproduction in Ascomycetes is well described in several model organisms such as Neurospora crassa or Podospora anserina. Deciphering the biological process of sexual reproduction (from the recognition between compatible partners to the formation of zygote) can be a major advantage to better control sexually reproducing pathogenic fungi. In Pyricularia oryzae, the fungal pathogen causing blast diseases on several Poaceae species, the biology of sexual reproduction remains poorly documented. Besides the well-documented production of asexual macroconidia, the production of microconidia was seldom reported in P. oryzae, and their role as male gamete (i.e., spermatia) and in male fertility has never been explored. Here, we characterised the morphological features of microconidia and demonstrated that they are bona fide spermatia. Contrary to macroconidia, microconidia are not able to germinate and seem to be the only male gametes in P. oryzae. We show that fruiting body (perithecium) formation requires microconidia to get in contact with mycelium of strains of opposite mating type, to presumably fertilise the female gametes.
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Affiliation(s)
- Alexandre Lassagne
- Plant Health Institute of Montpellier (PHIM), CIRAD, Montpellier, France.,Plant Health Institute of Montpellier (PHIM), University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Sylvain Brun
- Institut Jacques Monod, Université Paris Cité, CNRS, Paris, France
| | - Fabienne Malagnac
- Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, CEA, CNRS, Gif-sur-Yvette, France
| | - Henri Adreit
- Plant Health Institute of Montpellier (PHIM), CIRAD, Montpellier, France
| | - Joëlle Milazzo
- Plant Health Institute of Montpellier (PHIM), CIRAD, Montpellier, France
| | - Elisabeth Fournier
- Plant Health Institute of Montpellier (PHIM), University of Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Didier Tharreau
- Plant Health Institute of Montpellier (PHIM), CIRAD, Montpellier, France
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Orellana-Torrejon C, Vidal T, Gazeau G, Boixel AL, Gélisse S, Lageyre J, Saint-Jean S, Suffert F. Multiple scenarios for sexual crosses in the fungal pathogen Zymoseptoria tritici on wheat residues: Potential consequences for virulence gene transmission. Fungal Genet Biol 2022; 163:103744. [PMID: 36209959 DOI: 10.1016/j.fgb.2022.103744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/31/2022] [Accepted: 09/30/2022] [Indexed: 01/06/2023]
Abstract
Little is known about the impact of host immunity on sexual reproduction in fungal pathogens. In particular, it is unclear whether crossing requires both sexual partners to infect living plant tissues. We addressed this issue in a three-year experiment investigating different scenarios of Zymoseptoria tritici crosses according to the virulence ('vir') or avirulence ('avr') of the parents against a qualitative resistance gene. Co-inoculations ('vir × vir', 'avr × vir', 'avr × avr') and single inoculations were performed on a wheat cultivar carrying the Stb16q resistance gene (Cellule) and a susceptible cultivar (Apache), in the greenhouse. We assessed the intensity of asexual reproduction by scoring disease severity, and the intensity of sexual reproduction by counting the ascospores discharged from wheat residues. As expected, disease severity was more intense on Cellule for 'vir × vir' co-inoculations than for 'avr × vir' co-inoculations, with no disease for 'avr × avr'. However, all types of co-inoculation yielded sexual offspring, whether or not the parental strains caused plant symptoms. Parenthood was confirmed by genotyping (SSR markers), and the occurrence of crosses between (co-)inoculated and exogenous strains (other strains from the experiment, or from far away) was determined. We showed that symptomatic asexual infection was not required for a strain to participate in sexual reproduction, and deduced from this result that avirulent strains could be maintained asymptomatically "on" or "in" leaf tissues of plants carrying the corresponding resistant gene for long enough to reproduce sexually. In two of the three years, the intensity of sexual reproduction did not differ between the three types of co-inoculation in Cellule, suggesting that crosses involving avirulent strains are not anecdotal. We discuss the possible mechanisms explaining the maintenance of avirulence in Z. tritici populations and the potential impact of particular resistance deployments such as cultivar mixtures for limiting resistance breakdown.
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Affiliation(s)
- Carolina Orellana-Torrejon
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France; Université Paris-Saclay, INRAE, AgroParisTech, UMR ECOSYS, 91120 Palaiseau, France
| | - Tiphaine Vidal
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Gwilherm Gazeau
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Anne-Lise Boixel
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Sandrine Gélisse
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France
| | - Jérôme Lageyre
- Université Paris-Saclay, INRAE, AgroParisTech, UMR ECOSYS, 91120 Palaiseau, France
| | - Sébastien Saint-Jean
- Université Paris-Saclay, INRAE, AgroParisTech, UMR ECOSYS, 91120 Palaiseau, France
| | - Frédéric Suffert
- Université Paris-Saclay, INRAE, UR BIOGER, 91120 Palaiseau, France.
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Hossain MM. Wheat blast: A review from a genetic and genomic perspective. Front Microbiol 2022; 13:983243. [PMID: 36160203 PMCID: PMC9493272 DOI: 10.3389/fmicb.2022.983243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/12/2022] [Indexed: 12/11/2022] Open
Abstract
The newly emerged wheat blast fungus Magnaporthe oryzae Triticum (MoT) is a severe threat to global wheat production. The fungus is a distinct, exceptionally diverse lineage of the M. oryzae, causing rice blast disease. Genome-based approaches employing MoT-specific markers are used to detect MoT field isolates. Sequencing the whole genome indicates the presence of core chromosome and mini-chromosome sequences that harbor effector genes and undergo divergent evolutionary routes. Significant genetic and pathotype diversity within the fungus population gives ample potential for evolutionary change. Identifying and refining genetic markers allows for tracking genomic regions with stable blast resistance. Introgression of quantitative and R gene resistance into popular cultivars is crucial to controlling disease in areas where the pathogen population is diverse and well established. Novel approaches such as CRISPR/Cas-9 genome editing could generate resistant varieties in wheat within a short time. This chapter provides an extensive summary of the genetic and genomic aspects of the wheat blast fungus MoT and offers an essential resource for wheat blast research in the affected areas.
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Thierry M, Charriat F, Milazzo J, Adreit H, Ravel S, Cros-Arteil S, borron S, Sella V, Kroj T, Ioos R, Fournier E, Tharreau D, Gladieux P. Maintenance of divergent lineages of the Rice Blast Fungus Pyricularia oryzae through niche separation, loss of sex and post-mating genetic incompatibilities. PLoS Pathog 2022; 18:e1010687. [PMID: 35877779 PMCID: PMC9352207 DOI: 10.1371/journal.ppat.1010687] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 08/04/2022] [Accepted: 06/17/2022] [Indexed: 11/18/2022] Open
Abstract
Many species of fungal plant pathogens coexist as multiple lineages on the same host, but the factors underlying the origin and maintenance of population structure remain largely unknown. The rice blast fungus Pyricularia oryzae is a widespread model plant pathogen displaying population subdivision. However, most studies of natural variation in P. oryzae have been limited in genomic or geographic resolution, and host adaptation is the only factor that has been investigated extensively as a contributor to population subdivision. In an effort to complement previous studies, we analyzed genetic and phenotypic diversity in isolates of the rice blast fungus covering a broad geographical range. Using single-nucleotide polymorphism genotyping data for 886 isolates sampled from 152 sites in 51 countries, we showed that population subdivision of P. oryzae in one recombining and three clonal lineages with broad distributions persisted with deeper sampling. We also extended previous findings by showing further population subdivision of the recombining lineage into one international and three Asian clusters, and by providing evidence that the three clonal lineages of P. oryzae were found in areas with different prevailing environmental conditions, indicating niche separation. Pathogenicity tests and bioinformatic analyses using an extended set of isolates and rice varieties indicated that partial specialization to rice subgroups contributed to niche separation between lineages, and differences in repertoires of putative virulence effectors were consistent with differences in host range. Experimental crosses revealed that female sterility and early post-mating genetic incompatibilities acted as strong additional barriers to gene flow between clonal lineages. Our results demonstrate that the spread of a fungal pathogen across heterogeneous habitats and divergent populations of a crop species can lead to niche separation and reproductive isolation between distinct, widely distributed, lineages.
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Affiliation(s)
- Maud Thierry
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Florian Charriat
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Joëlle Milazzo
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Henri Adreit
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Sébastien Ravel
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
| | - Sandrine Cros-Arteil
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Sonia borron
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Violaine Sella
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Renaud Ioos
- ANSES Plant Health Laboratory, Mycology Unit, Malzéville, France
| | - Elisabeth Fournier
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
| | - Didier Tharreau
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- CIRAD, UMR PHIM, Montpellier, France
- * E-mail: (DT); (PG)
| | - Pierre Gladieux
- PHIM Plant Health Institute, Univ Montpellier, INRAE, CIRAD, Institut Agro, IRD, Montpellier, France
- * E-mail: (DT); (PG)
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Li F, Liu X, Zhu J, Li J, Gao K, Zhao C. The Role of Genetic Factors in the Differential Invasion Success of Two Spartina Species in China. FRONTIERS IN PLANT SCIENCE 2022; 13:909429. [PMID: 35712568 PMCID: PMC9196123 DOI: 10.3389/fpls.2022.909429] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
Biological invasions have become one of the greatest threats to global biodiversity and ecosystem conservation. Most previous studies have revealed how successful invasive species adapt to new environments and climate change through phenotypic and genetic evolution. Some researchers suggested that understanding unsuccessful or less successful biological invasions might be important for understanding the relationships between invasion adaptability and climate factors. We compared the sexual reproduction ability, genetic diversity, and gene × environment interaction in two intentionally introduced alien species in China (Spartina anglica and Spartina alterniflora) based on restriction site-associated DNA (RAD) sequencing. After more than 50 years, the distribution of S. alterniflora has rapidly expanded, while S. anglica has experienced extreme dieback. A total of 212,939 single nucleotide polymorphisms (SNPs) for the two Spartina species were used for analysis. The multilocus genotype (MLG) analysis revealed that clonal reproduction was the prevalent mode of reproduction in both species, indicating that a change in the mode of reproduction was not the key factor enabling successful invasion by Spartina. All genetic diversity indicators (He, Ho, π) in S. alterniflora populations were at least two times higher than those in S. anglica populations, respectively (p < 0.001). Furthermore, the population genetic structure and stronger patterns of climate-associated loci provided support for rapid adaptive evolution in the populations of S. alterniflora in China. Altogether, our results highlight the importance of genetic diversity and local adaptation, which were driven by multiple source populations, in increasing the invasiveness of S. alterniflora.
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Chittaragi A, Pramesh D, Naik GR, Naik MK, Yadav MK, Ngangkham U, Siddepalli ME, Nayak A, Prasannakumar MK, Eranna C. Multilocus sequence analysis and identification of mating-type idiomorphs distribution in Magnaporthe oryzae population of Karnataka state of India. J Appl Microbiol 2022; 132:4413-4429. [PMID: 35332630 DOI: 10.1111/jam.15546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 02/17/2022] [Accepted: 03/22/2022] [Indexed: 11/27/2022]
Abstract
AIMS To investigate the genetic diversity, population structure, and mating-type distribution among the eco-distinct isolates of Magnaporthe oryzae from Karnataka, India. METHODS AND RESULTS A set of 38 isolates of M. oryzae associated with leaf blast disease of rice were collected from different rice ecosystems of Karnataka, India, and analyzed for their diversity at actin, β-tubulin, calmodulin, translation elongation factor 1-α (TEF-1-α), and internal transcribed spacer (ITS) genes/region. The isolates were grouped into two clusters based on the multilocus sequence diversity, the majority being in cluster-IA (n=37), and only one isolate formed cluster-IB. Population structure was analyzed using 123 SNP data to understand the genetic relationship. Based on K=2 and ancestry threshold of >70%, blast strains were classified into two subgroups (SG1 and SG2) whereas, based on K=4 and ancestry threshold of >70%, blast strains were classified into four subgroups (SG1, SG2, SG3, and SG4). We have identified 13 haplotype groups where haplotype-group-2 was predominant (n=20) in the population. The Tajima's and Fu's Fs neutrality tests exhibited many rare alleles. Further, the mating-type analysis was also performed using MAT1 gene-specific primers to find the potentiality of sexual reproduction in different ecosystems. The majority of the isolates (54.5%) had MAT1-2 idiomorph, whereas 45.5 per cent of the isolates possessed MAT1-1 idiomorph. CONCLUSIONS The present study found the genetically homogenous population of M. oryzae by multilocus sequence analysis. Both mating types, MAT1-1 and MAT1-2, were found within the M. oryzae population of Karnataka. SIGNIFICANCE AND IMPACT OF STUDY The study on the population structure and sexual mating behavior of M. oryzae is important in developing region-specific blast-resistant rice cultivars. This is the first report of MAT1 idiomorphs distribution in the M. oryzae population in any Southern state of India.
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Affiliation(s)
- Amoghavarsha Chittaragi
- Department of Plant Pathology, University of Agricultural and Horticultural Sciences, Shivamogga, Karnataka, India.,Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Karnataka, India
| | - Devanna Pramesh
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Karnataka, India
| | - Ganesha R Naik
- Department of Plant Pathology, University of Agricultural and Horticultural Sciences, Shivamogga, Karnataka, India
| | - Manjunath K Naik
- Department of Plant Pathology, University of Agricultural and Horticultural Sciences, Shivamogga, Karnataka, India
| | - Manoj K Yadav
- ICAR-National Rice Research Institute, Cuttack, India
| | - Umakanta Ngangkham
- ICAR-Research Complex for North-Eastern Hill Region, Manipur Centre, Imphal, Manipur, India
| | - Manjunatha E Siddepalli
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Karnataka, India
| | - Anusha Nayak
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Karnataka, India
| | - M K Prasannakumar
- Department of Plant Pathology, University of Agricultural Sciences, Bengaluru, India
| | - Chidanandappa Eranna
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Karnataka, India
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11
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Hu ZJ, Huang YY, Lin XY, Feng H, Zhou SX, Xie Y, Liu XX, Liu C, Zhao RM, Zhao WS, Feng CH, Pu M, Ji YP, Hu XH, Li GB, Zhao JH, Zhao ZX, Wang H, Zhang JW, Fan J, Li Y, Peng YL, He M, Li DQ, Huang F, Peng YL, Wang WM. Loss and Natural Variations of Blast Fungal Avirulence Genes Breakdown Rice Resistance Genes in the Sichuan Basin of China. FRONTIERS IN PLANT SCIENCE 2022; 13:788876. [PMID: 35498644 PMCID: PMC9040519 DOI: 10.3389/fpls.2022.788876] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 03/10/2022] [Indexed: 05/11/2023]
Abstract
Magnaporthe oryzae is the causative agent of rice blast, a devastating disease in rice worldwide. Based on the gene-for-gene paradigm, resistance (R) proteins can recognize their cognate avirulence (AVR) effectors to activate effector-triggered immunity. AVR genes have been demonstrated to evolve rapidly, leading to breakdown of the cognate resistance genes. Therefore, understanding the variation of AVR genes is essential to the deployment of resistant cultivars harboring the cognate R genes. In this study, we analyzed the nucleotide sequence polymorphisms of eight known AVR genes, namely, AVR-Pita1, AVR-Pii, AVR-Pia, AVR-Pik, AVR-Pizt, AVR-Pi9, AVR-Pib, and AVR-Pi54 in a total of 383 isolates from 13 prefectures in the Sichuan Basin. We detected the presence of AVR-Pik, AVR-Pi54, AVR-Pizt, AVR-Pi9, and AVR-Pib in the isolates of all the prefectures, but not AVR-Pita1, AVR-Pii, and AVR-Pia in at least seven prefectures, indicating loss of the three AVRs. We also detected insertions of Pot3, Mg-SINE, and indels in AVR-Pib, solo-LTR of Inago2 in AVR-Pizt, and gene duplications in AVR-Pik. Consistently, the isolates that did not harboring AVR-Pia were virulent to IRBLa-A, the monogenic line containing Pia, and the isolates with variants of AVR-Pib and AVR-Pizt were virulent to IRBLb-B and IRBLzt-t, the monogenic lines harboring Pib and Piz-t, respectively, indicating breakdown of resistance by the loss and variations of the avirulence genes. Therefore, the use of blast resistance genes should be alarmed by the loss and nature variations of avirulence genes in the blast fungal population in the Sichuan Basin.
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Affiliation(s)
- Zi-Jin Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yan-Yan Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Yan-Yan Huang
| | - Xiao-Yu Lin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Hui Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Shi-Xin Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Ying Xie
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Xin-Xian Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Chen Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Ru-Meng Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Wen-Sheng Zhao
- State Key Laboratory of Agrobiotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Chuan-Hong Feng
- Plant Protection Station, Department of Agriculture Sichuan Province, Chengdu, China
| | - Mei Pu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yun-Peng Ji
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Xiao-Hong Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Guo-Bang Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Jing-Hao Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Zhi-Xue Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - He Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Ji-Wei Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Jing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yan Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yun-Liang Peng
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Min He
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - De-Qiang Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Fu Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - You-Liang Peng
- State Key Laboratory of Agrobiotechnology and Ministry of Agriculture Key Laboratory of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Wen-Ming Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Wen-Ming Wang
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12
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MAT Loci Play Crucial Roles in Sexual Development but Are Dispensable for Asexual Reproduction and Pathogenicity in Rice Blast Fungus Magnaporthe oryzae. J Fungi (Basel) 2021; 7:jof7100858. [PMID: 34682279 PMCID: PMC8539793 DOI: 10.3390/jof7100858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/07/2021] [Accepted: 10/10/2021] [Indexed: 11/30/2022] Open
Abstract
Magnaporthe oryzae, a fungal pathogen that causes rice blast, which is the most destructive disease of rice worldwide, has the potential to perform both asexual and sexual reproduction. MAT loci, consisting of MAT genes, were deemed to determine the mating types of M. oryzae strains. However, investigation was rarely performed on the development and molecular mechanisms of the sexual reproduction of the fungus. In the present work, we analyzed the roles of two MAT loci and five individual MAT genes in the sex determination, sexual development and pathogenicity of M. oryzae. Both of the MAT1-1 and MAT1-2 loci are required for sex determination and the development of sexual structures. MAT1-1-1, MAT1-1-3 and MAT1-2-1 genes are crucial for the formation of perithecium. MAT1-1-2 impacts the generation of asci and ascospores, while MAT1-2-2 is dispensable for sexual development. A GFP fusion experiment indicated that the protein of MAT1-1-3 is distributed in the nucleus. However, all of the MAT loci or MAT genes are dispensable for vegetative growth, asexual reproduction, pathogenicity and pathogenicity-related developments of the fungus, suggesting that sexual reproduction is regulated relatively independently in the development of the fungus. The data and methods of this work may be helpful to further understand the life cycle and the variation of the fungus.
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13
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Sheoran N, Ganesan P, Mughal NM, Yadav IS, Kumar A. Genome assisted molecular typing and pathotyping of rice blast pathogen, Magnaporthe oryzae, reveals a genetically homogenous population with high virulence diversity. Fungal Biol 2021; 125:733-747. [PMID: 34420700 DOI: 10.1016/j.funbio.2021.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 04/19/2021] [Accepted: 04/26/2021] [Indexed: 01/25/2023]
Abstract
Genome sequence-driven molecular typing tools have the potential to uncover the population biology and genetic diversity of rapidly evolving plant pathogens like Magnaporthe oryzae. Here, we report a new molecular typing technique -a digitally portable tool for population genetic analysis of M. oryzae to decipher the genetic diversity. Our genotyping tool exploiting allelic variations in housekeeping and virulence genes coupled with pathotyping revealed a prevalence of genetically homogenous populations within a single-field and plant niches such as leaf and panicle. The M. oryzae inciting leaf-blast and panicle-blast were confirmed to be genetically identical with no or minor nucleotide polymorphism in 17 genomic loci analyzed. Genetic loci such as Mlc1, Mpg1, Mps1, Slp1, Cal, Ef-Tu, Pfk, and Pgk were highly polymorphic as indicated by the haplotype-diversity, the number of polymorphic sites, and the number of mutations. The genetically homogenous single field population showed high virulence variability or diversity on monogenic rice differentials. The study indicated that the genetic similarity displayed by the isolates collected from a particular geographical location had no consequence on their virulence pattern on rice differentials carrying single/multiple resistance genes. The data on virulence diversity showed by the identical Sequence Types (STs) is indicative of no congruence between polymorphic virulence genes-based pathotyping and conserved housekeeping genes-based genotyping.
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Affiliation(s)
- Neelam Sheoran
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Prakash Ganesan
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
| | - Najeeb M Mughal
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, India.
| | - Inderjit Singh Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India.
| | - Aundy Kumar
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, India.
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14
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Odjo T, Diagne D, Adreit H, Milazzo J, Raveloson H, Andriantsimialona D, Kassankogno AI, Ravel S, Gumedzoé YMD, Ouedraogo I, Koita O, Silué D, Tharreau D. Structure of African Populations of Pyricularia oryzae from Rice. PHYTOPATHOLOGY 2021; 111:1428-1437. [PMID: 33386066 DOI: 10.1094/phyto-05-20-0186-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Rice blast, caused by the filamentous ascomycete Pyricularia oryzae, is one of the most devastating diseases of rice. Four genetic clusters were previously identified, and three have a large geographic distribution. Asia is the center of diversity and the origin of most migrations to other continents, and sexual reproduction persisted only in the South China-Laos-North Thailand region, which was identified as the putative center of origin of all P. oryzae populations on rice. Despite the importance of rice blast disease, little is known about the diversity and the population structure of the pathogen in Africa (including Madagascar). The present study was intended to describe the structure of African populations of P. oryzae and identify the relationship between African and worldwide genetic clusters. A set of 2,057 strains (937 African and 1,120 Madagascan strains) were genotyped with 12 simple sequence repeat markers to assess the diversity and the population structure of P. oryzae. Four genetic clusters were identified in Africa and Madagascar. All four clusters previously identified are present in Africa. Populations from West Africa, East Africa, and Madagascar are highly differentiated. The geographic structure is consistent with limited dispersion and with some migration events between neighboring countries. The two mating types are present in Africa with a dominance of Mat1.2, but no female-fertile strain was detected, supporting the absence of sexual reproduction on this continent. This study showed an unsuspected high level of genetic diversity of P. oryzae in Africa and suggested several independent introductions.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Théophile Odjo
- Faculté des Sciences Agronomiques de l'Université d'Abomey-Calavi, 01 BP526 Cotonou, Bénin
| | - Diariatou Diagne
- Laboratoire de Biologie Moléculaire Appliquée, Université des Sciences, des Techniques et des Technologies de Bamako, Faculté des Sciences et Techniques, BP E 3206 Bamako, Mali
| | - Henri Adreit
- UMR BGPI, CIRAD, TA A54/K, 34398 Montpellier, France. BGPI, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Joëlle Milazzo
- UMR BGPI, CIRAD, TA A54/K, 34398 Montpellier, France. BGPI, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Dodelys Andriantsimialona
- Centre Régional de Recherches Fofifa, 110 BP230 Antsirabe, Madagascar
- South Green Bioinformatics Platform, Bioversity, CIRAD, INRA, IRD, 34398 Montpellier, France
| | | | - Sébastien Ravel
- UMR BGPI, CIRAD, TA A54/K, 34398 Montpellier, France. BGPI, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Ibrahima Ouedraogo
- Institut de l'Environnement et Recherches Agricoles, BP 910 Bobo-Dioulasso, Burkina Faso
| | - Ousmane Koita
- Laboratoire de Biologie Moléculaire Appliquée, Université des Sciences, des Techniques et des Technologies de Bamako, Faculté des Sciences et Techniques, BP E 3206 Bamako, Mali
| | | | - Didier Tharreau
- UMR BGPI, CIRAD, TA A54/K, 34398 Montpellier, France. BGPI, Université de Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
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15
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D'Ávila LS, De Filippi MCC, Café-Filho AC. Sensitivity of Pyricularia oryzae Populations to Fungicides Over a 26-Year Time Frame in Brazil. PLANT DISEASE 2021; 105:1771-1780. [PMID: 33135989 DOI: 10.1094/pdis-08-20-1806-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The long-term dynamics of fungicide resistance of the rice blast fungus Pyricularia oryzae was monitored by examining the reaction of the fungal field isolates, collected over a period of 26 years, to the active ingredients of commercially relevant fungicides. The in vitro sensitivity of all isolates was measured against quinone outside inhibitors (QoI), melanin biosynthesis inhibitors, and sterol demethylation inhibitor (DMI) fungicides, namely azoxystrobin (as a QoI), tricyclazole (as a melanin biosynthesis inhibitor), tebuconazole (as a DMI), and trifloxystrobin + tebuconazole (QoI + DMI). Over the 26-year collection period, a gradual rise in the EC50 estimates for mycelial growth sensitivity was observed for all fungicides, but most strikingly for azoxystrobin. A rise in conidial germination and appressorium formation was also noted, most markedly for azoxystrobin. Consistently, the earlier isolates were much more sensitive to the active ingredients than the more contemporary isolates. The sequencing of the amplified cyt b fragment distinguished two haplotypes, H1 and H2. Haplotype H1 (six isolates) contained the G to C transversion at codon 143 (resulting in change G143A), linked to the resistant phenotype QoI-R. Haplotype H2 (40 isolates), gathered the isolates sensitive to QoI. This work documents the gradual rise in the frequency of fungicide-resistant isolates in P. oryzae rice populations on a long-term basis.
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Affiliation(s)
- Leilane S D'Ávila
- Graduate Program in Plant Pathology, Universidade de Brasília, 70910-900, Brasília, DF, Brazil
| | - Marta C Corsi De Filippi
- Graduate Program in Plant Pathology, Universidade de Brasília, 70910-900, Brasília, DF, Brazil
- Embrapa Rice and Beans, 75375-000, Santo Antônio de Goiás, GO, Brazil
| | - Adalberto C Café-Filho
- Graduate Program in Plant Pathology, Universidade de Brasília, 70910-900, Brasília, DF, Brazil
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16
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Ament-Velásquez SL, Tuovinen V, Bergström L, Spribille T, Vanderpool D, Nascimbene J, Yamamoto Y, Thor G, Johannesson H. The Plot Thickens: Haploid and Triploid-Like Thalli, Hybridization, and Biased Mating Type Ratios in Letharia. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:656386. [PMID: 37744149 PMCID: PMC10512270 DOI: 10.3389/ffunb.2021.656386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/24/2021] [Indexed: 09/26/2023]
Abstract
The study of the reproductive biology of lichen fungal symbionts has been traditionally challenging due to their complex lifestyles. Against the common belief of haploidy, a recent genomic study found a triploid-like signal in Letharia. Here, we infer the genome organization and reproduction in Letharia by analyzing genomic data from a pure culture and from thalli, and performing a PCR survey of the MAT locus in natural populations. We found that the read count variation in the four Letharia specimens, including the pure culture derived from a single sexual spore of L. lupina, is consistent with haploidy. By contrast, the L. lupina read counts from a thallus' metagenome are triploid-like. Characterization of the mating-type locus revealed a conserved heterothallic configuration across the genus, along with auxiliary genes that we identified. We found that the mating-type distributions are balanced in North America for L. vulpina and L. lupina, suggesting widespread sexual reproduction, but highly skewed in Europe for L. vulpina, consistent with predominant asexuality. Taken together, we propose that Letharia fungi are heterothallic and typically haploid, and provide evidence that triploid-like individuals are hybrids between L. lupina and an unknown Letharia lineage, reconciling classic systematic and genetic studies with recent genomic observations.
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Affiliation(s)
| | - Veera Tuovinen
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Linnea Bergström
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Toby Spribille
- Biological Sciences CW 405, University of Alberta, Edmonton, AB, Canada
| | - Dan Vanderpool
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Juri Nascimbene
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Yoshikazu Yamamoto
- Department of Bioproduction Science, Faculty of Bioresource Sciences, Akita Prefectural University, Akita, Japan
| | - Göran Thor
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hanna Johannesson
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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17
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Duan G, Bao J, Chen X, Xie J, Liu Y, Chen H, Zheng H, Tang W, Wang Z. Large-Scale Genome Scanning within Exonic Regions Revealed the Contributions of Selective Sweep Prone Genes to Host Divergence and Adaptation in Magnaporthe oryzae Species Complex. Microorganisms 2021; 9:562. [PMID: 33803140 PMCID: PMC8000120 DOI: 10.3390/microorganisms9030562] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 03/05/2021] [Accepted: 03/06/2021] [Indexed: 11/30/2022] Open
Abstract
Magnaporthe oryzae, one of the most notorious plant pathogens in the agronomic ecosystem, causes a destructive rice blast disease around the world. The blast fungus infects wide arrays of cultivated and non-cultivated plants within the Poaceae. Studies have shown that host speciation exerts selection pressure that drives the evolution and divergence of the M. oryzae population. Population genetic relationship deducted by genome-wide single nucleotide polymorphisms showed that M. oryzae differentiation is highly consistent with the host speciation process. In particular, the rice-infecting population of M. oryzae is distinct from populations from other hosts. However, how genome regions prone to host-mediated selection pressures associated with speciation in M. oryzae, especially at a large-scale population level, has not been extensively characterized. Here, we detected strong evidence of sweep selection throughout the genomes of rice and non-rice pathotypes of M. oryzae population using integrated haplotype score (iHS), cross population extended haplotype homozygosity (XPEHH), and cross population composite likelihood ratio (XPCLR) tests. Functional annotation analyses of the genes associated with host-mediated selection pressure showed that 14 pathogenicity-related genes are under positive selection pressure. Additionally, we showed that 17 candidate effector proteins are under positive and divergent selection among the blast fungus population through sweep selection analysis. Specifically, we find that a divergent selective gene, MGG_13871, is experiencing host-directed mutation in two amino acid residues in rice and non-rice infecting populations. These results provide a crucial insight into the impact of selective sweeping on the differentiation of M. oryzae populations and the dynamic influences of genomic regions in promoting host adaptation and speciation among M. oryzae species.
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Affiliation(s)
- Guohua Duan
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiandong Bao
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
| | - Xiaomin Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiahui Xie
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuchan Liu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
| | - Huiquan Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Huakun Zheng
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wei Tang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zonghua Wang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, The School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.D.); (J.B.); (X.C.); (J.X.); (Y.L.); (H.C.); (H.Z.)
- Fujian Universities Key Laboratory for Plant-Microbe Interaction, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
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18
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Ebbole DJ, Chen M, Zhong Z, Farmer N, Zheng W, Han Y, Lu G, Wang Z. Evolution and Regulation of a Large Effector Family of Pyricularia oryzae. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2021; 34:255-269. [PMID: 33211639 DOI: 10.1094/mpmi-07-20-0210-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Plant pathogen effectors play important roles in parasitism, including countering plant immunity. However, investigations of the emergence and diversification of fungal effectors across host-adapted populations has been limited. We previously identified a gene encoding a suppressor of plant cell death in Pyricularia oryzae (syn. Magnaporthe oryzae). Here, we report the gene is one of a 21-member gene family and we characterize sequence diversity in different populations. Within the rice pathogen population, nucleotide diversity is low, however; the majority of gene family members display presence-absence polymorphism or other null alleles. Gene family allelic diversity is greater between host-adapted populations and, thus, we named them host-adapted genes (HAGs). Multiple copies of HAGs were found in some genome assemblies and sequence divergence between the alleles in two cases suggested they were the result of repeat-induced point mutagenesis. Transfer of family members between populations and novel HAG haplotypes resulting from apparent recombination were observed. HAG family transcripts were induced in planta and a subset of HAGs are dependent on a key regulator of pathogenesis, PMK1. We also found differential intron splicing for some HAGs that would prevent ex planta protein expression. For some genes, spliced transcript was expressed in antiphase with an overlapping antisense transcript. Characterization of HAG expression patterns and allelic diversity reveal novel mechanisms for HAG regulation and mechanisms generating sequence diversity and novel allele combinations. This evidence of strong in planta-specific expression and selection operating on the HAG family is suggestive of a role in parasitism.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Daniel J Ebbole
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, 77843, U.S.A
| | - Meilian Chen
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, 77843, U.S.A
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Zhenhui Zhong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian 350002, China
| | - Nicholas Farmer
- Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, 77843, U.S.A
| | - Wenhui Zheng
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian 350002, China
| | - Yijuan Han
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian 350002, China
| | - Zonghua Wang
- Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fujian 350002, China
- Fujian Universities Key Laboratory of Plant-Microbe Interactions, College of Life Science, Fujian Agriculture and Forestry University, Fujian 350002, China
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19
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Abstract
Rice blast disease is both the most explosive and potentially damaging disease of the world's rice (Oryza sativa) crop and a model system for research on the molecular mechanisms that fungi use to cause plant disease. The blast fungus, Magnaporthe oryzae, is highly evolved to sense when it is on a leaf surface; to develop a pressurized cell, the appressorium, to punch through the leaf cuticle; and then to hijack living rice cells to assist it in causing disease. Host specificity, determining which plants particular fungal strains can infect, is also an important topic for research. The blast fungus is a moving target, quickly overcoming rice resistance genes we deploy to control it, and recently emerging to cause devastating disease on an entirely new cereal crop, wheat. M. oryzae is highly adaptable, with multiple examples of genetic instability at certain gene loci and in certain genomic regions. Understanding the biology of the fungus in the field, and its potential for genetic and genome variability, is key to keep it from adapting to life in the research laboratory and losing relevance to the significant impact it has on global food security.
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Affiliation(s)
- Barbara Valent
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
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20
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LeBlanc N, Cubeta MA, Crouch JA. Population Genomics Trace Clonal Diversification and Intercontinental Migration of an Emerging Fungal Pathogen of Boxwood. PHYTOPATHOLOGY 2021; 111:184-193. [PMID: 33048629 DOI: 10.1094/phyto-06-20-0219-fi] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Boxwood blight was first documented in Europe, prior to its recent colonization of North America, where it continues to have significant negative impacts on the ornamental industry. Due to near genetic uniformity in the two sister species of fungal plant pathogens that cause boxwood blight, understanding historical disease emergence and predicting future outbreaks is limited. The goal of this research was to apply population genomics to understand the role of pathogen diversification and migration in disease emergence. Specifically, we tested whether the primary pathogen species Calonectria pseudonaviculata has remained genetically isolated from its European-limited sister species C. henricotiae, while diversifying into clonal lineages that have migrated among continents. Whole-genome sequencing identified 1,608 single-nucleotide polymorphisms (SNPs) in 67 C. pseudonaviculata isolates from four continents and 1,017 SNPs in 13 C. henricotiae isolates from Europe. Interspecific genetic differentiation and an absence of shared polymorphisms indicated lack of gene flow between the sister species. Tests for intraspecific genetic structure in C. pseudonaviculata identified four genetic clusters, three of which corresponded to monophyletic phylogenetic clades. Comparison of evolutionary divergence scenarios among the four genetic clusters using approximate Bayesian computation indicated that the two C. pseudonaviculata genetic clusters currently found in the United States were derived from different sources, one from the first genetic cluster found in Europe and the second from an unidentified population. Evidence for multiple introductions of this pathogen into the United States and intercontinental migration indicates that future introductions are likely to occur and should be considered in plant disease quarantine regulation.
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Affiliation(s)
- Nicholas LeBlanc
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN
- Department of Entomology and Plant Pathology, North Carolina State University, Center for Integrated Fungal Research, Raleigh, NC
| | - Marc A Cubeta
- Department of Entomology and Plant Pathology, North Carolina State University, Center for Integrated Fungal Research, Raleigh, NC
| | - Jo Anne Crouch
- Mycology and Nematology Genetic Diversity and Biology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD
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21
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Microconidia: Understanding Its Role in the Fungus Magnaporthe oryzae Inciting Rice Blast Disease. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60585-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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St. Leger RJ, Wang JB. Metarhizium: jack of all trades, master of many. Open Biol 2020; 10:200307. [PMID: 33292103 PMCID: PMC7776561 DOI: 10.1098/rsob.200307] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023] Open
Abstract
The genus Metarhizium and Pochonia chlamydosporia comprise a monophyletic clade of highly abundant globally distributed fungi that can transition between long-term beneficial associations with plants to transitory pathogenic associations with frequently encountered protozoans, nematodes or insects. Some very common 'specialist generalist' species are adapted to particular soil and plant ecologies, but can overpower a wide spectrum of insects with numerous enzymes and toxins that result from extensive gene duplications made possible by loss of meiosis and associated genome defence mechanisms. These species use parasexuality instead of sex to combine beneficial mutations from separate clonal individuals into one genome (Vicar of Bray dynamics). More weakly endophytic species which kill a narrow range of insects retain sexuality to facilitate host-pathogen coevolution (Red Queen dynamics). Metarhizium species can fit into numerous environments because they are very flexible at the genetic, physiological and ecological levels, providing tractable models to address how new mechanisms for econutritional heterogeneity, host switching and virulence are acquired and relate to diverse sexual life histories and speciation. Many new molecules and functions have been discovered that underpin Metarhizium associations, and have furthered our understanding of the crucial ecology of these fungi in multiple habitats.
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23
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Castroagudín VL, Weiland JE, Baysal-Gurel F, Cubeta MA, Daughtrey ML, Gauthier NW, LaMondia J, Luster DG, Hand FP, Shishkoff N, Williams-Woodward J, Yang X, LeBlanc N, Crouch JA. One Clonal Lineage of Calonectria pseudonaviculata Is Primarily Responsible for the Boxwood Blight Epidemic in the United States. PHYTOPATHOLOGY 2020; 110:1845-1853. [PMID: 32584205 DOI: 10.1094/phyto-04-20-0130-r] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Boxwood blight caused by Calonectria pseudonaviculata and C. henricotiae is destroying cultivated and native boxwood worldwide, with profound negative economic impacts on the horticulture industry. First documented in the United States in 2011, the disease has now occurred in 30 states. Previous research showed that global C. pseudonaviculata populations prior to 2014 had a clonal structure, and only the MAT1-2 idiomorph was observed. In this study, we examined C. pseudonaviculata genetic diversity and population structure in the United States after 2014, following the expansion of the disease across the country over the past 5 years. Two hundred eighteen isolates from 21 states were genotyped by sequencing 11 simple sequence repeat (SSR) loci and by MAT1 idiomorph typing. All isolates presented C. pseudonaviculata-specific alleles, indicating that C. henricotiae is still absent in the U.S. states sampled. The presence of only the MAT1-2 idiomorph and gametic linkage disequilibrium suggests the prevalence of asexual reproduction. The contemporary C. pseudonaviculata population is characterized by a clonal structure and composed of 13 multilocus genotypes (SSR-MLGs) unevenly distributed across the United States. These SSR-MLGs grouped into two clonal lineages (CLs). The predominant lineage CL2 (93% of isolates) is the primary contributor to U.S. disease expansion. The contemporary U.S. C. pseudonaviculata population is not geographically subdivided and not genetically differentiated from the U.S. population prior to 2014, but is significantly differentiated from the main European population, which is largely composed of CL1. Our findings provide insights into the boxwood blight epidemic that are critical for disease management and breeding of resistant boxwood cultivars.
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Affiliation(s)
- Vanina L Castroagudín
- U.S. Department of Agriculture-Agricultural Research Service, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN 37830
| | - Jerry E Weiland
- U.S. Department of Agriculture-Agricultural Research Service, Horticultural Crops Research Laboratory, Corvallis, OR 97339
| | - Fulya Baysal-Gurel
- Department of Agricultural and Environmental Sciences, Otis L. Floyd Nursery Research Center, Tennessee State University, McMinnville, TN 37110
| | - Marc A Cubeta
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606
| | - Margery L Daughtrey
- School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853
| | | | - James LaMondia
- Connecticut Agricultural Experiment Station, Valley Laboratory, Windsor, CT 06095
| | - Douglas G Luster
- U.S. Department of Agriculture-Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Frederick, MD 21702
| | | | - Nina Shishkoff
- U.S. Department of Agriculture-Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Frederick, MD 21702
| | | | - Xiao Yang
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN 37830
- U.S. Department of Agriculture-Agricultural Research Service, Foreign Disease-Weed Science Research Unit, Frederick, MD 21702
| | - Nicholas LeBlanc
- U.S. Department of Agriculture-Agricultural Research Service, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705
- Oak Ridge Institute for Science and Education, ARS Research Participation Program, Oak Ridge, TN 37830
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27606
| | - Jo Anne Crouch
- U.S. Department of Agriculture-Agricultural Research Service, Mycology and Nematology Genetic Diversity and Biology Laboratory, Beltsville, MD 20705
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24
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Latorre SM, Reyes-Avila CS, Malmgren A, Win J, Kamoun S, Burbano HA. Differential loss of effector genes in three recently expanded pandemic clonal lineages of the rice blast fungus. BMC Biol 2020; 18:88. [PMID: 32677941 PMCID: PMC7364606 DOI: 10.1186/s12915-020-00818-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/22/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Understanding the mechanisms and timescales of plant pathogen outbreaks requires a detailed genome-scale analysis of their population history. The fungus Magnaporthe (Syn. Pyricularia) oryzae-the causal agent of blast disease of cereals- is among the most destructive plant pathogens to world agriculture and a major threat to the production of rice, wheat, and other cereals. Although M. oryzae is a multihost pathogen that infects more than 50 species of cereals and grasses, all rice-infecting isolates belong to a single genetically defined lineage. Here, we combined the two largest genomic datasets to reconstruct the genetic history of the rice-infecting lineage of M. oryzae based on 131 isolates from 21 countries. RESULTS The global population of the rice blast fungus consists mainly of three well-defined genetic groups and a diverse set of individuals. Multiple population genetic tests revealed that the rice-infecting lineage of the blast fungus probably originated from a recombining diverse group in Southeast Asia followed by three independent clonal expansions that took place over the last ~ 200 years. Patterns of allele sharing identified a subpopulation from the recombining diverse group that introgressed with one of the clonal lineages before its global expansion. Remarkably, the four genetic lineages of the rice blast fungus vary in the number and patterns of presence and absence of candidate effector genes. These genes encode secreted proteins that modulate plant defense and allow pathogen colonization. In particular, clonal lineages carry a reduced repertoire of effector genes compared with the diverse group, and specific combinations of presence and absence of effector genes define each of the pandemic clonal lineages. CONCLUSIONS Our analyses reconstruct the genetic history of the rice-infecting lineage of M. oryzae revealing three clonal lineages associated with rice blast pandemics. Each of these lineages displays a specific pattern of presence and absence of effector genes that may have shaped their adaptation to the rice host and their evolutionary history.
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Affiliation(s)
- Sergio M Latorre
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tuebingen, Germany
| | - C Sarai Reyes-Avila
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Angus Malmgren
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Joe Win
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, UK.
| | - Hernán A Burbano
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tuebingen, Germany.
- Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
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25
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Abstract
In diverse parasite taxa, from scale insects to root-knot nematodes, asexual lineages have exceptionally large host ranges, larger than those of their sexual relatives. Phylogenetic comparative studies of parasite taxa indicate that increases in host range and geographic range increase the probability of establishment of asexual lineages. At first pass, this convergence of traits appears counter-intuitive: intimate, antagonistic association with an enormous range of host taxa correlates with asexual reproduction, which should limit genetic variation within populations. Why would narrow host ranges favor sexual parasites and large host ranges favor asexual parasites? To take on this problem I link theory on ecological specialization to the two predominant hypotheses for the evolution of sex. I argue that both hypotheses predict a positive association between host range and the probability of invasion of asexual parasites, mediated either by variation in population size or in the strength of antagonistic coevolution. I also review hypotheses on colonization and the evolution of niche breadth in asexual lineages. I emphasize parasite taxa, with their diversity of reproductive modes and ecological strategies, as valuable assets in the hunt for solutions to the classic problems of the evolution of sex and geographic parthenogenesis.
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Affiliation(s)
- Amanda K Gibson
- Wissenschaftskolleg zu Berlin, Berlin, Germany.,Department of Biology, University of Virginia, Charlottesville, VA, USA
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26
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D'Ávila L, De Filippi M, Café‐Filho A. Both MAT1‐1 and MAT 1‐2 idiomorphs present in rice blast populations (
Magnaporthe oryzae
) collected in rice fields in northern Brazil. ACTA ACUST UNITED AC 2019. [DOI: 10.5197/j.2044-0588.2019.040.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- L.S. D'Ávila
- Graduate Programme in Plant PathologyUniversity of BrasíliaDF70910‐900Brazil
| | | | - A.C. Café‐Filho
- Graduate Programme in Plant PathologyUniversity of BrasíliaDF70910‐900Brazil
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27
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Laine AL, Barrès B, Numminen E, Siren JP. Variable opportunities for outcrossing result in hotspots of novel genetic variation in a pathogen metapopulation. eLife 2019; 8:47091. [PMID: 31210640 PMCID: PMC6667214 DOI: 10.7554/elife.47091] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 06/18/2019] [Indexed: 11/17/2022] Open
Abstract
Many pathogens possess the capacity for sex through outcrossing, despite being able to reproduce also asexually and/or via selfing. Given that sex is assumed to come at a cost, these mixed reproductive strategies typical of pathogens have remained puzzling. While the ecological and evolutionary benefits of outcrossing are theoretically well-supported, support for such benefits in pathogen populations are still scarce. Here, we analyze the epidemiology and genetic structure of natural populations of an obligate fungal pathogen, Podosphaera plantaginis. We find that the opportunities for outcrossing vary spatially. Populations supporting high levels of coinfection –a prerequisite of sex – result in hotspots of novel genetic diversity. Pathogen populations supporting coinfection also have a higher probability of surviving winter. Jointly our results show that outcrossing has direct epidemiological consequences as well as a major impact on pathogen population genetic diversity, thereby providing evidence of ecological and evolutionary benefits of outcrossing in pathogens. The existence of sex – broadly defined as the coming together of genes from different individuals – is one of the big evolutionary puzzles. Reproduction allows an organism to pass on its genes to future generations. However, while asexual and self-fertilizing individuals transmit all of their genes to their offspring, individuals that reproduce through sex transmit only half of their genome. This is considered the cost of sex. Many pathogens reproduce through sex, despite often also being able to reproduce asexually or by self-fertilization. Typically a pre-requisite of sex in pathogens is for at least two different strains to infect the same host. Aside from this limitation, little is known about when, where and why pathogens have sex. It has been tricky to study due to the microscopic size of pathogens and the difficulties of identifying different sexes. Moreover, sexual reproduction may be triggered by environmental cues that are difficult to mimic under controlled experimental conditions. Are there any benefits associated with pathogen sex? To find out, Laine et al. analyzed data collected over the course of four years from thousands of populations of a powdery mildew fungus that infected plants across the Åland islands. This revealed that the opportunities for pathogen sex vary in different locations. Areas where multiple strains of the fungus commonly infect the same plants result in hotspots of new genetic diversity. These mixed populations are also more likely to survive winter. This demonstrates the potential for pathogen sexual reproduction to provide an ecological benefit. Identifying areas and populations where pathogens have sex can help to identify when and where new strains are most likely to emerge. In the future, studies that use similar methods to Laine et al. could help to predict where infections and diseases are highly likely to arise.
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Affiliation(s)
- Anna-Liisa Laine
- Research Centre for Ecological Change, Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse, Switzerland
| | - Benoit Barrès
- Research Centre for Ecological Change, Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - Elina Numminen
- Research Centre for Ecological Change, Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland
| | - Jukka P Siren
- Research Centre for Ecological Change, Organismal and Evolutionary Biology, University of Helsinki, Helsinki, Finland.,Helsinki Institute for Information Technology, Department of Computer Science, Aalto University, Espoo, Finland
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28
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Olukayode T, Quime B, Shen YC, Yanoria MJ, Zhang S, Yang J, Zhu X, Shen WC, von Tiedemann A, Zhou B. Dynamic Insertion of Pot3 in AvrPib Prevailing in a Field Rice Blast Population in the Philippines Led to the High Virulence Frequency Against the Resistance Gene Pib in Rice. PHYTOPATHOLOGY 2019; 109:870-877. [PMID: 30501464 DOI: 10.1094/phyto-06-18-0198-r] [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] [Indexed: 05/25/2023]
Abstract
The Magnaporthe oryzae avirulence gene AvrPib is required for the resistance mediated by its cognate resistance gene Pib, which has been intensively used in indica rice breeding programs in many Asian countries. However, the sequence diversity of AvrPib among geographically distinct M. oryzae populations was recently shown to be increasing. Here, we selected a field population consisting of 248 rice blast isolates collected from a disease hotspot in Philippine for the analysis of AvrPib haplotypes and their pathogenicity against Pib. We found that all of the isolates were virulent to Pib and each of them contained an insertion of Pot3 transposon in AvrPib. Moreover, Pot3 insertion was detected in different genomic positions, resulting in three different AvrPib haplotypes, designated avrPib-H1 to H3. We further conducted a genome-wide Pot2 fingerprinting analysis by repetitive element palindromic polymerase chain reaction (PCR) and identified seven different lineages out of 47 representative isolates. The isolates belonging to the same lineage often had the same AvrPib haplotype. In contrast, the isolates having the same AvrPib haplotypes did not always belong to the same lineages. Both mating types MAT1-1 and MAT1-2 were identified in the population in Bohol and the latter appeared dominant. On the host side, we found that 32 of 52 released rice varieties in the Philippines contained Pib diagnosed by PCR gene-specific primers and DNA sequencing of gene amplicons, suggesting that it was widely incorporated in different rice varieties. Our study highlights the genetic dynamics of rice blast population at both the AvrPib locus and the genome-wide levels, providing insight into the mechanisms of the mutations in AvrPib leading to the breakdown of Pib-mediated resistance in rice.
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Affiliation(s)
- Toluwase Olukayode
- 1 Division of Plant Pathology and Crop Protection, Department of Crop Sciences, Faculty of Agricultural Sciences, Georg-August University, Grisebachstraße 6, D-37077 Göttingen, Germany
- 2 International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Berlaine Quime
- 2 International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Yin-Chi Shen
- 2 International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- 3 Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617 Taiwan
| | - Mary Jeannie Yanoria
- 2 International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Suobing Zhang
- 2 International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- 4 Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; and
| | - Jianyuan Yang
- 5 Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xiaoyuan Zhu
- 5 Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Wei-Chiang Shen
- 3 Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, 10617 Taiwan
| | - Andreas von Tiedemann
- 1 Division of Plant Pathology and Crop Protection, Department of Crop Sciences, Faculty of Agricultural Sciences, Georg-August University, Grisebachstraße 6, D-37077 Göttingen, Germany
| | - Bo Zhou
- 2 International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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29
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Ceresini PC, Castroagudín VL, Rodrigues FÁ, Rios JA, Aucique‐Pérez CE, Moreira SI, Croll D, Alves E, de Carvalho G, Maciel JLN, McDonald BA. Wheat blast: from its origins in South America to its emergence as a global threat. MOLECULAR PLANT PATHOLOGY 2019; 20:155-172. [PMID: 30187616 PMCID: PMC6637873 DOI: 10.1111/mpp.12747] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Wheat blast was first reported in Brazil in 1985. It spread rapidly across the wheat cropping areas of Brazil to become the most important biotic constraint on wheat production in the region. The alarming appearance of wheat blast in Bangladesh in 2016 greatly increased the urgency to understand this disease, including its causes and consequences. Here, we summarize the current state of knowledge of wheat blast and aim to identify the most important gaps in our understanding of the disease. We also propose a research agenda that aims to improve the management of wheat blast and limit its threat to global wheat production.
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Affiliation(s)
- Paulo Cezar Ceresini
- Department of Crop Protection, Agricultural Engineering, and SoilsUNESP University of São Paulo StateIlha Solteira CampusSão PauloBrazil15385-000
| | - Vanina Lilián Castroagudín
- Department of Crop Protection, Agricultural Engineering, and SoilsUNESP University of São Paulo StateIlha Solteira CampusSão PauloBrazil15385-000
- Present address:
Department of Plant PathologyUniversity of ArkansasARUSA
| | - Fabrício Ávila Rodrigues
- Department of Plant Pathology, Lab. of Host‐Parasite InteractionUFV Federal University of ViçosaViçosaMinas GeraisBrazil36570-000
| | - Jonas Alberto Rios
- Department of Plant Pathology, Lab. of Host‐Parasite InteractionUFV Federal University of ViçosaViçosaMinas GeraisBrazil36570-000
| | - Carlos Eduardo Aucique‐Pérez
- Department of Plant Pathology, Lab. of Host‐Parasite InteractionUFV Federal University of ViçosaViçosaMinas GeraisBrazil36570-000
| | - Silvino Intra Moreira
- Department of Plant PathologyUFLA Federal University of LavrasLavrasMinas GeraisBrazil37200-000
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of BiologyUniversity of NeuchâtelNeuchâtelSwitzerlandCH-2000
| | - Eduardo Alves
- Department of Plant PathologyUFLA Federal University of LavrasLavrasMinas GeraisBrazil37200-000
| | - Giselle de Carvalho
- Department of Crop Protection, Agricultural Engineering, and SoilsUNESP University of São Paulo StateIlha Solteira CampusSão PauloBrazil15385-000
| | - João Leodato Nunes Maciel
- Brazilian Agriculture Research Corporation, Embrapa Wheat (Embrapa Trigo)Passo FundoRio Grande do SulBrazil99050-970
| | - Bruce Alan McDonald
- Plant Pathology Group, Institute of Integrative BiologySwiss Federal Institute of Technology, ETH ZurichZurichSwitzerlandCH-8092
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30
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Rushworth CA, Windham MD, Keith RA, Mitchell-Olds T. Ecological differentiation facilitates fine-scale coexistence of sexual and asexual Boechera. AMERICAN JOURNAL OF BOTANY 2018; 105:2051-2064. [PMID: 30548985 PMCID: PMC6685206 DOI: 10.1002/ajb2.1201] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 09/10/2018] [Indexed: 05/28/2023]
Abstract
PREMISE OF THE STUDY Ecological differentiation (ED) between sexual and asexual organisms may permit the maintenance of reproductive polymorphism. Several studies of sexual/asexual ED in plants have shown that the geographic ranges of asexuals extend beyond those of sexuals, often in areas of higher latitude or elevation. But very little is known about ED at fine scales, wherein coexistence of sexuals and asexuals may be permitted by differential niche occupation. METHODS We used 149 populations of sexual and apomictic lineages in the genus Boechera (rock cress) collected across a portion of this mustard's vast range. We characterized reproductive mode, ploidy, and species identity or hybrid parentage of each individual, and then used a multipronged statistical approach to (1) identify ED between sexuals and asexuals; (2) investigate the impacts of two confounding factors, polyploidy and hybridization, on ED; and (3) determine the environmental variables underlying ED. KEY RESULTS We found that sexuals and asexuals are significantly ecologically differentiated across the landscape, despite fine-scale interdigitation of these two reproductive forms. Asexual reproduction was strongly associated with greater disturbance, reduced slope, and greater environmental variability. Although ploidy had little effect on the patterns observed, hybridization has a unique impact on the relationships between asexual reproduction and specific environmental variables. CONCLUSIONS Ecological differentiation along the axes of disturbance, slope, and climatic variability, as well as the effects of heterozygosity, may contribute to the maintenance of sexuality and asexuality across the landscape, ultimately impacting the establishment and spread of asexual lineages.
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Affiliation(s)
- Catherine A. Rushworth
- Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
- University and Jepson Herbaria and Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Michael D. Windham
- Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
| | - Rose A. Keith
- Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
| | - Tom Mitchell-Olds
- Department of Biology, Box 90338, Duke University, Durham, NC 27708, USA
- Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA
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31
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Ceresini PC, Castroagudín VL, Rodrigues FÁ, Rios JA, Eduardo Aucique-Pérez C, Moreira SI, Alves E, Croll D, Maciel JLN. Wheat Blast: Past, Present, and Future. ANNUAL REVIEW OF PHYTOPATHOLOGY 2018; 56:427-456. [PMID: 29975608 DOI: 10.1146/annurev-phyto-080417-050036] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The devastating wheat blast disease first emerged in Brazil in 1985. The disease was restricted to South America until 2016, when a series of grain imports from Brazil led to a wheat blast outbreak in Bangladesh. Wheat blast is caused by Pyricularia graminis-tritici ( Pygt), a species genetically distinct from the Pyricularia oryzae species that causes rice blast. Pygt has high genetic and phenotypic diversity and a broad host range that enables it to move back and forth between wheat and other grass hosts. Recombination is thought to occur mainly on the other grass hosts, giving rise to the highly diverse Pygt population observed in wheat fields. This review brings together past and current knowledge about the history, etiology, epidemiology, physiology, and genetics of wheat blast and discusses the future need for integrated management strategies. The most urgent current need is to strengthen quarantine and biosafety regulations to avoid additional spread of the pathogen to disease-free countries. International breeding efforts will be needed to develop wheat varieties with more durable resistance.
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Affiliation(s)
- Paulo Cezar Ceresini
- Department of Crop Protection, Agricultural Engineering, and Soils, São Paulo State University, 15385-000, Ilha Solteira, São Paulo, Brazil;
| | - Vanina Lilián Castroagudín
- Department of Crop Protection, Agricultural Engineering, and Soils, São Paulo State University, 15385-000, Ilha Solteira, São Paulo, Brazil;
| | - Fabrício Ávila Rodrigues
- Laboratory of Host-Parasite Interaction, Department of Plant Pathology, Federal University of Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Jonas Alberto Rios
- Laboratory of Host-Parasite Interaction, Department of Plant Pathology, Federal University of Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Carlos Eduardo Aucique-Pérez
- Laboratory of Host-Parasite Interaction, Department of Plant Pathology, Federal University of Viçosa, 36570-900, Viçosa, Minas Gerais, Brazil
| | - Silvino Intra Moreira
- Department of Plant Pathology, Federal University of Lavras, 37200-000, Lavras, Minas Gerais, Brazil
| | - Eduardo Alves
- Department of Plant Pathology, Federal University of Lavras, 37200-000, Lavras, Minas Gerais, Brazil
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, 2000 Neuchâtel, Switzerland
| | - João Leodato Nunes Maciel
- Embrapa Wheat (Embrapa Trigo), Brazilian Agricultural Research Corporation, Passo 99050-970, Fundo, Rio Grande do Sul, Brazil
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32
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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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33
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Zhong Z, Chen M, Lin L, Han Y, Bao J, Tang W, Lin L, Lin Y, Somai R, Lu L, Zhang W, Chen J, Hong Y, Chen X, Wang B, Shen WC, Lu G, Norvienyeku J, Ebbole DJ, Wang Z. Population genomic analysis of the rice blast fungus reveals specific events associated with expansion of three main clades. ISME JOURNAL 2018; 12:1867-1878. [PMID: 29568114 PMCID: PMC6051997 DOI: 10.1038/s41396-018-0100-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 02/10/2018] [Accepted: 02/20/2018] [Indexed: 12/30/2022]
Abstract
We examined the genomes of 100 isolates of Magnaporthe oryzae (Pyricularia oryzae), the causal agent of rice blast disease. We grouped current field populations of M. oryzae into three major globally distributed groups. A genetically diverse group, clade 1, which may represent a group of closely related lineages, contains isolates of both mating types. Two well-separated clades, clades 2 and 3, appear to have arisen as clonal lineages distinct from the genetically diverse clade. Examination of genes involved in mating pathways identified clade-specific diversification of several genes with orthologs involved in mating behavior in other fungi. All isolates within each clonal lineage are of the same mating type. Clade 2 is distinguished by a unique deletion allele of a gene encoding a small cysteine-rich protein that we determined to be a virulence factor. Clade 3 isolates have a small deletion within the MFA2 pheromone precursor gene, and this allele is shared with an unusual group of isolates we placed within clade 1 that contain AVR1-CO39 alleles. These markers could be used for rapid screening of isolates and suggest specific events in evolution that shaped these populations. Our findings are consistent with the view that M. oryzae populations in Asia generate diversity through recombination and may have served as the source of the clades 2 and 3 isolates that comprise a large fraction of the global population.
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Affiliation(s)
- Zhenhui Zhong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Meilian Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lianyu Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yijuan Han
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiandong Bao
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei Tang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lili Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yahong Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rewish Somai
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lin Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenjing Zhang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jian Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yonghe Hong
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaofeng Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Baohua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei-Chiang Shen
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Republic of China.
| | - Guodong Lu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Justice Norvienyeku
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Daniel J Ebbole
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, USA.
| | - Zonghua Wang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Fujian-Taiwan Joint Center for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Institute of Ocean Science, Minjiang University, Fuzhou, 350108, China.
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34
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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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35
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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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36
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Pagliaccia D, Urak RZ, Wong F, Douhan LI, Greer CA, Vidalakis G, Douhan GW. Genetic Structure of the Rice Blast Pathogen (Magnaporthe oryzae) over a Decade in North Central California Rice Fields. MICROBIAL ECOLOGY 2018; 75:310-317. [PMID: 28755027 PMCID: PMC5742603 DOI: 10.1007/s00248-017-1029-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/28/2017] [Indexed: 06/07/2023]
Abstract
Rice blast, caused by the ascomycete Magnaporthe oryzae, is one of the most destructive rice diseases worldwide. Even though the disease has been present in California since 1996, there is no data for the pathogen population biology in the state. Using amplified fragment length polymorphisms and mating-type markers, the M. oryzae population diversity was investigated using isolates collected when the disease was first established in California and isolates collected a decade later. While in the 1990 samples, a single multilocus genotype (MLG) was identified (MLG1), over a decade later, we found 14 additional MLGs in the 2000 isolates. Some of these MLGs were found to infect the only rice blast-resistant cultivar (M-208) available for commercial production in California. The same samples also had a significant decrease of MLG1. MLG1 was found infecting the resistant rice cultivar M-208 on one occasion whereas MLG7 was the most common genotype infecting the M-208. MLG7 was identified in the 2000 samples, and it was not present in the M. oryzae population a decade earlier. Our results demonstrate a significant increase in genotypic diversity over time with no evidence of sexual reproduction and suggest a recent introduction of new virulent race(s) of the pathogen. In addition, our data could provide information regarding the durability of the Pi-z resistance gene of the M-208. This information will be critical to plant breeders in developing strategies for deployment of other rice blast resistance genes/cultivars in the future.
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Affiliation(s)
- Deborah Pagliaccia
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA.
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.
| | - Ryan Z Urak
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA
| | - Frank Wong
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA
- Bayer's Environmental Health Division, Bayer, Durham, NC, USA
| | - LeAnn I Douhan
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA
- Val Verde Unified School District, Perris, CA, USA
| | - Christopher A Greer
- Cooperative Extension, University of California, Sutter-Yuba, Yuba City, CA, 95991, USA
| | - Georgios Vidalakis
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA
| | - Greg W Douhan
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92521, USA
- Cooperative Extension Tulare County, Tulare, CA, USA
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37
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Soubeyrand S, Garreta V, Monteil C, Suffert F, Goyeau H, Berder J, Moinard J, Fournier E, Tharreau D, Morris CE, Sache I. Testing Differences Between Pathogen Compositions with Small Samples and Sparse Data. PHYTOPATHOLOGY 2017; 107:1199-1208. [PMID: 28677479 DOI: 10.1094/phyto-02-17-0070-fi] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The structure of pathogen populations is an important driver of epidemics affecting crops and natural plant communities. Comparing the composition of two pathogen populations consisting of assemblages of genotypes or phenotypes is a crucial, recurrent question encountered in many studies in plant disease epidemiology. Determining whether there is a significant difference between two sets of proportions is also a generic question for numerous biological fields. When samples are small and data are sparse, it is not straightforward to provide an accurate answer to this simple question because routine statistical tests may not be exactly calibrated. To tackle this issue, we built a computationally intensive testing procedure, the generalized Monte Carlo plug-in test with calibration test, which is implemented in an R package available at https://doi.org/10.5281/zenodo.635791 . A simulation study was carried out to assess the performance of the proposed methodology and to make a comparison with standard statistical tests. This study allows us to give advice on how to apply the proposed method, depending on the sample sizes. The proposed methodology was then applied to real datasets and the results of the analyses were discussed from an epidemiological perspective. The applications to real data sets deal with three topics in plant pathology: the reproduction of Magnaporthe oryzae, the spatial structure of Pseudomonas syringae, and the temporal recurrence of Puccinia triticina.
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Affiliation(s)
- Samuel Soubeyrand
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Vincent Garreta
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Caroline Monteil
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Frédéric Suffert
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Henriette Goyeau
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Julie Berder
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Jacques Moinard
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Elisabeth Fournier
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Didier Tharreau
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Cindy E Morris
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
| | - Ivan Sache
- First and second authors: BioSP, INRA, 84914, Avignon, France; second, fourth, fifth, and sixth authors: INRA, UMR1290 Bioger, AgroParisTech, Université Paris-Saclay 78850 Thiverval-Grignon, France; third and tenth authors: INRA, UR0407 Plant Pathology, 84143 Montfavet, France; seventh author: DRAAF Midi-Pyrénées, 31074 Toulouse Cedex, France; eighth author: INRA, UMR BGPI, 34398 Montpellier, France; ninth author: CIRAD, UMR BGPI, 34398 Montpellier, France; and eleventh author: AgroParisTech, UMR1290 Bioger, 78850 Thiverval-Grignon, France
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Möller M, Stukenbrock EH. Evolution and genome architecture in fungal plant pathogens. Nat Rev Microbiol 2017; 15:756-771. [DOI: 10.1038/nrmicro.2017.76] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Dutech C, Labbé F, Capdevielle X, Lung-Escarmant B. Genetic analysis reveals efficient sexual spore dispersal at a fine spatial scale in Armillaria ostoyae, the causal agent of root-rot disease in conifers. Fungal Biol 2017; 121:550-560. [PMID: 28606350 DOI: 10.1016/j.funbio.2017.03.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 03/10/2017] [Indexed: 11/24/2022]
Abstract
Armillaria ostoyae (sometimes named Armillaria solidipes) is a fungal species causing root diseases in numerous coniferous forests of the northern hemisphere. The importance of sexual spores for the establishment of new disease centres remains unclear, particularly in the large maritime pine plantations of southwestern France. An analysis of the genetic diversity of a local fungal population distributed over 500 ha in this French forest showed genetic recombination between genotypes to be frequent, consistent with regular sexual reproduction within the population. The estimated spatial genetic structure displayed a significant pattern of isolation by distance, consistent with the dispersal of sexual spores mostly at the spatial scale studied. Using these genetic data, we inferred an effective density of reproductive individuals of 0.1-0.3 individuals/ha, and a second moment of parent-progeny dispersal distance of 130-800 m, compatible with the main models of fungal spore dispersal. These results contrast with those obtained for studies of A. ostoyae over larger spatial scales, suggesting that inferences about mean spore dispersal may be best performed at fine spatial scales (i.e. a few kilometres) for most fungal species.
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Affiliation(s)
- Cyril Dutech
- BIOGECO, INRA, Univ. Bordeaux, UMR 1202, F-33610 Cestas, France.
| | - Frédéric Labbé
- BIOGECO, INRA, Univ. Bordeaux, UMR 1202, F-33610 Cestas, France
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40
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Wang J, Fernández‐Pavía SP, Larsen MM, Garay‐Serrano E, Gregorio‐Cipriano R, Rodríguez‐Alvarado G, Grünwald NJ, Goss EM. High levels of diversity and population structure in the potato late blight pathogen at the Mexico centre of origin. Mol Ecol 2017; 26:1091-1107. [DOI: 10.1111/mec.14000] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 12/11/2016] [Accepted: 12/21/2016] [Indexed: 01/15/2023]
Affiliation(s)
- Jianan Wang
- Department of Plant Pathology and Emerging Pathogens Institute University of Florida Gainesville FL 32611 USA
| | - Sylvia P. Fernández‐Pavía
- Laboratorio de Patología Vegetal Universidad Michoacana de San Nicolás de Hidalgo IIAF Tarímbaro Michoacán 58880 México
| | | | - Edith Garay‐Serrano
- Laboratorio de Patología Vegetal Universidad Michoacana de San Nicolás de Hidalgo IIAF Tarímbaro Michoacán 58880 México
| | - Rosario Gregorio‐Cipriano
- Laboratorio de Patología Vegetal Universidad Michoacana de San Nicolás de Hidalgo IIAF Tarímbaro Michoacán 58880 México
| | - Gerardo Rodríguez‐Alvarado
- Laboratorio de Patología Vegetal Universidad Michoacana de San Nicolás de Hidalgo IIAF Tarímbaro Michoacán 58880 México
| | | | - Erica M. Goss
- Department of Plant Pathology and Emerging Pathogens Institute University of Florida Gainesville FL 32611 USA
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McDonald BA, Stukenbrock EH. Rapid emergence of pathogens in agro-ecosystems: global threats to agricultural sustainability and food security. Philos Trans R Soc Lond B Biol Sci 2016; 371:20160026. [PMID: 28080995 PMCID: PMC5095548 DOI: 10.1098/rstb.2016.0026] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2016] [Indexed: 01/06/2023] Open
Abstract
Agricultural ecosystems are composed of genetically depauperate populations of crop plants grown at a high density and over large spatial scales, with the regional composition of crop species changing little from year to year. These environments are highly conducive for the emergence and dissemination of pathogens. The uniform host populations facilitate the specialization of pathogens to particular crop cultivars and allow the build-up of large population sizes. Population genetic and genomic studies have shed light on the evolutionary mechanisms underlying speciation processes, adaptive evolution and long-distance dispersal of highly damaging pathogens in agro-ecosystems. These studies document the speed with which pathogens evolve to overcome crop resistance genes and pesticides. They also show that crop pathogens can be disseminated very quickly across and among continents through human activities. In this review, we discuss how the peculiar architecture of agro-ecosystems facilitates pathogen emergence, evolution and dispersal. We present four example pathosystems that illustrate both pathogen specialization and pathogen speciation, including different time frames for emergence and different mechanisms underlying the emergence process. Lastly, we argue for a re-design of agro-ecosystems that embraces the concept of dynamic diversity to improve their resilience to pathogens. This article is part of the themed issue 'Tackling emerging fungal threats to animal health, food security and ecosystem resilience'.
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Affiliation(s)
- Bruce A McDonald
- Plant Pathology Group, ETH Zurich, Universitätstrasse 2, 8092 Zürich, Switzerland
| | - Eva H Stukenbrock
- Environmental Genomics Group, Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306 Plön, Germany
- Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, 24118 Kiel, Germany
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Janoušek J, Wingfield MJ, Monsivais JGM, Jankovský L, Stauffer C, Konečný A, Barnes I. Genetic Analyses Suggest Separate Introductions of the Pine Pathogen Lecanosticta acicola Into Europe. PHYTOPATHOLOGY 2016; 106:1413-1425. [PMID: 26714104 DOI: 10.1094/phyto-10-15-0271-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Lecanosticta acicola is a heterothallic ascomycete that causes brown spot needle blight on native and nonnative Pinus spp. in many regions of the world. In this study we investigated the origin of European L. acicola populations and estimated the level of random mating of the pathogen in affected areas. Part of the elongation factor 1-α gene was sequenced, 11 microsatellite regions were screened, and the mating type idiomorphs were determined for 201 isolates of L. acicola collected from three continents and 17 host species. The isolates from Mexico and Guatemala were unique, highly diverse and could represent cryptic species of Lecanosticta. The isolates from East Asia formed a uniform and discrete group. Two distinct populations were identified in both North America and Europe. Approximate Bayesian computation analyses strongly suggest independent introductions of two populations from North America into Europe. Microsatellite data and mating type distributions indicated random recombination in the populations of North America and Europe. Its intercontinental introduction can most likely be explained as a consequence of the movement of infected plant material. In contrast, the spread of L. acicola within Europe appears to be primarily due to conidial dispersion and probably also ascospore dissemination.
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Affiliation(s)
- Josef Janoušek
- First and fourth authors: Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno 613 00, Czech Republic; second and seventh authors: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; third author: Facultad de Ciencias Forestales, UANL, Nuevo León 67700, Mexico; fifth author: Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna 1190, Austria; and sixth author: Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Michael J Wingfield
- First and fourth authors: Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno 613 00, Czech Republic; second and seventh authors: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; third author: Facultad de Ciencias Forestales, UANL, Nuevo León 67700, Mexico; fifth author: Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna 1190, Austria; and sixth author: Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - José G Marmolejo Monsivais
- First and fourth authors: Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno 613 00, Czech Republic; second and seventh authors: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; third author: Facultad de Ciencias Forestales, UANL, Nuevo León 67700, Mexico; fifth author: Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna 1190, Austria; and sixth author: Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Libor Jankovský
- First and fourth authors: Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno 613 00, Czech Republic; second and seventh authors: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; third author: Facultad de Ciencias Forestales, UANL, Nuevo León 67700, Mexico; fifth author: Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna 1190, Austria; and sixth author: Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Christian Stauffer
- First and fourth authors: Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno 613 00, Czech Republic; second and seventh authors: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; third author: Facultad de Ciencias Forestales, UANL, Nuevo León 67700, Mexico; fifth author: Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna 1190, Austria; and sixth author: Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Adam Konečný
- First and fourth authors: Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno 613 00, Czech Republic; second and seventh authors: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; third author: Facultad de Ciencias Forestales, UANL, Nuevo León 67700, Mexico; fifth author: Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna 1190, Austria; and sixth author: Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Irene Barnes
- First and fourth authors: Department of Forest Protection and Wildlife Management, Faculty of Forestry and Wood Technology, Mendel University in Brno, Brno 613 00, Czech Republic; second and seventh authors: Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa; third author: Facultad de Ciencias Forestales, UANL, Nuevo León 67700, Mexico; fifth author: Department of Forest and Soil Sciences, University of Natural Resources and Life Sciences, Vienna 1190, Austria; and sixth author: Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
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Tilquin A, Kokko H. What does the geography of parthenogenesis teach us about sex? Philos Trans R Soc Lond B Biol Sci 2016; 371:20150538. [PMID: 27619701 PMCID: PMC5031622 DOI: 10.1098/rstb.2015.0538] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2016] [Indexed: 11/12/2022] Open
Abstract
Theory predicts that sexual reproduction is difficult to maintain if asexuality is an option, yet sex is very common. To understand why, it is important to pay attention to repeatably occurring conditions that favour transitions to, or persistence of, asexuality. Geographic parthenogenesis is a term that has been applied to describe a large variety of patterns where sexual and related asexual forms differ in their geographic distribution. Often asexuality is stated to occur in a habitat that is, in some sense, marginal, but the interpretation differs across studies: parthenogens might not only predominate near the margin of the sexuals' distribution, but might also extend far beyond the sexual range; they may be disproportionately found in newly colonizable areas (e.g. areas previously glaciated), or in habitats where abiotic selection pressures are relatively stronger than biotic ones (e.g. cold, dry). Here, we review the various patterns proposed in the literature, the hypotheses put forward to explain them, and the assumptions they rely on. Surprisingly, few mathematical models consider geographic parthenogenesis as their focal question, but all models for the evolution of sex could be evaluated in this framework if the (often ecological) causal factors vary predictably with geography. We also recommend broadening the taxa studied beyond the traditional favourites.This article is part of the themed issue 'Weird sex: the underappreciated diversity of sexual reproduction'.
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Affiliation(s)
- Anaïs Tilquin
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland Centre of Excellence in Biological Interactions, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Hanna Kokko
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland Centre of Excellence in Biological Interactions, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
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Liu XH, Ning GA, Huang LY, Zhao YH, Dong B, Lu JP, Lin FC. Calpains are involved in asexual and sexual development, cell wall integrity and pathogenicity of the rice blast fungus. Sci Rep 2016; 6:31204. [PMID: 27502542 PMCID: PMC4977516 DOI: 10.1038/srep31204] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 07/14/2016] [Indexed: 01/03/2023] Open
Abstract
Calpains are ubiquitous and well-conserved proteins that belong to the calcium-dependent, non-lysosomal cysteine protease family. In this study, 8 putative calpains were identified using Pfam domain analysis and BlastP searches in M. oryzae. Three single gene deletion mutants (ΔMocapn7, ΔMocapn9 and ΔMocapn14) and two double gene deletion mutants (ΔMocapn4ΔMocapn7 and ΔMocapn9ΔMocapn7) were obtained using the high-throughput gene knockout system. The calpain disruption mutants showed defects in colony characteristics, conidiation, sexual reproduction and cell wall integrity. The mycelia of the ΔMocapn7, ΔMocapn4ΔMocapn7 and ΔMocapn9ΔMocapn7 mutants showed reduced pathogenicity on rice and barley.
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Affiliation(s)
- Xiao-Hong Liu
- State Key Laboratory for Rice Biology, Biotechnology Institute, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Guo-Ao Ning
- State Key Laboratory for Rice Biology, Biotechnology Institute, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Lu-Yao Huang
- State Key Laboratory for Rice Biology, Biotechnology Institute, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Ya-Hui Zhao
- State Key Laboratory for Rice Biology, Biotechnology Institute, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Bo Dong
- State Key Laboratory of Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang Province, China
| | - Jian-Ping Lu
- College of Life Sciences, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Fu-Cheng Lin
- State Key Laboratory for Rice Biology, Biotechnology Institute, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
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Yoshida K, Saunders DGO, Mitsuoka C, Natsume S, Kosugi S, Saitoh H, Inoue Y, Chuma I, Tosa Y, Cano LM, Kamoun S, Terauchi R. Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements. BMC Genomics 2016; 17:370. [PMID: 27194050 PMCID: PMC4870811 DOI: 10.1186/s12864-016-2690-6] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Accepted: 05/05/2016] [Indexed: 01/17/2023] Open
Abstract
Background Magnaporthe oryzae (anamorph Pyricularia oryzae) is the causal agent of blast disease of Poaceae crops and their wild relatives. To understand the genetic mechanisms that drive host specialization of M. oryzae, we carried out whole genome resequencing of four M. oryzae isolates from rice (Oryza sativa), one from foxtail millet (Setaria italica), three from wild foxtail millet S. viridis, and one isolate each from finger millet (Eleusine coracana), wheat (Triticum aestivum) and oat (Avena sativa), in addition to an isolate of a sister species M. grisea, that infects the wild grass Digitaria sanguinalis. Results Whole genome sequence comparison confirmed that M. oryzae Oryza and Setaria isolates form a monophyletic and close to another monophyletic group consisting of isolates from Triticum and Avena. This supports previous phylogenetic analysis based on a small number of genes and molecular markers. When comparing the host specific subgroups, 1.2–3.5 % of genes showed presence/absence polymorphisms and 0–6.5 % showed an excess of non-synonymous substitutions. Most of these genes encoded proteins whose functional domains are present in multiple copies in each genome. Therefore, the deleterious effects of these mutations could potentially be compensated by functional redundancy. Unlike the accumulation of nonsynonymous nucleotide substitutions, gene loss appeared to be independent of divergence time. Interestingly, the loss and gain of genes in pathogens from the Oryza and Setaria infecting lineages occurred more frequently when compared to those infecting Triticum and Avena even though the genetic distance between Oryza and Setaria lineages was smaller than that between Triticum and Avena lineages. In addition, genes showing gain/loss and nucleotide polymorphisms are linked to transposable elements highlighting the relationship between genome position and gene evolution in this pathogen species. Conclusion Our comparative genomics analyses of host-specific M. oryzae isolates revealed gain and loss of genes as a major evolutionary mechanism driving specialization to Oryza and Setaria. Transposable elements appear to facilitate gene evolution possibly by enhancing chromosomal rearrangements and other forms of genetic variation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2690-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kentaro Yoshida
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan. .,The Sainsbury Laboratory, Norwich Research Park, Norwich, UK. .,Graduate School of Agricultural Science, Kobe University, Kobe, Japan.
| | - Diane G O Saunders
- The Genome Analysis Centre, Norwich Research Park, Noriwich, UK.,John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | | | | | - Yoshihiro Inoue
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Izumi Chuma
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Yukio Tosa
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Liliana M Cano
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK.,Department of Plant Pathology, Indian River Research and Education Center, University of Florida, Fort Pierce, USA
| | - Sophien Kamoun
- The Sainsbury Laboratory, Norwich Research Park, Norwich, UK
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan.
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Zimmerman KCK, Levitis DA, Pringle A. Beyond animals and plants: dynamic maternal effects in the fungus Neurospora crassa. J Evol Biol 2016; 29:1379-93. [PMID: 27062053 DOI: 10.1111/jeb.12878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/05/2016] [Indexed: 11/28/2022]
Abstract
Maternal effects are widely documented in animals and plants, but not in fungi or other eukaryotes. A principal cause of maternal effects is asymmetrical parental investment in a zygote, creating greater maternal vs. paternal influence on offspring phenotypes. Asymmetrical investments are not limited to animals and plants, but are also prevalent in fungi and groups including apicomplexans, dinoflagellates and red algae. Evidence suggesting maternal effects among fungi is sparse and anecdotal. In an experiment designed to test for maternal effects across sexual reproduction in the model fungus Neurospora crassa, we measured offspring phenotypes from crosses of all possible pairs of 22 individuals. Crosses encompassed reciprocals of 11 mating-type 'A' and 11 mating-type 'a' wild strains. After controlling for the genetic and geographic distances between strains in any individual cross, we found strong evidence for maternal control of perithecia (sporocarp) production, as well as maternal effects on spore numbers and spore germination. However, both parents exert equal influence on the percentage of spores that are pigmented and size of pigmented spores. We propose a model linking the stage-specific presence or absence of maternal effects to cellular developmental processes: effects appear to be mediated primarily through the maternal cytoplasm, and, after spore cell walls form, maternal influence on spore development is limited. Maternal effects in fungi, thus far largely ignored, are likely to shape species' evolution and ecologies. Moreover, the association of anisogamy and maternal effects in a fungus suggests maternal effects may also influence the biology of other anisogamous eukaryotes.
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Affiliation(s)
- K C K Zimmerman
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - D A Levitis
- Department of Biology, Bates College, Lewiston, ME, USA
| | - A Pringle
- Departments of Botany and Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
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Li J, Lu L, Jia Y, Wang Q, Fukuta Y, Li C. Characterization of Field Isolates of Magnaporthe oryzae with Mating Type, DNA Fingerprinting, and Pathogenicity Assays. PLANT DISEASE 2016; 100:298-303. [PMID: 30694130 DOI: 10.1094/pdis-06-15-0660-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Due to the harmful nature of the rice blast fungus, Magnaporthe oryzae, it is beneficial to characterize field isolates to help aid in the deployment of resistance (R) genes in rice. In the present study, 252 field isolates of M. oryzae, collected from rice fields of Yunnan Province in China, were assessed for mating type, DNA fingerprinting, and disease reactions to differential rice lines. In total, 94 isolates (37.3%) were MAT1-1 and 158 (62.7%) were MAT1-2 based on polymerase chain reaction assays, and some of them were verified with the tester isolates. All MAT1-1 and MAT1-2 isolates were virulent to some of the International Rice Research Institute-Japan International Research Center for Agricultural Sciences monogenic lines harboring 22 major resistance genes as differential varieties. Three simple-sequence repeat markers were used to examine genetic diversity in all isolates. The existence of regional patterns of genetic diversity, sexual reproduction potential, and pathogenicity suggests that M. oryzae populations have been independently asexually adapted in rice fields during crop cultivation.
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Affiliation(s)
- Jinbin Li
- Agricultural Environment and Resources Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, Yunnan Province 650205, China
| | - Lin Lu
- Flower Research Institute, YAAS, Kunming, China
| | - Yulin Jia
- United States Department of Agriculture-Agriculture Research Service, Dale Bumpers National Rice Research Center, Stuttgart, AR
| | - Qun Wang
- Agricultural Environment and Resources Research Institute, YAAS, Kunming, China
| | - Yoshimichi Fukuta
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, Ishigaki, Okinawa 907-0002, Japan
| | - Chengyun Li
- The Ministry of Education Key Laboratory for Agricultural Biodiversity and Pest Management, Yunnan Agricultural University, Kunming, Yunnan Province 650201, China
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Chiapello H, Mallet L, Guérin C, Aguileta G, Amselem J, Kroj T, Ortega-Abboud E, Lebrun MH, Henrissat B, Gendrault A, Rodolphe F, Tharreau D, Fournier E. Deciphering Genome Content and Evolutionary Relationships of Isolates from the Fungus Magnaporthe oryzae Attacking Different Host Plants. Genome Biol Evol 2015; 7:2896-912. [PMID: 26454013 PMCID: PMC4684704 DOI: 10.1093/gbe/evv187] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Deciphering the genetic bases of pathogen adaptation to its host is a key question in ecology and evolution. To understand how the fungus Magnaporthe oryzae adapts to different plants, we sequenced eight M. oryzae isolates differing in host specificity (rice, foxtail millet, wheat, and goosegrass), and one Magnaporthe grisea isolate specific of crabgrass. Analysis of Magnaporthe genomes revealed small variation in genome sizes (39–43 Mb) and gene content (12,283–14,781 genes) between isolates. The whole set of Magnaporthe genes comprised 14,966 shared families, 63% of which included genes present in all the nine M. oryzae genomes. The evolutionary relationships among Magnaporthe isolates were inferred using 6,878 single-copy orthologs. The resulting genealogy was mostly bifurcating among the different host-specific lineages, but was reticulate inside the rice lineage. We detected traces of introgression from a nonrice genome in the rice reference 70-15 genome. Among M. oryzae isolates and host-specific lineages, the genome composition in terms of frequencies of genes putatively involved in pathogenicity (effectors, secondary metabolism, cazome) was conserved. However, 529 shared families were found only in nonrice lineages, whereas the rice lineage possessed 86 specific families absent from the nonrice genomes. Our results confirmed that the host specificity of M. oryzae isolates was associated with a divergence between lineages without major gene flow and that, despite the strong conservation of gene families between lineages, adaptation to different hosts, especially to rice, was associated with the presence of a small number of specific gene families. All information was gathered in a public database (http://genome.jouy.inra.fr/gemo).
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Affiliation(s)
- Hélène Chiapello
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France INRA, UR 875, Unité Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France
| | - Ludovic Mallet
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France INRA, UR 875, Unité Mathématiques et Informatique Appliquées de Toulouse, Castanet-Tolosan, France INRA, UR 1164, Unité de Recherche Génomique Info, Versailles, France
| | - Cyprien Guérin
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France
| | - Gabriela Aguileta
- CNRS, UMR 8079, Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay, France Center for Genomic Regulation, Barcelona, Spain
| | - Joëlle Amselem
- INRA, UR 1164, Unité de Recherche Génomique Info, Versailles, France
| | - Thomas Kroj
- INRA, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
| | - Enrique Ortega-Abboud
- CIRAD, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
| | - Marc-Henri Lebrun
- INRA-AgroParisTech, UMR 1190, Biologie et Gestion des Risques en Agriculture BIOGER-CPP, Campus AgroParisTech, Thiverval-Grignon, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Université d'Aix Marseille, France Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Annie Gendrault
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France
| | - François Rodolphe
- INRA, UR 1404, Unité Mathématiques et Informatique Appliquées du Génome à l'Environnement, Jouy-en-Josas, France
| | - Didier Tharreau
- CIRAD, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
| | - Elisabeth Fournier
- INRA, UMR 385, Biologie et Génétique des Interactions Plantes-Pathogènes BGPI, INRA-CIRAD-Montpellier SupAgro, Campus International de Baillarguet, Montpellier, France
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49
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Nougué O, Rode NO, Jabbour-zahab R, Ségard A, Chevin LM, Haag CR, Lenormand T. Automixis in Artemia: solving a century-old controversy. J Evol Biol 2015; 28:2337-48. [DOI: 10.1111/jeb.12757] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 08/26/2015] [Accepted: 09/07/2015] [Indexed: 12/11/2022]
Affiliation(s)
- O. Nougué
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
| | - N. O. Rode
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
- INRA - UMR 1334 AGAP; Montpellier France
| | - R. Jabbour-zahab
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
| | - A. Ségard
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
| | - L.-M. Chevin
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
| | - C. R. Haag
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
| | - T. Lenormand
- UMR 5175 CEFE; CNRS - Université Montpellier - Université P. Valéry - EPHE; Montpellier Cedex 5 France
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50
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Abstract
Trade in plant and plant products has profoundly affected the global distribution and diversity of plant pathogens. Identification of migration pathways can be used to monitor or manage pathogen movement for proactive disease management or quarantine measures. Genomics-based genetic marker discovery is allowing unprecedented collection of population genetic data for plant pathogens. These data can be used for detailed analysis of the ancestry of population samples and therefore for analysis of migration. Reconstruction of migration histories has confirmed previous hypotheses based on observational data and led to unexpected new findings on the origins of pathogens and source populations for past and recent migration. The choice of software for analysis depends on the type of migration being studied and the reproductive mode of the pathogen. Biased sampling and complex population structures are potential challenges to accurate inference of migration pathways.
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Affiliation(s)
- Erica M Goss
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32611;
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