Whole-genome sequencing reveals recent and frequent genetic recombination between clonal lineages of Cryphonectria parasitica in western Europe

Demené, Arthur; Legrand, Ludovic; Gouzy, Jérôme; Debuchy, Robert; Saint-Jean, Gilles; Fabreguettes, Olivier; Dutech, Cyril

doi:10.1016/j.fgb.2019.06.002

Cited by 18 publications

(33 citation statements)

References 74 publications

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“…Other European populations of C. parasitica were also found to mainly reproduce asexually and have a higher degree of clonality [11,37,61] compared to the native populations of Asia and America [12]. However, a whole-genome sequencing study revealed the frequent recombination between the clonal lineages of C. parasitica and suggested that a clonal population does not necessarily involve the absence of sexual reproduction [70], as was observed in other fungal species [71,72]. Prospero and Rigling [56] also stated that sexual reproduction could have been underestimated in Europe because a high genetic similarity among the individuals of an introduced pathogen is usually observed, which can only lead to a few new haplotypes through sexual reproduction.…”

Section: Discussionmentioning

confidence: 99%

Microsatellite Analysis Revealing High Genetic Diversity of the Chestnut Blight Fungus in South Tyrol (Northern Italy)

Ahmad

Baric

2022

Forests

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Cryphonectria parasitica, which causes chestnut blight, is one of the most important pathogens of forest trees. In Europe, mycovirus-mediated biocontrol is the most efficient method to control the disease but can be impeded by the lack of information about the population structure of the fungus within a region. In particular, sexual reproduction and the new introduction of the pathogen can complicate biocontrol strategies. For this reason, this study aimed to determine the population structure of C. parasitica, which causes chestnut blight, in the northern Italian region of South Tyrol, using eleven multilocus microsatellite markers. Fifty-one haplotypes were found across South Tyrol, belonging to three divergent clusters. Recombinant genotypes demonstrated that sexual reproduction occurs across the different clusters. The most dominant genotypes in the region were also the most dominant in neighboring areas, such as Switzerland, northern Italy and France. All of the clusters from South Tyrol were related to the Italian genotype pool and are thought to have been introduced from northern Italian and other European populations due to naturally occurring gene flow or human-mediated introduction. At least three separate introduction events of C. parasitica might have happened in South Tyrol that could be separated by time. This study demonstrated a high genetic diversity of C. parasitica in South Tyrol and helped to shed light on the sexual reproduction and introduction events in the local populations.

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Section: Discussionmentioning

confidence: 99%

Microsatellite Analysis Revealing High Genetic Diversity of the Chestnut Blight Fungus in South Tyrol (Northern Italy)

Ahmad

Baric

2022

Forests

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“…We used ClonalFrameML v1.11-3 ( 65 ) to detect and quantify the number of recombination events, with phylogenetic relationships generated using RAxML v8.2.1 ( 66 ) as described previously ( 67 , 68 ). Additionally, we interpreted ClonalFrameML estimates of the ratio of the recombination rate to the mutation rate ( R /θ), the average size of recombination events (δ), the average divergence between donor and recipient ( v ), and the relative importance of recombination and mutation ( r/m ), which is calculated as the product of these three estimates (Table S2 in reference 33 ).…”

Section: Methodsmentioning

confidence: 99%

The Frequency of Sex: Population Genomics Reveals Differences in Recombination and Population Structure of the Aflatoxin-Producing Fungus Aspergillus flavus

Drott

Satterlee

Skerker

et al. 2020

mBio

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The apparent rarity of sex in many fungal species has raised questions about how much sex is needed to purge deleterious mutations and how differences in frequency of sex impact fungal evolution. We sought to determine how differences in the extent of recombination between populations of Aspergillus flavus impact the evolution of genes associated with the synthesis of aflatoxin, a notoriously potent carcinogen. We sequenced the genomes of, and quantified aflatoxin production in, 94 isolates of A. flavus sampled from seven states in eastern and central latitudinal transects of the United States. The overall population is subdivided into three genetically differentiated populations (A, B, and C) that differ greatly in their extent of recombination, diversity, and aflatoxin-producing ability. Estimates of the number of recombination events and linkage disequilibrium decay suggest relatively frequent sex only in population A. Population B is sympatric with population A but produces significantly less aflatoxin and is the only population where the inability of nonaflatoxigenic isolates to produce aflatoxin was explained by multiple gene deletions. Population expansion evident in population B suggests a recent introduction or range expansion. Population C is largely nonaflatoxigenic and restricted mainly to northern sampling locations through restricted migration and/or selection. Despite differences in the number and type of mutations in the aflatoxin gene cluster, codon optimization and site frequency differences in synonymous and nonsynonymous mutations suggest that low levels of recombination in some A. flavus populations are sufficient to purge deleterious mutations. IMPORTANCE Differences in the relative frequencies of sexual and asexual reproduction have profound implications for the accumulation of deleterious mutations (Muller’s ratchet), but little is known about how these differences impact the evolution of ecologically important phenotypes. Aspergillus flavus is the main producer of aflatoxin, a notoriously potent carcinogen that often contaminates food. We investigated if differences in the levels of production of aflatoxin by A. flavus could be explained by the accumulation of deleterious mutations due to a lack of recombination. Despite differences in the extent of recombination, variation in aflatoxin production is better explained by the demography and history of specific populations and may suggest important differences in the ecological roles of aflatoxin among populations. Furthermore, the association of aflatoxin production and populations provides a means of predicting the risk of aflatoxin contamination by determining the frequencies of isolates from low- and high-production populations.

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“…stewartii so as to pinpoint likely pathways of past introductions (invasion history) of the pathogen to regions where it is not endemic, as recently done for other plant pests (e.g. Anoplophora glabripennis : Javal et al., ; Cryphonectria parasitic a: Demené et al., ; Phytophthora cinnamomi : Socorro Serrano et al., ; Pieris rapae : Ryan et al., ; Seiridium cardinale : Della Rocca et al., ). Furthermore, it would be useful to clarify the origin of the seed associated with current outbreaks in Italy and Slovenia.…”

Section: Discussionmentioning

confidence: 99%

Risk assessment of the entry of Pantoea stewartii subsp. stewartii on maize seed imported by the EU from the USA

Bragard¹,

Dehnen‐Schmutz²,

Serio³

et al. 2019

EFS2

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Following a request from the European Commission, the EFSA Panel on Plant Health performed a risk assessment of the entry of Pantoea stewartii subsp. stewartii on maize seed imported by the EU from the USA. This pest is a Gram-negative bacterium which causes Stewart's vascular wilt and leaf blight of maize (including sweet corn), a disease responsible for serious crop losses throughout the world. The following scenarios were considered: scenario A0 (current practice), scenario A1 (US request for modification of EU conditions for derogation), and scenario A2 (EU conditions for derogation). Results from the quantitative seed pathway model presented here show that, despite the low rates of plant-to-seed and seed-toseedling transmission that have been reported in the literature for Stewart's wilt, given the amount of traded seed, and in the case of voluntary (i.e. not mandatory) inspections of seed production fields at the origin (i.e. scenario A0), the frequency of introducing the disease is in the order of magnitude of some hundred introductions per year (median number). The EU conditions for derogation would lead to a decrease in the likelihood of entry compared to scenarios A0 (about 10,000 times fewer introductions) and A1 (about 2,000 times fewer introductions). This protective effect is mainly due to the requirement that only genotypes resistant to Stewart's wilt are traded, with the additional field inspection (two instead of one per season) providing additional reassurance. The Panel also concluded that seed lot inspections, as currently carried out (e.g. with a sample of 400 seeds) are not likely to lead to a relevant reduction in the level of infected imported maize seed, given the low prevalence of Stewart's wilt at the origin. If, however, there is aggregation in infection among consignments, inspection would work towards identifying the highly infected consignments. Recently, outbreaks of Stewart's wilt have occurred in Italy (Emilia Romagna, Friuli, Lombardy and Veneto). A review is provided of the available information to assess the possible role of seed imports in these outbreaks.

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Whole-genome sequencing reveals recent and frequent genetic recombination between clonal lineages of Cryphonectria parasitica in western Europe

Cited by 18 publications

References 74 publications

Microsatellite Analysis Revealing High Genetic Diversity of the Chestnut Blight Fungus in South Tyrol (Northern Italy)

Microsatellite Analysis Revealing High Genetic Diversity of the Chestnut Blight Fungus in South Tyrol (Northern Italy)

The Frequency of Sex: Population Genomics Reveals Differences in Recombination and Population Structure of the Aflatoxin-Producing Fungus Aspergillus flavus

Risk assessment of the entry of Pantoea stewartii subsp. stewartii on maize seed imported by the EU from the USA

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