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

Open research practices have been highlighted extensively during the last 10 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 analyses were conducted. Openly sharing protocols, data, and computational code is central to 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 did not follow protocols for open science and failed to share data or code in a reproducible way. We propose that use of open-source tools facilitates computationally reproducible work and analyses, benefitting not just readers but the authors as well. Finally, we provide ideas and suggest tools to promote open, reproducible computational research practices among plant pathologists. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Timing of Triazole-Based Spray Schedules for Managing Mungbean Powdery Mildew in Australia: A Meta-Analysis.

Powdery mildew (PM), caused by two fungal species, Podosphaera xanthii and Erysiphe vignae, is a yield-limiting foliar disease commonly found in mungbean (Vigna radiata) cropping areas of the eastern region of Australia. Effective control of the disease relies largely on fungicide applications, mainly of the triazole group. Uncertainty in the current fungicide spray schedule recommendations, which advise commencing with a spray at the first signs of PM, prompted this study to evaluate PM severity and crop yield data obtained from fungicide trials, which also tested spray schedules starting before (early) or after (late) first signs, applied singly or combined with a follow-up spray. A meta-analytic approach was used to obtain mean differences of the PM severity and crop yield between plots sprayed with specific triazole-based spray schedules and nontreated plots. From 26 trials, 14 trials and 15 trials met the criteria for inclusion in PM severity and yield analyses, respectively. The schedule with the first spray starting at first sign, with a follow-up spray 14 days later, resulted in significantly lower disease severity compared with all other schedules. However, the yield protected was only numerically higher and not statistically different compared with single-spray at first sign, single-spray late, or two-spray starting late. PM severity and yield in the early sprayed plots did not differ from the nontreated plots. These findings support the current recommendations and provide additional evidence that yields are still protected when delaying the first spray up to a week after disease onset. They also suggest that additional sprays may not always be necessary, thus reducing direct fungicide costs, indirect costs related to fungicide insensitivity, and potential adverse effects to the environment.

Whole-Genome Data from Curtobacterium flaccumfaciens pv. flaccumfaciens Strains Associated with Tan Spot of Mungbean and Soybean Reveal Diverse Plasmid Profiles.

Despite the substantial economic impact of Curtobacterium flaccumfaciens pv. flaccumfaciens on legume production worldwide, the genetic basis of its pathogenicity and potential host association is poorly understood. The production of high-quality reference genome assemblies of C. flaccumfaciens pv. flaccumfaciens strains associated with different hosts sheds light on the genetic basis of its pathogenic variability and host association. Moreover, the study of recent outbreaks of bacterial wilt and microevolution of the pathogen in Australia requires access to high-quality reference genomes that are sufficiently closely related to the population being studied within Australia. We provide the first genome assemblies of C. flaccumfaciens pv. flaccumfaciens strains associated with mungbean and soybean, which revealed high variability in their plasmid composition. The analysis of C. flaccumfaciens pv. flaccumfaciens genomes revealed an extensive suite of carbohydrate-active enzymes potentially associated with pathogenicity, including four carbohydrate esterases, 50 glycoside hydrolases, 23 glycosyl transferases, and a polysaccharide lyase. We also identified 11 serine peptidases, three of which were located within a linear plasmid, pCff119. These high-quality assemblies and annotations will provide a foundation for population genomics studies of C. flaccumfaciens pv. flaccumfaciens in Australia and for answering fundamental questions regarding pathogenicity factors and adaptation of C. flaccumfaciens pv. flaccumfaciens to various hosts worldwide and, at a broader scale, contribute to unraveling genomic features of gram-positive, xylem-inhabiting bacterial pathogens.[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.

The skin crawls, the stomach turns: ectoparasites and pathogens elicit distinct defensive responses in humans.

Disgust has long been viewed as a primary motivator of defensive responses to threats posed by both microscopic pathogens and macroscopic ectoparasites. Although disgust can defend effectively against pathogens encountered through ingestion or incidental contact, it offers limited protection against ectoparasites, which actively pursue a host and attach to its surface. Humans might, therefore, possess a distinct ectoparasite defence system-including cutaneous sensory mechanisms and grooming behaviours-functionally suited to guard the body's surface. In two US studies and one in China, participants (N = 1079) viewed a range of ectoparasite- and pathogen-relevant video stimuli and reported their feelings, physiological sensations, and behavioural motivations. Participants reported more surface-guarding responses towards ectoparasite stimuli than towards pathogen stimuli, and more ingestion/contamination-reduction responses towards pathogen stimuli than towards ectoparasite stimuli. Like other species, humans appear to possess evolved psychobehavioural ectoparasite defence mechanisms that are distinct from pathogen defence mechanisms.

Semi-automated measurement of vascular tortuosity and its implications for mechanical thrombectomy performance.

PURPOSE: Few studies have examined the geometry of endovascular mechanical thrombectomy pathways. Here we examine the tortuosity and angulations of catheter pathways from the aortic arch to the termination of the internal carotid artery (ICA) and its association with thrombectomy performance. METHODS: We included 100 consecutive anterior circulation large vessel occlusion thrombectomy patients over 12 months. Computed tomography angiograms (CTA) were used for 3D segmentation of catheter pathway from the aortic arch to ICA termination. Tortuosity index (TI) and angulations of the catheter pathway were measured in a semi-automated fashion. TI and angulation degree were compared between sides and correlated with age and procedural measures. RESULTS: We analyzed 188 catheter pathways in 100 patients. Severe angulation (≤ 30°) was present in 5.8% and 39.4% of common carotid artery (CCA) and extracranial ICA segments, respectively. Five pathways (2.6%) had 360° loop. CCA and extracranial ICA tortuosity had a weak but significant correlation with age (r = 0.17, 0.21, p value = 0.05, 0.02 respectively), time from groin puncture to the site of occlusion (r = 0.29, 0.25, p values = 0.008, 0.026 respectively), and fluoroscopy time (r = 0.022, 0.31, p values = 0.016, 0.001 respectively). There was a significant difference in the pattern of angulation (p value = 0.04) and tortuosity between right and left side in CCA segment (TI = 0.20 ± 0.086 vs. 0.15 ± 0.82, p value < 0.001). CONCLUSIONS: There was a significant difference in CCA angulation between right and left sides. TI of extracranial CCA and ICA correlated with age and influenced time from groin puncture to the occlusion site and total fluoroscopy time.

Fungal diversity notes 1387-1511: taxonomic and phylogenetic contributions on genera and species of fungal taxa.

This article is the 13th contribution in the Fungal Diversity Notes series, wherein 125 taxa from four phyla, ten classes, 31 orders, 69 families, 92 genera and three genera incertae sedis are treated, demonstrating worldwide and geographic distribution. Fungal taxa described and illustrated in the present study include three new genera, 69 new species, one new combination, one reference specimen and 51 new records on new hosts and new geographical distributions. Three new genera, Cylindrotorula (Torulaceae), Scolecoleotia (Leotiales genus incertae sedis) and Xenovaginatispora (Lindomycetaceae) are introduced based on distinct phylogenetic lineages and unique morphologies. Newly described species are Aspergillus lannaensis, Cercophora dulciaquae, Cladophialophora aquatica, Coprinellus punjabensis, Cortinarius alutarius, C. mammillatus, C. quercoflocculosus, Coryneum fagi, Cruentomycena uttarakhandina, Cryptocoryneum rosae, Cyathus uniperidiolus, Cylindrotorula indica, Diaporthe chamaeropicola, Didymella azollae, Diplodia alanphillipsii, Dothiora coronicola, Efibula rodriguezarmasiae, Erysiphe salicicola, Fusarium queenslandicum, Geastrum gorgonicum, G. hansagiense, Helicosporium sexualis, Helminthosporium chiangraiensis, Hongkongmyces kokensis, Hydrophilomyces hydraenae, Hygrocybe boertmannii, Hyphoderma australosetigerum, Hyphodontia yunnanensis, Khaleijomyces umikazeana, Laboulbenia divisa, Laboulbenia triarthronis, Laccaria populina, Lactarius pallidozonarius, Lepidosphaeria strobelii, Longipedicellata megafusiformis, Lophiotrema lincangensis, Marasmius benghalensis, M. jinfoshanensis, M. subtropicus, Mariannaea camelliae, Melanographium smilaxii, Microbotryum polycnemoides, Mimeomyces digitatus, Minutisphaera thailandensis, Mortierella solitaria, Mucor harpali, Nigrograna jinghongensis, Odontia huanrenensis, O. parvispina, Paraconiothyrium ajrekarii, Parafuscosporella niloticus, Phaeocytostroma yomensis, Phaeoisaria synnematicus, Phanerochaete hainanensis, Pleopunctum thailandicum, Pleurotheciella dimorphospora, Pseudochaetosphaeronema chiangraiense, Pseudodactylaria albicolonia, Rhexoacrodictys nigrospora, Russula paravioleipes, Scolecoleotia eriocamporesi, Seriascoma honghense, Synandromyces makranczyi, Thyridaria aureobrunnea, Torula lancangjiangensis, Tubeufia longihelicospora, Wicklowia fusiformispora, Xenovaginatispora phichaiensis and Xylaria apiospora. One new combination, Pseudobactrodesmium stilboideus is proposed. A reference specimen of Comoclathris permunda is designated. New host or distribution records are provided for Acrocalymma fici, Aliquandostipite khaoyaiensis, Camarosporidiella laburni, Canalisporium caribense, Chaetoscutula juniperi, Chlorophyllum demangei, C. globosum, C. hortense, Cladophialophora abundans, Dendryphion hydei, Diaporthe foeniculina, D. pseudophoenicicola, D. pyracanthae, Dictyosporium pandanicola, Dyfrolomyces distoseptatus, Ernakulamia tanakae, Eutypa flavovirens, E. lata, Favolus septatus, Fusarium atrovinosum, F. clavum, Helicosporium luteosporum, Hermatomyces nabanheensis, Hermatomyces sphaericoides, Longipedicellata aquatica, Lophiostoma caudata, L. clematidis-vitalbae, Lophiotrema hydei, L. neoarundinaria, Marasmiellus palmivorus, Megacapitula villosa, Micropsalliota globocystis, M. gracilis, Montagnula thailandica, Neohelicosporium irregulare, N. parisporum, Paradictyoarthrinium diffractum, Phaeoisaria aquatica, Poaceascoma taiwanense, Saproamanita manicata, Spegazzinia camelliae, Submersispora variabilis, Thyronectria caudata, T. mackenziei, Tubeufia chiangmaiensis, T. roseohelicospora, Vaginatispora nypae, Wicklowia submersa, Xanthagaricus necopinatus and Xylaria haemorrhoidalis. The data presented herein are based on morphological examination of fresh specimens, coupled with analysis of phylogenetic sequence data to better integrate taxa into appropriate taxonomic ranks and infer their evolutionary relationships.

Draft Genome Resource for Macrophomina phaseolina Associated With Charcoal Rot in Sorghum.

Macrophomina phaseolina is a soil-borne phytopathogenic fungus that causes charcoal rot in several plant species, including sorghum. We constructed a draft genome of M. phaseolina isolate BRIP 70780a from sorghum, using long-read native DNA from MinION sequencing, which was error-corrected using short-read Illumina MiSeq reads. The draft genome, consisting of 22 contigs with an N50 of 4,257,441 bp, 99.3% complete benchmarking universal single-copy orthologs, and 14,471 genes, is a valuable resource to aid future studies in population genomics and molecular diagnostic marker development for rapid detection of the pathogen.

Feelings of obligation are valuations of signaling-mediated social payoffs.

We extend Tomasello's framework by addressing the functional challenge of obligation. If the long-run social consequences of a decision are sufficiently costly, obligation motivates the actor to forgo potential immediate benefits in favor of long-term social interests. Thus, obligation psychology balances the downstream socially-mediated payoffs from a decision. This perspective can predict when and why obligation will be experienced.

hagis, an R Package Resource for Pathotype Analysis of Phytophthora sojae Populations Causing Stem and Root Rot of Soybean.

Phytophthora sojae is a significant pathogen of soybean worldwide. Pathotype surveys for Phytophthora sojae are conducted to monitor resistance gene efficacy and determine if new resistance genes are needed. Valuable measurements for pathotype analysis include the distribution of susceptible reactions, pathotype complexity, pathotype frequency, and diversity indices for pathotype distributions. Previously the Habgood-Gilmour Spreadsheet (HaGiS), written in Microsoft Excel, was used for data analysis. However, the growing popularity of the R programming language in plant pathology and desire for reproducible research made HaGiS a prime candidate for conversion into an R package. Here we report on the development and use of an R package, hagis, that can be used to produce all outputs from the HaGiS Excel sheet for P. sojae or other gene-for-gene pathosystem studies.

State-dependent risk-taking.

Who takes risks, and when? The relative state model proposes two non-independent selection pressures governing risk-taking: need-based and ability-based. The need-based account suggests that actors take risks when they cannot reach target states with low-risk options (consistent with risk-sensitivity theory). The ability-based account suggests that actors engage in risk-taking when they possess traits or abilities that increase the expected value of risk-taking (by increasing the probability of success, enhancing payoffs for success or buffering against failure). Adaptive risk-taking involves integrating both considerations. Risk-takers compute the expected value of risk-taking based on their state-the interaction of embodied capital relative to one's situation, to the same individual in other circumstances or to other individuals. We provide mathematical support for this dual pathway model, and show that it can predict who will take the most risks and when (e.g. when risk-taking will be performed by those in good, poor, intermediate or extreme state only). Results confirm and elaborate on the initial verbal model of state-dependent risk-taking: selection favours agents who calibrate risk-taking based on implicit computations of condition and/or competitive (dis)advantage, which in turn drives patterned individual differences in risk-taking behaviour.

The Relative State Model: Integrating Need-Based and Ability-Based Pathways to Risk-Taking.

Who takes risks, and why? Does risk-taking in one context predict risk-taking in other contexts? We seek to address these questions by considering two non-independent pathways to risk: need-based and ability-based. The need-based pathway suggests that risk-taking is a product of competitive disadvantage consistent with risk-sensitivity theory. The ability-based pathway suggests that people engage in risk-taking when they possess abilities or traits that increase the probability of successful risk-taking, the expected value of the risky behavior itself, and/or have signaling value. We provide a conceptual model of decision-making under risk-the relative state model-that integrates both pathways and explicates how situational and embodied factors influence the estimated costs and benefits of risk-taking in different contexts. This model may help to reconcile long-standing disagreements and issues regarding the etiology of risk-taking, such as the domain-generality versus domain-specificity of risk or differential engagement in antisocial and non-antisocial risk-taking.

Climate change may have limited effect on global risk of potato late blight.

Weather affects the severity of many plant diseases, and climate change is likely to alter the patterns of crop disease severity. Evaluating possible future patterns can help focus crop breeding and disease management research. We examined the global effect of climate change on potato late blight, the disease that caused the Irish potato famine and still is a common potato disease around the world. We used a metamodel and considered three global climate models for the A2 greenhouse gas emission scenario for three 20-year time-slices: 2000-2019, 2040-2059 and 2080-2099. In addition to global analyses, five regions were evaluated where potato is an important crop: the Andean Highlands, Indo-Gangetic Plain and Himalayan Highlands, Southeast Asian Highlands, Ethiopian Highlands, and Lake Kivu Highlands in Sub-Saharan Africa. We found that the average global risk of potato late blight increases initially, when compared with historic climate data, and then declines as planting dates shift to cooler seasons. Risk in the agro-ecosystems analyzed, varied from a large increase in risk in the Lake Kivu Highlands in Rwanda to decreases in the Southeast Asian Highlands of Indonesia.

Taking transgenic rice drought screening to the field.

Numerous transgenes have been reported to increase rice drought resistance, mostly in small-scale experiments under vegetative-stage drought stress, but few studies have included grain yield or field evaluations. Different definitions of drought resistance are currently in use for field-based and laboratory evaluations of transgenics, the former emphasizing plant responses that may not be linked to yield under drought. Although those fundamental studies use efficient protocols to uncover and validate gene functions, screening conditions differ greatly from field drought environments where the onset of drought stress symptoms is slow (2-3 weeks). Simplified screening methods, including severely stressed survival studies, are therefore not likely to identify transgenic events with better yield performance under drought in the target environment. As biosafety regulations are becoming established to allow field trials in some rice-producing countries, there is a need to develop relevant screening procedures that scale from preliminary event selection to greenhouse and field trials. Multilocation testing in a range of drought environments may reveal that different transgenes are necessary for different types of drought-prone field conditions. We describe here a pipeline to improve the selection efficiency and reproducibility of results across drought treatments and test the potential of transgenic rice for the development of drought-resistant material for agricultural purposes.

Fundamental freedoms and the psychology of threat, bargaining, and inequality.

Van de Vliert's findings may be explained by the psychology of threat and bargaining. Poor people facing extreme threats must cope by surrendering individual freedom in service of shared group needs. Wealthier people are more able to flee from threats and/or resist authoritarianism, so their leaders must concede greater freedom. Incorporating these factors (plus inequality) can sharpen researchers' predictions.

Coalitionality shapes moral elevation: evidence from the U.S. Black Lives Matter protest and counter-protest movements.

Witnessing altruistic behaviour can elicit moral elevation, an emotion that motivates prosocial cooperation. This emotion is evoked more strongly when the observer anticipates that other people will be reciprocally cooperative. Coalitionality should therefore moderate feelings of elevation, as whether the observer shares the coalitional affiliation of those observed should influence the observer's assessment of the likelihood that the latter will cooperate with the observer. We examined this thesis in studies contemporaneous with the 2020 Black Lives Matter (BLM) protests. Although BLM protests were predominantly peaceful, they were depicted by conservative media as destructive and antisocial. In two large-scale, pre-registered online studies (total N = 2172), political orientation strongly moderated feelings of state elevation elicited by a video of a peaceful BLM protest (Studies 1 and 2) or a peaceful Back the Blue (BtB) counter-protest (Study 2). Political conservatism predicted less elevation following the BLM video and more elevation following the BtB video. Elevation elicited by the BLM video correlated with preferences to defund police, whereas elevation elicited by the BtB video correlated with preferences to increase police funding. These findings extend prior work on elevation into the area of prosocial cooperation in the context of coalitional conflict.

A global-temporal analysis on Phytophthora sojae resistance-gene efficacy.

Plant disease resistance genes are widely used in agriculture to reduce disease outbreaks and epidemics and ensure global food security. In soybean, Rps (Resistance to Phytophthora sojae) genes are used to manage Phytophthora sojae, a major oomycete pathogen that causes Phytophthora stem and root rot (PRR) worldwide. This study aims to identify temporal changes in P. sojae pathotype complexity, diversity, and Rps gene efficacy. Pathotype data was collected from 5121 isolates of P. sojae, derived from 29 surveys conducted between 1990 and 2019 across the United States, Argentina, Canada, and China. This systematic review shows a loss of efficacy of specific Rps genes utilized for disease management and a significant increase in the pathotype diversity of isolates over time. This study finds that the most widely deployed Rps genes used to manage PRR globally, Rps1a, Rps1c and Rps1k, are no longer effective for PRR management in the United States, Argentina, and Canada. This systematic review emphasizes the need to widely introduce new sources of resistance to P. sojae, such as Rps3a, Rps6, or Rps11, into commercial cultivars to effectively manage PRR going forward.

Greater traditionalism predicts COVID-19 precautionary behaviors across 27 societies.

People vary both in their embrace of their society's traditions, and in their perception of hazards as salient and necessitating a response. Over evolutionary time, traditions have offered avenues for addressing hazards, plausibly resulting in linkages between orientations toward tradition and orientations toward danger. Emerging research documents connections between traditionalism and threat responsivity, including pathogen-avoidance motivations. Additionally, because hazard-mitigating behaviors can conflict with competing priorities, associations between traditionalism and pathogen avoidance may hinge on contextually contingent tradeoffs. The COVID-19 pandemic provides a real-world test of the posited relationship between traditionalism and hazard avoidance. Across 27 societies (N = 7844), we find that, in a majority of countries, individuals' endorsement of tradition positively correlates with their adherence to costly COVID-19-avoidance behaviors; accounting for some of the conflicts that arise between public health precautions and other objectives further strengthens this evidence that traditionalism is associated with greater attention to hazards.

The relationship between natural rain intensity and Ascochyta blight in chickpea development.

Ascochyta blight management strategy in chickpea standing crops in Australia is solely based on applying protective fungicides before a forecast rainfall event. Despite this, studies on the likely interaction between natural rain (as well as simulated rain) amount, duration and Ascochyta blight development are rare. This study was conducted to investigate the relationship between natural rain intensity (mm/h) and Ascochyta blight development. Infested chickpea residue were placed at the soil surface, and three pots of a susceptible chickpea cultivar were randomly placed on each side of the plot (total 12 pots and 36 plants), preceding a forecast rainfall event. Trap plants were transferred to a controlled temperature room after rain events. After a 48 h incubation period, trap plants were transferred to a glasshouse to allow lesion development. The number of lesions on all plant parts were counted after two weeks. Lesions developed in rain amounts as low as 1.4 mm and rain durations as short as 0.7 h. The number of lesions significantly increased with increasing rain amount. There was a positive effect of increasing rain duration and a negative effect of increasing wind speed. This study suggests that small rain amounts, shorter duration rains or a limited amount of primary inoculum are not barriers to conidial dispersal or host infection, and that the current value of a rainfallthreshold (2 mm) for conidial spread and host infection is not accurate for susceptible cultivars.

The First Annotated Genome Assembly of Macrophomina tecta Associated with Charcoal Rot of Sorghum.

Charcoal rot is an important soilborne disease caused by a range of Macrophomina species, which affects a broad range of commercially important crops worldwide. Even though Macrophomina species are fungal pathogens of substantial economic importance, their mechanism of pathogenicity and host spectrum are poorly understood. There is an urgent need to better understand the biology, epidemiology, and evolution of Macrophomina species, which, in turn, will aid in improving charcoal rot management strategies. Here, we present the first high-quality genome assembly and annotation of Macrophomina tecta strain BRIP 70781 associated with charcoal rot symptoms on sorghum. Hybrid assembly integrating long reads generated by Oxford Nanopore Technology and short Illumina paired-end reads resulted in 43 contigs with a total assembly size of ∼54 Mb, and an N50 of 3.4 Mb. In total, 12,926 protein-coding genes and 7,036 repeats were predicted. Genome comparisons detected accumulation of DNA transposons in Macrophomina species associated with sorghum. The first reference genome of M. tecta generated in this study will contribute to more comparative and population genomics studies of Macrophomina species.