Emerson M. Del Ponte

Universidade Federal de Viçosa

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Kaique S. Alves

Universidade Federal de Viçosa

Piérri Spolti

Universidade Federal de Viçosa

Franklin Jackson Machado

Universidade Federal de Viçosa

João Paulo Ascari

Fundação de Amparo à Pesquisa do Estado de Mato Grosso

C. V. Godoy

Brazilian Agricultural Research Corporation

J. M. C. Fernandes

Universidade Federal de Pernambuco

Jhonatan Paulo Barro

Universidade Federal de Viçosa

Dauri José Tessmann

Universidade Estadual de Maringá

Camila P. Nicolli

University of Wisconsin–Madison

Clive H. Bock

Agricultural Research Service

Cooperative Institutions

Universidade Federal de Viçosa

101

Agricultural Research Service

United States Department of Agriculture

Universidade Federal do Rio Grande do Sul

Brazilian Agricultural Research Corporation

Plant (United States)

Cornell University

University of California, Davis

Pennsylvania State University

Universidade Federal de Pelotas

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Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a MonophyleticFusariumthat Includes theFusarium solaniSpecies Complex

Phytopathology (2020)

David M. Geiser Abdullah M. S. Al‐Hatmi Takayuki Aoki Tsutomu Arie Virgilio Balmas

Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.

Monophyly

Polyphyly

Fusarium solani

10.1094/phyto-08-20-0330-le

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Heterogeneidade da relação entre produtividade da soja e severidade da ferrugem asiática: uma análise exploratória.

A. de H. N. Maia Emerson M. Del Ponte C. V. Godoy

This work aimed to conduct an exploratory, prior to meta-analysis, assessment of the heterogeneity of the linear relationship between soybean yield (Y) and the severity (X) of a foliar fungal disease (soybean rust) from 144 fungicide trials conducted in five years and 45 locations in Brazil. We used graphical analysis to explore the within- and between-trial variability of model parameter estimates (effect sizes) and summary measures for model goodness-of-fit and influence analysis. In the estimation of the weighted mean regression coefficients, following the metaanalysis concept, we propose a method that takes into account the magnitude of influence measures as well as the uncertainties of parameters estimates, usually the inverse of the standard error of for the parameter estimate. High between-trial heterogeneity was observed for parameter estimates, standard errors (within trial variability), determination coefficient and influence measures. Graphical analysis suggested influence of timing of disease onset and control yield class on model slope, which will be quantified further using a meta-analytical approach.

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Fusarium subtropicale, sp. nov., a novel nivalenol mycotoxin–producing species isolated from barley (Hordeum vulgare) in Brazil and sister to F. praegraminearum

Mycologia (2018)

Carolina Bertuzzi Pereira Todd J. Ward Dauri José Tessmann Emerson M. Del Ponte Imane Laraba

Surveys were conducted in commercial wheat and barley fields in the south central production regions of state of Paraná, Brazil, from 2011 to 2015. Spikes displaying visible Fusarium head blight symptoms were collected and the pathogen isolated from the tissues. The 754 Fusarium isolates recovered were identified by a high-throughput multilocus genotyping assay (MLGT) designed to identify trichothecene toxin–producing fusaria (i.e., formerly B-clade, but referred to here as F. sambucinum species complex lineage 1 [FSAMSC-1]) together with sequencing a portion of the translation elongation factor 1-α (TEF1) gene. One strain was discovered that appeared to be closely related to but phylogenetically distinct from F. praegraminearum based on the relatively low 97.7% TEF1 identity and positive genotype obtained with one of the two F. praegraminearum species–specific MLGT probes. Molecular phylogenetic analyses of a 10-gene data set resolved this novel FSAMSC-1 species and F. praegraminearum as sisters. Formally described herein as F. subtropicale, it is phenotypically distinct from the 22 other FSAMSC-1 species in that it produces mostly 1–3-septate macroconidia. Whole-genome sequence data were used to predict its potential to produce mycotoxins. Chemical analyses confirmed that F. subtropicale could produce the mycotoxins 4,15-diacetylnivalenol, butenolide, culmorin, and fusarin C in vitro, and the pathogenicity experiment revealed that F. subtropicale could infect but not spread in susceptible hard red spring wheat cultivar “Norm.”

Species complex

10.1080/00275514.2018.1512296

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Altitude is the Main Driver of Coffee Leaf Rust Epidemics: a Large-scale Survey in Ethiopia

Kifle Belachew Girma Adugna Senbeta Weyessa Garedew Robert W. Barreto Emerson M. Del Ponte

Arabica coffee (Coffea arabica L.) is native from Africa and Ethiopia is often regarded as its birthplace. Previously of little concern to Ethiopian farmers, coffee leaf rust (CLR) caused by the fungus Hemileia vastatrix is an emergent disease globally. To update the status of CLR, a large survey was conducted in 405 coffee fields across nine production zones of Oromia and Southern Nations Nationalities and Peoples (SNNP) regions. The disease, evaluated one time during the month of the peak for CLR intensity for each region, was present in every single field; mean incidence and severity ranged from 5 to 86.7% (mean = 35.3%) and 0.22 to 55.5 (mean = 9.09), respectively. A complementary log-log model predicted mean field severity from mean field incidence. Altitude, a known surrogate for temperature, was the main driver of the epidemics. Incidence and severity were highest at the lowland fields, where poorly managed plantations of local varieties grown under open sun were also more dominant. CLR intensity decreased with the increase in altitude at the highlands where well-managed improved varieties grown under the shade in forest systems dominate the scenario. This survey contributes to increase awareness of a growing problem in Ethiopia, especially for coffee fields at the highlands should temperatures rise and farmers cut forest to grow plantations of susceptible cultivars. Improving genetic resistance and adoption of best management practices are urgent to prevent the rapid surge of new races and mitigate crop losses currently overlooked by coffee farmers at the lowlands.

Arabica coffee

Low altitude

Rust (programming language)

10.31219/osf.io/gdr5v

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Spatial Patterns of Fusarium Head Blight in New York Wheat Fields Suggest Role of Airborne Inoculum

Plant Health Progress (2003)

Emerson M. Del Ponte D. A. Shah Gary C. Bergstrom

The spatial pattern of Fusarium head blight (FHB) incidence was studied in 70 winter wheat fields in New York over a period of 3 years. Incidence of FHB was randomly distributed among 60 sampling areas in 64 of the 70 fields. Fields with random FHB ranged from 0.05 to 23% in average incidence of FHB and followed bean, cabbage, corn, oat, pea, sorghum, and soybean. There was strong evidence of aggregation in FHB only in three fields that had large concentrations of corn debris. Many fields had small, scattered fragments of corn debris in evidence from a corn crop two or more years prior to wheat. The lack of aggregation in FHB and low incidences of FHB in these fields suggests that weathered corn debris contributed relatively little within-field inoculum for FHB. Based on the predominantly random patterns of FHB, disease in rotational wheat fields of New York appears to be initiated primarily by deposition of spores from diffuse atmospheric populations of G. zeae. We hypothesize that these airborne spores may originate largely from inoculum sources external to wheat fields. Over-wintered corn residue, especially from the preceding crop season, on the soil surface is the most likely potential source of regional atmospheric inoculum for FHB in New York. Accepted for publication 10 March 2003. Published 18 April 2003.

Growing season

10.1094/php-2003-0418-01-rs

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Openness and Computational Reproducibility in Plant Pathology: Where we Stand and a Way Forward

Adam Sparks Emerson M. Del Ponte Kaique S. Alves Zachary Foster Niklaus J. Grünwald

Openness and computational reproducibility in plant pathology: where do we stand and a way forward. Abstract Open research practices have been highlighted extensively during the last ten years in many fields of scientific study as essential standards needed to promote transparency and reproducibility of scientific results. Scientific claims can only be evaluated based on how protocols, materials, equipment and methods were described; data were collected and prepared; and analyzes were conducted. Openly sharing protocols, data and computational code is central for current scholarly dissemination and communication, but in many fields, including plant pathology, adoption of these practices has been slow. We randomly selected 450 articles published from 2012 to 2021 across 21 journals representative of the plant pathology discipline and assigned them scores reflecting their openness and computational reproducibility. We found that most of the articles were not following protocols for open science and were failing to share data or code in a reproducible way. We also propose that use of open-source tools facilitates computationally reproducible work and analyzes benefitting not just readers, but the authors as well. Finally, we also provide ideas and tools to promote open, reproducible computational research practices among plant pathologists. Open preprint This article is a preprint and has not been peer reviewed

Openness to experience

Preprint

Open Science

Best practice

10.31220/agrirxiv.2021.00082

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Citations (1)

Web-Based System to True-Forecast Disease Epidemics — Case Study for Fusarium Head Blight of Wheat

Springer eBooks (2007)

J. M. C. Fernandes Emerson M. Del Ponte Willingthon Pavan G. R. da Cunha

Presumption

Plant disease

10.1007/978-3-540-44650-7_25

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Incidence-severity relationships in non-treated and fungicide-treated wheat head blast epidemics in Brazil

Gustavo Bilíbio dos Santos Maurício Antônio de Oliveira Coelho Emerson M. Del Ponte

The relationship between wheat head blast incidence (I; proportion of diseased heads in a sample) and severity (S; the average diseased area in a sample of heads) was studied with the aim of determining whether severity could be reliably predicted from incidence. Data were collected from two main sources: a) the EPAMIG (non-treated) field experiments spanning seven years (2013-2019 with three cultivars) designed to evaluate the effect of planting dates on wheat blast (no fungicide use); and b) the UFTs (fungicide-treated) field experiments conducted by researchers of the network of uniform fungicide trials conducted during nine years (2012-2020) across 10 locations (totaling 14 cultivars). An ordinary linear regression model fitted to the complementary log-log transformation of the data provided a good fit to the data based on the square correlation of the predicted Ŝ, and the observed S (R2): The R2 was 0.95 for the pooled (all years) non-treated dataset and 0.88 for the pooled fungicide-treated dataset. A covariance analysis indicated that year, but not cultivar, significantly affected the parameters of the I-S relationship in the non-treated dataset. We conclude that wheat head blast S can be predicted from I but more reliably in non-treated epidemics given the larger influence of chemical treatments on the relationship than cultivar or year, a surrogate for varying weather.

Winter wheat

Field trial

10.31219/osf.io/jhtmv

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Recent co-evolution of two pandemic plant diseases in a multi-hybrid swarm

Nature Ecology & Evolution (2023)

Mostafa Rahnama Bradford Condon João Paulo Ascari Julian R. Dupuis Emerson M. Del Ponte

Abstract Most plant pathogens exhibit host specificity but when former barriers to infection break down, new diseases can rapidly emerge. For a number of fungal diseases, there is increasing evidence that hybridization plays a major role in driving host jumps. However, the relative contributions of existing variation versus new mutations in adapting to new host(s) is unclear. Here we reconstruct the evolutionary history of two recently emerged populations of the fungus Pyricularia oryzae that are responsible for two new plant diseases: wheat blast and grey leaf spot of ryegrasses. We provide evidence that wheat blast/grey leaf spot evolved through two distinct mating episodes: the first occurred ~60 years ago, when a fungal individual adapted to Eleusine mated with another individual from Urochloa . Then, about 10 years later, a single progeny from this cross underwent a series of matings with a small number of individuals from three additional host-specialized populations. These matings introduced non-functional alleles of two key host-specificity factors, whose recombination in a multi-hybrid swarm probably facilitated the host jump. We show that very few mutations have arisen since the founding event and a majority are private to individual isolates. Thus, adaptation to the wheat or Lolium hosts appears to have been instantaneous, and driven entirely by selection on repartitioned standing variation, with no obvious role for newly formed mutations.

Pyricularia

10.1038/s41559-023-02237-z

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Taxonomic and pathogenic diversity of the blast pathogen populations infecting wheat and grasses in Minas Gerais

João Paulo Ascari Emerson M. Del Ponte

The blast disease of Poaceae is caused by a large species complex, among which P. oryzae is composed of several host-specialized lineages. The Pyricularia oryzae Triticum pathotype (PoT) causes the blast disease in wheat, but is also capable of infecting other grasses, which may serve as an inoculum reservoir for epidemics in wheat. In Brazil, severe wheat blast epidemics are most common in the Cerrado region. The dominant hypothesis is that signal grass (Urochloa sp.) and other gramineous plants harbor the wheat blast pathogen, thus serving as a major reservoir of inoculum for epidemics in wheat. A two-year survey of the Pyricularia blast pathogens was conducted in both wheat and non-wheat areas as well as prior (February) and during (May) the wheat growing season in Minas Gerais. A total of 1,368 plant samples representative of 31 Poaceae species, including wheat, were collected and inspected for the presence of blast symptoms. During the isolations, 932 isolates were obtained, being one fourth obtained from gramineous plants. A subset of 572 isolates was selected for identification at the species level based on portions of the CH7-BAC9 gene sequences. Most of the isolates (n = 494) were P. oryzae, within which 68% were PoT and 32% non-PoT based on two PCR assays targeting (MoT3 and C17 PCR assays). The PoT lineage was found predominantly (97%) in wheat and rarely in the other hosts, even nearby wheat fields (2.1%), as well as at longer distances from wheat regions (0.1%). The blast pathogen population isolated from signal grass grouped in different clades from PoT, and therefore referred to Urochloa lineage (PoU). A series of cross-inoculation greenhouse experiments was conducted using wheat (cv. BRS Guamirim and BR 18-Terena) and signal grass (cv. Marandu) as host and 14 PoT and six PoU isolates as pathogen factor. In the first leaf-inoculation experiment, results showed a significant interaction between host and pathogen; PoT was strongly/weakly aggressive towards wheat/signal grass and PoU was strongly/weakly aggressive towards signal grass/wheat. In inoculated wheat heads, PoT was more aggressive (>91% infected spikelets) than PoU (52% infected spikelets). In a third experiment, four signal grass cultivars (Marandu, Basilisk, Piatã, and Xaraés) were inoculated with the same set of 20 isolates. Similarly, signal grass cultivars were generally more susceptible to PoU than PoT. Severity induced by PoU was twice (7.7% severity) as high as PoT (3.8%) and so was the number of conidia/leaf produced by PoU (47,500) and PoT (23,200). Two groups of signal grass cultivars were formed, the most susceptible composed of Marandu and Basilisk and the least susceptible composed of Piatã and Xaraés. Results of our study confirm the host-specialization and the shaping of the blast populations according to the host. We further suggest that grasses in general, especially signal grass, may not play a major role as an inoculum reservoir for PoT, as it harbors mainly the PoU population. However, due to the large extent of pasture-growing regions and cross-infection ability in wheat, signal grass may harbor amounts of PoT inoculum that are sufficient for initiating leaf and head blast epidemics in wheat blast in Minas Gerais state.

Pyricularia

Blast disease

10.31219/osf.io/ydqsz

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Citations (2)