Large-scale genomic analyses with machine learning uncover predictive patterns associated with fungal phytopathogenic lifestyles and traits

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: Oct. 11, 2023

Invasive plant pathogenic fungi have a global impact, with devastating economic and environmental effects on crops forests. Biosurveillance, critical component of threat mitigation, requires risk prediction based fungal lifestyles traits. Recent studies revealed distinct genomic patterns associated specific groups fungi. We sought to establish whether these phytopathogenic hold across diverse taxonomic ecological from the Ascomycota Basidiomycota, furthermore, if those can be used in predictive capacity for biosurveillance. Using supervised machine learning approach that integrates phylogenetic data, we analyzed 387 genomes test proof-of-concept use signatures predicting traits during biosurveillance activities. Our feature sets were derived genome annotation data carbohydrate-active enzymes (CAZymes), peptidases, secondary metabolite clusters (SMCs), transporters, transcription factors. found could successfully predict groups, best performance coming comprising CAZyme, peptidase, SMC data. While phylogeny was an important most predictions, inclusion improved every lifestyle trait tested. Plant pathogenicity one best-predicted traits, showing promise genomics applications. Furthermore, our expansions number genes CAZyme peptidase families pathogens compared non-phytopathogenic (saprotrophs, endo- ectomycorrhizal fungi). Such profiles give insight into evolution phytopathogenicity useful risks unknown future

Language: Английский

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High‐resolution biomonitoring of plant pathogens and plant species using metabarcoding of pollen pellet contents collected from a honey bee hive

Environmental DNA, Journal Year: 2019, Volume and Issue: 1(2), P. 155 - 175

Published: June 19, 2019

Abstract The Canadian beekeeping industry is spread across the country, with greatest proportion of managed honey bee colonies occurring in Prairie Provinces. Nationally, number beekeepers has recently been trending upwards. Simultaneously, agronomic and environmental plant pest incidents are increasing due to a factors, including introduction exotic organisms through international trade, which major pathway for potentially invasive alien species quarantine pests. Therefore, regulatory agencies interested developing high‐throughput tools achieve earlier detection unwanted order expedite application mitigating measures limit impacts their introduction. This study evaluates potential pollen pellet contents collected by bees monitor pests using metabarcoding, sequencing (HTS) approach monitoring complex samples. used ITS1 intergenic region target oomycetes fungi, ATP9‐NAD9 spacer specifically Phytophthora species, ITS2 species. From HTS results, plants that were detected corresponded known hosts certain pathogens or closely related Genera phytopathogenic found samples comprised Fusarium sp., Ophiostoma Peronospora Pythium sp. Correlations, high entropy, co‐occurrences between fungi observed. bee‐collected pellets phytopathogens given environment demonstrated here, this concept could represent promising complementary tool surveillance previously described air insect sampling methods if protocol was applied additional genetic markers.

Language: Английский

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Genome‐scale phylogeography resolves the native population structure of the Asian longhorned beetle, Anoplophora glabripennis (Motschulsky)

Evolutionary Applications, Journal Year: 2022, Volume and Issue: 15(6), P. 934 - 953

Published: April 11, 2022

Human-assisted movement has allowed the Asian longhorned beetle (ALB, Anoplophora glabripennis (Motschulsky)) to spread beyond its native range and become a globally regulated invasive pest. Within of China Korean peninsula, human-mediated dispersal also caused cryptic translocation insects, resulting in population structure complexity. Previous studies used genetic methods detangle this complexity but were unable clearly delimit populations which is needed develop downstream biosurveillance tools. We genome-wide markers define historical ALB contemporary between regions. genotyping-by-sequencing generate 6102 single-nucleotide polymorphisms (SNPs) amplicon sequencing genotype 53 microsatellites. In total, we genotyped 712 individuals from ALB's distribution. observed six distinct clusters among populations, with clear delineation northern southern groups. Most South Korea China. Our results indicate divergence suggest limited large-scale admixture, did identify restricted number cases identified SNPs under selection describe clinal allele frequency pattern missense variant associated glycerol kinase, an important enzyme utilization insect cryoprotectant. further demonstrate that small numbers can assign geographic regions high probability, paving way for novel

Language: Английский

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Meta-Omics Tools in the World of Insect-Microorganism Interactions

Biology, Journal Year: 2018, Volume and Issue: 7(4), P. 50 - 50

Published: Nov. 27, 2018

Microorganisms are able to influence several aspects of insects’ life, and this statement is gaining increasing strength, as research demonstrates it daily. At the same time, new sequencing technologies now available at a lower cost per base, bioinformatic procedures becoming more user-friendly. This triggering huge effort in studying microbial diversity associated insects, especially economically important insect pests. The importance microbiome has been widely acknowledged for wide range animals, also insects topic considerable importance. In addition bacterial-associates, insect-associated fungal communities attention, those including plant pathogens. use meta-omics tools not restricted description world, but can be used bio-surveillance, food safety assessment, or even bring novelties industry. mini-review aims give overview how fostering advances on insect-microorganism interactions.

Language: Английский

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Capacity of United States federal government and its partners to rapidly and accurately report the identity (taxonomy) of non-native organisms intercepted in early detection programs

Biological Invasions, Journal Year: 2019, Volume and Issue: 22(1), P. 101 - 127

Published: Dec. 31, 2019

Abstract The early detection of and rapid response to invasive species (EDRR) depends on accurate identification non-native species. 2016–2018 National Invasive Species Council Management Plan called for an assessment US government (federal) capacity report the identity organisms intercepted through programs. This paper serves as that action item. Here we summarize survey-based findings make recommendations improving federal government’s identify authoritatively in a timely manner. We conclude with improve within context EDRR by increasing coordination, maintaining taxonomic expertise, creating tools clearinghouse, developing using standards naming protocols, expanding content DNA Barcode libraries, ensuring long-term sustainability biological collections, engaging empowering citizens citizen science groups.

Language: Английский

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In Situ Processing and Efficient Environmental Detection (iSPEED) of tree pests and pathogens using point-of-use real-time PCR

PLoS ONE, Journal Year: 2020, Volume and Issue: 15(4), P. e0226863 - e0226863

Published: April 2, 2020

Global trade and climate change are responsible for a surge in foreign invasive species emerging pests pathogens across the world. Early detection surveillance activities essential to monitor environment prevent or mitigate future ecosystem impacts. Molecular diagnostics by DNA testing has become an integral part of this process. However, environmental applications, there is need cost-effective efficient point-of-use obtain accurate results from remote sites real-time. This requires development simple fast sample processing extraction, room-temperature stable reagents portable instrument. We developed real-time Polymerase Chain Reaction system using crude buffer-based extraction protocol lyophilized, pre-made, reactions on-site applications. demonstrate use approach with covering broad spectrum known undesirable forest enemies: fungi Sphaerulina musiva, Cronartium ribicola comandrae, oomycete Phytophthora ramorum insect Lymantria dispar. obtained positive identification variety different tissues, including infected leaves, pathogen spores, legs antenna. The assays were yielded no false nor negative. shelf-life lyophilized was confirmed after one year at room temperature. Finally, successful tests conducted thermocyclers disposable instruments suitability method, named Situ Processing Efficient Environmental Detection (iSPEED), field testing. kit fits backpack can be carried locations rapid pathogens.

Language: Английский

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Molecular Identification of Anoplophora glabripennis (Coleoptera: Cerambycidae) From Frass by Loop-Mediated Isothermal Amplification

Journal of Economic Entomology, Journal Year: 2020, Volume and Issue: 113(6), P. 2911 - 2919

Published: Aug. 25, 2020

Abstract Anoplophora glabripennis (Motschulsky, 1853), native to eastern Asia, is a destructive woodborer of many ornamental species, leading the decline and death attacked trees. In outbreak areas as Europe or North America, this pest usually identified using morphological molecular analyses adult larval specimens. However, procedures for collecting A. specimens from infested plants are too expensive time consuming routine screening. A noninvasive diagnostic tool based on frass discrimination therefore crucial rapid identification at different development stages in host. This article describes protocol loop-mediated isothermal amplification (LAMP). DNA extracted was amplified with both visual real-time LAMP compared those nontarget species. The results show that method reliable accurate could be promising phytosanitary surveys.

Language: Английский

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Range‐wide population genomics of the spongy moth, Lymantria dispar (Erebidae): Implications for biosurveillance, subspecies classification and phylogeography of a destructive moth

Evolutionary Applications, Journal Year: 2023, Volume and Issue: 16(3), P. 638 - 656

Published: Jan. 13, 2023

The spongy moth, Lymantria dispar, is an irruptive forest pest native to Eurasia where its range extends from coast and overspills into northern Africa. Accidentally introduced Europe in Massachusetts 1868-1869, it now established North America considered a highly destructive invasive pest. A fine-scale characterization of population genetic structure would facilitate identification source populations for specimens intercepted during ship inspections enable mapping introduction pathways help prevent future incursions novel environments. In addition, detailed knowledge L. dispar's global provide new insight the adequacy current subspecies classification system phylogeographic history. To address these issues, we generated >2000 genotyping-by-sequencing-derived SNPs 1445 contemporary sampled at 65 locations 25 countries/3 continents. Using multiple analytical approaches, identified eight subpopulations that could be further partitioned 28 groups, achieving unprecedented resolution this species' structure. Although reconciliation between groupings three currently recognized proved challenging, our data confirmed circumscription japonica Japan. However, cline observed across continental Eurasia, dispar asiatica East Asia d. Western Europe, points absence sharp geographical boundary (e.g., Ural Mountains) two subspecies, as suggested earlier. Importantly, moths Caucasus/Middle displayed high enough distances other warrant their consideration separate dispar. Finally, contrast with earlier mtDNA-based investigations Caucasus place origin, analyses suggest evolutionary cradle, spread Central Japan through Korea.

Language: Английский

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Important alien and potential native invasive insect pests of key fruit trees in Sub-Saharan Africa: advances in sustainable pre- and post-harvest management approaches

CABI Agriculture and Bioscience, Journal Year: 2022, Volume and Issue: 3(1)

Published: Feb. 12, 2022

Abstract Fruit production in Sub-Saharan Africa is of paramount importance both socially and economically. Millions farmers derive livelihoods from mango, avocado, citrus, cashew, coconut farming, but native alien invasive species constrain The region’s capacity to contain invasives weak due the absence national institutional support systems for early detection, containment, eradication, or management pests. Climate change expected play a huge role influx more shift ecological requirements some species. Though fair share pre-and post-management pest techniques several insect pests has been developed, adoption adaptation options are limited. Data on economic social implications largely lacking, making it challenging implement informed policy decisions. existence “Strategy Managing Invasive Species 2021–2030” promises paradigm invasives, reactive thinking coordinated proactive approaches. uncoordinated deployment measures region lack funding, negative managing effectively. Prospects enhanced future research wide, efforts currently being channeled Area-Wide-Integrated Pest Management bottom-up approach with stakeholders owning process. Participatory development technologies also taking centre stage, paving way increased adaptation. Postharvest promise provide adequate phytosanitary assurance required by countries importing fruit Africa.

Language: Английский

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An Applied Empirical Framework for Invasion Science: Confronting Biological Invasion Through Collaborative Research Aimed at Tool Production

Annals of the Entomological Society of America, Journal Year: 2020, Volume and Issue: 113(4), P. 230 - 245

Published: Feb. 6, 2020

Abstract Global ecosystem functions, services, and commodities are increasingly threatened by biological invasions. As a result, there is an urgent need to manage invasive species through global collaborative research. We propose ‘applied empirical framework’ (AEF) aggressively confront the current invasion crisis. The AEF builds on existing models for science that advocate 1) standardized research designs reveal key aspects of invasion, 2) facilitate sharing resources information. further emphasizes 3) production ‘tools’ (e.g., data, methodologies, technical instruments) designed direct uptake agencies 4) taxonomically targeted approach in which task forces conduct rapid, in-depth top-priority across their entire geographic range. review distinctive roles played different collaborator types. then provide example action BioSAFE initiative (Biosurveillance Alien Forest Enemies), highly project aimed at developing genomic tools biosurveillance intervention forest species. illustrate our two polyphagous insect species: wood-borer Anoplophora glabripennis, Motschusky (Coleoptera: Cerambycidae; Asian longhorned beetle) defoliator Lymantria dispar, Linnaeus spp. (Lepidoptera: Lymantriidae; gypsy moth). These examples how can focus accelerate response crisis applying resource capabilities groups generate management

Language: Английский

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