The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed

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Abstract

Ambrosia artemisiifolia and Ambrosia trifida (Asteraceae) are important pest species and the two greatest sources of aeroallergens globally. Here, we took advantage of a hybrid to simplify genome assembly and present chromosome-level assemblies for both species. These assemblies show high levels of completeness with Benchmarking Universal Single-Copy Ortholog (BUSCO) scores of 94.5% for A. artemisiifolia and 96.1% for A. trifida and long terminal repeat (LTR) Assembly Index values of 26.6 and 23.6, respectively. The genomes were annotated using RNA data identifying 41,642 genes in A. artemisiifolia and 50,203 in A. trifida. More than half of the genome is composed of repetitive elements, with 62% in A. artemisiifolia and 69% in A. trifida. Single copies of herbicide resistance-associated genes PPX2L, HPPD, and ALS were found, while two copies of the EPSPS gene were identified; this latter observation may reveal a possible mechanism of resistance to the herbicide glyphosate. Ten of the 12 main allergenicity genes were also localized, some forming clusters with several copies, especially in A. artemisiifolia. The evolution of genome structure has differed among these two species. The genome of A. trifida has undergone greater rearrangement, possibly the result of chromoplexy. In contrast, the genome of A. artemisiifolia retains a structure that makes the allotetraploidization of the most recent common ancestor of the Heliantheae Alliance the clearest feature of its genome. When compared to other Heliantheae Alliance species, this allowed us to reconstruct the common ancestor's karyotype—a key step for furthering of our understanding of the evolution and diversification of this economically and allergenically important group.

A simulation study comparing common methods for analyzing species–habitat associations of plants

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A simulation study comparing common methods for analyzing species–habitat associations of plants

Our simulation study explored various methodologies for studying species–habitat associations through spatial point pattern analyses. The results indicate that all methods performed equally well, and their performance was mostly influenced by the initial point pattern characteristics. Therefore, we suggest applying the method that is most suitable for the available data.


Abstract

Question

Species-specific habitat associations are one of several processes that lead to a clustered spatial pattern of plant populations. This pattern occurs in tropical and temperate forests. To analyze species–habitat associations, four methods are commonly used when determining species–habitat associations from spatial point pattern and environmental raster data. Two of the methods randomize the spatial point pattern of plants, and two randomize the raster data of habitat patches. However, the strengths and weaknesses of the four methods have never been analyzed in detail.

Methods

We conducted a simulation study to analyze the strengths and weaknesses of the four most used methods. The methods are the gamma test, pattern reconstruction, the torus-translation test and the randomized-habitats procedure. We simulated neutral landscapes representing habitat patches and point patterns representing fine-scale plant distributions. We built into our simulations known positive and negative species–habitat associations.

Results

All four methods were equally good at detecting species–habitat associations. Detected positive associations better than negative ones. Furthermore, correct detections were mostly influenced by the initial spatial distribution of the point patterns, landscape fragmentation and the number of simulated null model randomizations.

Conclusions

The four methods have advantages and disadvantages, and which is the most suitable method largely depends on the characteristics of the available data. However, our simulation study shows that the results are consistent between methods.

Comparative omics analysis for novel target discovery in plant pathogens: A case study for Magnaporthe oryzae

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Comparative omics analysis for novel target discovery in plant pathogens: A case study for Magnaporthe oryzae

A novel strategy, integrating omics and bioinformatics, identifies distinct fungal pathways, revealing a promising target for precision fungicides against Magnaporthe oryzae, causing rice blast disease.


Abstract

The central concern surrounding chemical pesticide application is its potential adverse effects on non-target organisms. For fungal pathogens, the search for specific targets has been complicated by the similarities in pathways shared between these pathogens and humans. We present a comprehensive strategy, integrating comparative omics and bioinformatics, to pinpoint precise targets for fungicides effective against the fungal pathogen Magnaporthe oryzae, responsible for rice blast disease. Our approach involves subtractive metabolic pathways, homology screening and target prioritization. Through subtractive metabolic analysis, we identified three unique M. oryzae pathways, distinct from human and rice. Nonredundant protein sequences were subsequently subjected to BLASTP screening against human and rice, as well as other databases from diverse organisms. Target subcellular localization was predicted using eight tools, including artificial intelligence and a deep-learning method. A comprehensive examination of biological processes was conducted, including gene expression, protein–protein interactions, network enrichment, broad-spectrum activity and physicochemical analysis. Glutamate 5-kinase emerged as the prime candidate for targeted fungicide development, promising progress in precision-oriented solutions.

The length of the 3′ UTR of the tomato torrado virus (ToTV) RNA1 affects virus accumulation in Solanum lycopersicum during mechanical passages from plant to plant

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The length of the 3′ UTR of the tomato torrado virus (ToTV) RNA1 affects virus accumulation in Solanum lycopersicum during mechanical passages from plant to plant

ToTV-Kra defective genomes with truncated 3′ untranslated region of RNA1 are infectious. Changes in RNA1 length affect viral replication and sap transmission and may have arisen spontaneously or as an adaptation to the mode of viral transmission.


Abstract

Tomato torrado virus (ToTV), a member of the Torradovirus genus, primarily infects tomatoes. Previous analyses revealed high heterogeneity in the 3′ untranslated region (3′ UTR) of RNA1 of isolate ToTV-Kra. In addition to the full-length 3′ UTR RNA1 (a wild-type, wt), four truncated versions (var2, var3, var4 and var5) were identified. Here, we investigated the biological importance of this phenomenon by assessing whether such defective genomes are infectious individually, and how the length of the 3′ UTR influences disease symptoms, virus transmission and viral RNA accumulation. Using the ToTVpJL-Kra infectious clone, we introduced deletions corresponding to the known RNA1 defective variants and examined their impact on ToTV virulence and sap transmission ability. Viral RNA accumulation was assessed in agroinfiltrated tomatoes, as well as during serial passages. We found that all defective genomes were infectious and the length of the 3′ UTR of RNA1 influenced viral RNA accumulation. Tomatoes agroinfiltrated with var2, var3 or var5 showed the highest copy numbers of genomic RNAs. However, during serial passages, ToTVpJL-Kra-var1 and -var2 (six nucleotides shorter) showed limited sap transmission ability compared to the other variants, which persisted and replicated well in tomatoes. Plants treated with ToTVpJL-Kra-var3, -var4 and a mixture of var1–var5 showed the highest viral RNA accumulation, which was not associated with increased symptom severity in comparison to the other variants. Additionally, we identified a further sequence insertion in the 3′ UTR of var3 RNA1. This insertion could have occurred spontaneously or as a result of virus adaptation to the mode of transmission.

The coffee leaf rust pandemic: An ever‐present danger to coffee production

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The coffee leaf rust pandemic: An ever-present danger to coffee production

The history of the fungal disease coffee leaf rust is highlighted along with recent epidemics and future scenarios. Possible causes of these outbreaks are also examined.


Abstract

Coffee leaf rust (CLR) is caused by the biotrophic pathogenic fungus Hemileia vastatrix. Despite being the most researched coffee disease, mysteries still exist relating to its epidemiology and biology. The objective of this work is to highlight past and present events concerning this prominent coffee disease. We start with an historical overview of the homeland of Coffea arabica, the Afromontane forest of south-west Ethiopia, and then follow its journey across the globe linked to colonial trade and power struggles. We report the relevance of CLR to coffee production today, with a focus on the Americas and summarize unproven hypotheses in relation to the cause of recent epidemics. We present an original hypothesis concerning the first major outbreak occurring in 1869 in Ceylon (Sri Lanka), based on geopolitical connections to global trade. We review old and new options for management of the disease. The likelihood of a yet undetected alternate host of H. vastatrix is also considered as an additional piece of the epidemiological puzzle. Finally, we reflect on the interactions between H. vastatrix and a changing climate. By better understanding past events, linked to CLR, we may be better prepared for future outbreaks.

Sensitivity of dominant UK Phytophthora infestans genotypes to a range of fungicide active ingredients

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Sensitivity of dominant UK Phytophthora infestans genotypes to a range of fungicide active ingredients

Dominant UK Phytophthora infestans genotypes (EU6, EU36 and EU37) were tested for sensitivity to seven fungicide active ingredients (2019–22). EU37 isolates were insensitive to fluazinam; no insensitivity to other fungicides was found.


Abstract

Late blight, caused by Phytophthora infestans, is a serious disease of potatoes worldwide and is predominantly controlled by repeated prophylactic use of fungicides throughout the growing season. Effective blight management and integrated pest management strategies rely on knowledge of the efficacy of available fungicides to control contemporary genotypes of P. infestans. Between 2019 and 2022, representative isolates of the newer dominant genotypes EU36, EU37 and the older dominant genotype EU6 were sampled from GB crops and tested for sensitivity to seven commonly used fungicide active ingredients (cyazofamid, fluopicolide, mandipropamid, propamocarb, oxathiapiprolin, amisulbrom and mancozeb) used preventatively in detached leaf tests and zoospore motility assays where appropriate. Dose–response curves based on lesion area (mm2) were constructed, and EC50 values calculated. Isolates of P. infestans genotype EU37 were insensitive to fluazinam as previously reported. No insensitivity, or progression towards resistance over time, to any of the other fungicides was observed in any isolates of the genotypes tested, and EC50 values were generally in line with previous testing. Zoospore motility tests with fluopicolide revealed significantly higher MIC values for isolates of genotype EU36 compared with EU37 and EU6, which, whilst not indicative of resistance at the low concentrations of active ingredient tested, may be a factor contributing to the overall dominance of that genotype in the wider population of P. infestans. The evidence suggests that the fungicides tested, with the exception of fluazinam and EU37, are effective for the control of P. infestans genotypes dominant in the GB population up until 2022.

An emergent plant‐parasitic nematode in Brazil: Aphelenchoides besseyi. Current status and research perspectives

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An emergent plant-parasitic nematode in Brazil: Aphelenchoides besseyi. Current status and research perspectives

We review the biology, life cycle, host range and management solutions of an emergent pathogen in Brazil, all in the context of the landmark events leading to the rise of Aphelenchoides besseyi (Created using Biorender).


Abstract

Aphelenchoides besseyi is an emerging and yet overlooked plant parasite of many economically important crops, including cotton, soybean and common bean. It presents an economic risk to these crops in several countries, notably in Brazil. Although first reported infecting strawberries in the United States as early as 1942, it was only identified to be the causal agent of green stem and foliar retention (GSFR) disease in Brazil in 2017. Currently, there are no chemical nematicides registered in Brazil against A. besseyi, and no known sources of genetic resistance. Here, we review the biology of A. besseyi, its spread across Brazil, its relevance to the country's current and future agriculture and the limited control measures. We describe control measures that have been successfully used to manage infestations of other plant-parasitic nematodes and could potentially be extended to use in the control of A. besseyi. We also review and discuss potential future control measures, such as RNA interference and genome editing, for the development of crops with enhanced resistance to A. besseyi.

Geographic distribution, host preference and phylogenetic relationships among Pyricularia species inciting millet and rice blast disease in India

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Geographic distribution, host preference and phylogenetic relationships among Pyricularia species inciting millet and rice blast disease in India

The study explores the diversity, host preferences and phylogeny of Pyricularia strains found in rice and millets in India.


Abstract

Blast disease causes significant damage to millets (pearl millet, finger millet and foxtail millet) and rice in India. This study investigates strains of Pyricularia, the causal agent of blast disease, in rice and millets in India in terms of their diversity, host preferences and phylogeny. One hundred and thirty-six Pyricularia isolates causing rice and millet blast were collected from 46 locations in India. They displayed morphological diversity irrespective of host or location. All Pyricularia isolates were separated into two major clusters by a multilocus sequence-based phylogenetic tree, which also demonstrated that most isolates are grouped according to their host associations. In contrast, a few finger millet isolates were found to be grouped with foxtail millet isolates. We explored how Pyricularia isolates behaved when exposed to rice and millets. Finger millet isolates were shown to be pathogenic on a wide variety of millets, whereas rice isolates were only found to infect rice and wheat. The majority of the blast isolates of millets were shown to be pathogenic on common weed species of the millet ecosystem, such as Echinochloa crusgalli, Eleusina indica and Erogrotis gagantica. Our findings emphasize the importance of pathogen surveillance in both cultivated crops and weed hosts, as well as the possible risk of blast fungus infection in Indian millets due to host expansion. Blast disease control programmes in India will be greatly enhanced by the knowledge gained in this study on the diversity and host association of Pyricularia strains.