VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center.

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.

PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions.

Since 2005, the Pathogen-Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to the identification and presentation of phenotype information on pathogenicity and effector genes and their host interactions. Specific gene alterations that did not alter the in host interaction phenotype are also presented. PHI-base is invaluable for comparative analyses and for the discovery of candidate targets in medically and agronomically important species for intervention. Version 4.12 (September 2021) contains 4387 references, and provides information on 8411 genes from 279 pathogens, tested on 228 hosts in 18, 190 interactions. This provides a 24% increase in gene content since Version 4.8 (September 2019). Bacterial and fungal pathogens represent the majority of the interaction data, with a 54:46 split of entries, whilst protists, protozoa, nematodes and insects represent 3.6% of entries. Host species consist of approximately 54% plants and 46% others of medical, veterinary and/or environmental importance. PHI-base data is disseminated to UniProtKB, FungiDB and Ensembl Genomes. PHI-base will migrate to a new gene-centric version (version 5.0) in early 2022. This major development is briefly described.

Quarantine supervision of Wood Packaging Materials (WPM) at Chinese ports of entry from 2003 to 2016.

Exotic pests have caused huge losses to agriculture, forestry, and human health. Analyzing information on all concerned pest species and their origin will help to improve the inspection procedures and will help to clarify the relative risks of imported cargo and formulate international trade policies. Records of intercepted pests from wood packaging materials (WPM) from 2003 to 2016 in the China Port Information Network (CPIN) database were analyzed. Results showed that the number of intercepted pests from WPM was lowest in the first quarter and highest in the fourth one. The total number of interceptions increased each year, with 53.33% of intercepted insects followed by nematodes (31.54%). The original continent of most intercepted pests was Asia (49.29%). Xylophagous insects were primarily intercepted from Southeast Asian countries, whereas nematodes were primarily intercepted from Korea, Australia, Mexico, and other countries. WPM interception records were mainly concentrated in China's coastal inspection stations (98.7%), with the largest number of interceptions documented in Shanghai, followed by the inspection stations of Jiangsu Province. The proportion of pest taxa intercepted by the Chinese provinces' stations each year is becoming increasingly balanced. The number of pest disposal treatment measures for intercepted cargoes with dead non-quarantine pests increased significantly from 2012 to 2016. This reflects the fact that Chinese customs inspection stations are becoming increasingly scientific and standardizing the interception and treatment of WPM pests. The issues reflected in the database, with a view to providing a reference for future work by customs officers and researchers.

Tuning Beforehand: A Foresight on RNA Interference (RNAi) and In Vitro-Derived dsRNAs to Enhance Crop Resilience to Biotic and Abiotic Stresses.

Crop yield is severely affected by biotic and abiotic stresses. Plants adapt to these stresses mainly through gene expression reprogramming at the transcriptional and post-transcriptional levels. Recently, the exogenous application of double-stranded RNAs (dsRNAs) and RNA interference (RNAi) technology has emerged as a sustainable and publicly acceptable alternative to genetic transformation, hence, small RNAs (micro-RNAs and small interfering RNAs) have an important role in combating biotic and abiotic stresses in plants. RNAi limits the transcript level by either suppressing transcription (transcriptional gene silencing) or activating sequence-specific RNA degradation (post-transcriptional gene silencing). Using RNAi tools and their respective targets in abiotic stress responses in many crops is well documented. Many miRNAs families are reported in plant tolerance response or adaptation to drought, salinity, and temperature stresses. In biotic stress, the spray-induced gene silencing (SIGS) provides an intelligent method of using dsRNA as a trigger to silence target genes in pests and pathogens without producing side effects such as those caused by chemical pesticides. In this review, we focus on the potential of SIGS as the most recent application of RNAi in agriculture and point out the trends, challenges, and risks of production technologies. Additionally, we provide insights into the potential applications of exogenous RNAi against biotic stresses. We also review the current status of RNAi/miRNA tools and their respective targets on abiotic stress and the most common responsive miRNA families triggered by stress conditions in different crop species.

Optimal Pest Control Strategies with Cost-effectiveness Analysis.

Pest and plant diseases cause damages and economic losses, threatening food security and ecosystem services. Thus, proper pest management is indispensable to mitigate the risk of losses. The risk of environmental hazards induced by toxic chemicals alongside the rapid development of chemical resistance by insects entails more resilient, sustainable, and ecologically sound approaches to chemical methods of control. This study evaluates the application of three dynamical measures of controls, namely, green insecticide, mating disruption, and the removal of infected plants, in controlling pest insects. A model was built to describe the interaction between plants and insects as well as the circulation of the pathogen. Optimal control measures are sought in such a way they maximize the healthy plant density jointly with the pests' density under the lowest possible control efforts. Our simulation study shows that all strategies succeed in controlling the insects. However, a cost-effectiveness analysis suggests that a strategy with two measures of green insecticide and plant removal is the most cost-effective, followed by one which applies all control measures. The best strategy projects the decrease of potential loss from 65.36% to 6.12%.

Evaluation on reprogramed biological processes in transgenic maize varieties using transcriptomics and metabolomics.

Genetic engineering (GM) has great potential to improve maize productivity, but rises some concerns on unintended effects, and equivalent as their comparators. There are some limitations through targeted analysis to detect the UE in genetically modified organisms in many previous studies. We here reported a case-study on the effects of introducing herbicides and insect resistance (HIR) gene cassette on molecular profiling (transcripts and metabolites) in a popular maize variety Zhengdan958 (ZD958) in China. We found that introducing HIR gene cassette bring a limited numbers of differential abundant genes (DAGs) or differential abundant metabolites (DAMs) between transgenic events and non-transgenic control. In contrast, averaged 10 times more DAGs and DAMs were observed when performed comparison under different growing environments in three different ecological regions of China than the numbers induced by gene effects. Major biological pathways relating to stress response or signaling transduction could explain somehow the effects of growing environments. We further compared two transgenic events mediated ZD958 (GM-ZD958) with either transgenic parent GM-Z58, and other genetic background nonGM-Z58, nonGM-ZD958, and Chang7-2. We found that the numbers of DAGs and DAMs between GM-ZD958 and its one parent maize variety, Z58 or GM-Z58 is equivalent, but not Chang7-2. These findings suggest that greater effects due to different genetic background on altered molecular profiling than gene modification itself. This study provides a case evidence indicating marginal effects of gene pleiotropic effects, and environmental effects should be emphasized.

DDRP: Real-time phenology and climatic suitability modeling of invasive insects.

Rapidly detecting and responding to new invasive species and the spread of those that are already established is essential for reducing their potential threat to food production, the economy, and the environment. We describe a new spatial modeling platform that integrates mapping of phenology and climatic suitability in real-time to provide timely and comprehensive guidance for stakeholders needing to know both where and when invasive insect species could potentially invade the conterminous United States. The Degree-Days, Risk, and Phenological event mapping (DDRP) platform serves as an open-source and relatively easy-to-parameterize decision support tool to help detect new invasive threats, schedule monitoring and management actions, optimize biological control, and predict potential impacts on agricultural production. DDRP uses a process-based modeling approach in which degree-days and temperature stress are calculated daily and accumulate over time to model phenology and climatic suitability, respectively. Outputs include predictions of the number of completed generations, life stages present, dates of phenological events, and climatically suitable areas based on two levels of climate stress. Species parameter values can be derived from laboratory and field studies or estimated through an additional modeling step. DDRP is written entirely in R, making it flexible and extensible, and capitalizes on multiple R packages to generate gridded and graphical outputs. We illustrate the DDRP modeling platform and the process of model parameterization using two invasive insect species as example threats to United States agriculture: the light brown apple moth, Epiphyas postvittana, and the small tomato borer, Neoleucinodes elegantalis. We then discuss example applications of DDRP as a decision support tool, review its potential limitations and sources of model error, and outline some ideas for future improvements to the platform.

Interacting effects of insect and ungulate herbivory on Scots pine growth.

Most plants are subjected to damage from multiple species of herbivores, and the combined impact on plant growth can be non-additive. Since plant response to herbivores tends to be species specific, and change with repeated damage, the outcome likely depend on the sequence and number of attacks. There is a high likelihood of non-additive effects on plant growth by damage from mammals and insects, as mammalian herbivory can alter insect herbivore damage levels, yet few studies have explored this. We report the growth response of young Scots pine trees to sequential mammal and insect herbivory, varying the sequence and number of damage events, using an ungulate-pine-sawfly system. Combined sawfly and ungulate herbivory had both additive and non-additive effects on pine growth-the growth response depended on the combination of ungulate browsing and sawfly defoliation (significant interaction effect). Repeated sawfly herbivory reduced growth (compared to single defoliation) on un-browsed trees. However, on browsed trees, depending on when sawfly defoliation was combined with browsing, trees exposed to repeated sawfly herbivory had both higher, lower and the same growth as trees exposed to a single defoliation event. We conclude that the sequence of attacks by multiple herbivores determine plant growth response.

Multiple wheat genomes reveal global variation in modern breeding.

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome1, and the lack of genome-assembly data for multiple wheat lines2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm16, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Genetic engineering of crops for insect resistance: An overview.

Phytophagous insect incidence is a serious threat for reduction of crop productivity globally. There is an estimation of one fourth of crop is being destroyed by insects annually. Indeed, the development of insect-resistant crops is a great milestone in agriculture to increase crop yield and reduce pesticide dependency. Genetic engineering facilitates development of insect resistant crops by expressing bacterial δ-endotoxins and vegetative insecticidal proteins and other plant genes like lectins, protease inhibitors, etc. In addition, RNA interference and genome editing through CRISPR Cas9 also provides new solutions for the development of insect-resistant crops. The resultant genetically modified crops showed resistance against lepidopteran, dipteran, homopteran and coleopteran insects. The insect-resistant crops have made a significant economic impact worldwide in terms of higher yield and low pesticide usage. In this review, we focus on different strategies for developing transgenics against insect pest control by expressing different insecticidal proteins in crops.

Review on Structures of Pesticide Targets.

Molecular targets play important roles in agrochemical discovery. Numerous pesticides target the key proteins in pathogens, insect, or plants. Investigating ligand-binding pockets and/or active sites in the proteins' structures is usually the first step in designing new green pesticides. Thus, molecular target structures are extremely important for the discovery and development of such pesticides. In this manuscript, we present a review of the molecular target structures, including those of antiviral, fungicidal, bactericidal, insecticidal, herbicidal, and plant growth-regulator targets, currently used in agrochemical research. The data will be helpful in pesticide design and the discovery of new green pesticides.

Deficiency of mitochondrial outer membrane protein 64 confers rice resistance to both piercing-sucking and chewing insects in rice.

The brown planthopper (BPH) and striped stem borer (SSB) are the most devastating insect pests in rice (Oryza sativa) producing areas. Screening for endogenous resistant genes is the most practical strategy for rice insect-resistance breeding. Forty-five mutants showing high resistance against BPH were identified in a rice T-DNA insertion population (11,000 putative homozygous lines) after 4 years of large-scale field BPH-resistance phenotype screening. Detailed analysis showed that deficiency of rice mitochondrial outer membrane protein 64 (OM64) gene resulted in increased resistance to BPH. Mitochondrial outer membrane protein 64 protein is located in the outer mitochondrial membrane by subcellular localization and its deficiency constitutively activated hydrogen peroxide (H2 O2 ) signaling, which stimulated antibiosis and tolerance to BPH. The om64 mutant also showed enhanced resistance to SSB, a chewing insect, which was due to promotion of Jasmonic acid biosynthesis and related responses. Importantly, om64 plants presented no significant changes in rice yield-related characters. This study confirmed OM64 as a negative regulator of rice herbivore resistance through regulating H2 O2 production. Mitochondrial outer membrane protein 64 is a potentially efficient candidate to improve BPH and SSB resistance through gene deletion. Why the om64 mutant was resistant to both piercing-sucking and chewing insects via a gene deficiency in mitochondria is discussed.

Legumes Protease Inhibitors as Biopesticides and Their Defense Mechanisms against Biotic Factors.

Legumes are affected by biotic factors such as insects, molds, bacteria, and viruses. These plants can produce many different molecules in response to the attack of phytopathogens. Protease inhibitors (PIs) are proteins produced by legumes that inhibit the protease activity of phytopathogens. PIs are known to reduce nutrient availability, which diminishes pathogen growth and can lead to the death of the pathogen. PIs are classified according to the specificity of the mechanistic activity of the proteolytic enzymes, with serine and cysteine protease inhibitors being studied the most. Previous investigations have reported the efficacy of these highly stable proteins against diverse biotic factors and the concomitant protective effects in crops, representing a possible replacement of toxic agrochemicals that harm the environment.

Population dynamics of Hippophae rhamnoides shrub in response of sea-level rise and insect outbreaks.

The coastal vegetation of islands is expected to be affected by future sea-level rise and other anthropogenic impacts. The biodiverse coastal vegetation on the eastern part of the Dutch Wadden Island of Ameland has experienced land subsidence caused by gas extraction since 1986. This subsidence mimics future sea-level rising through increased flooding and raising groundwater levels. We studied the effects of this relative sea-level rise and other environmental factors (i.e. insect outbreaks, temperature and precipitation) on the population dynamics (i.e. cover and age structure and annual growth) of the shrub sea-buckthorn (Hippophae rhamnoides L.) in young (formed after 1950) and old (formed before 1950) dune areas over a period of 56 years (1959-2015). We found an increase in sea-buckthorn cover in the young dune areas since 1959, while over time the population in the old dunes decreased due to successional replacement by other species. With the increasing age of the young dunes, we found also a decrease in sea-buckthorn after 2009. However the sharp decrease indicated that other environmental factors were also involved. The most important determinant of annual shrub growth appeared to be five outbreaks of the brown-tail moth (Euproctis chrysorrhoea L.), in the last decade. Relative sea-level rise caused more frequent flooding and reduced growth at lower elevations due to inundation or soil water saturation. This study clearly indicates that sea-buckthorn is affected by relative sea-level rise, but that other ecological events better explain its variation in growth. Although shrub distribution and growth can be monitored with robust methods, future predictions of vegetation dynamics are complicated by unpredictable extreme events caused by (a)biotic stressors such as insect outbreaks.

Offspring reverse transcriptome responses to maternal deprivation when reared with pathogens in an insect with facultative family life.

Offspring of species with facultative family life are able to live with and without parents (i.e. to adjust to extreme changes in their social environment). While these adjustments are well understood on a phenotypic level, their genetic underpinnings remain surprisingly understudied. Investigating gene expression changes in response to parental absence may elucidate the genetic constraints driving evolutionary transitions between solitary and family life. Here, we manipulated maternal presence to observe gene expression changes in the fat body of juvenile European earwigs, an insect with facultative family life. Because parents typically protect offspring against pathogens, expression changes were recorded in pathogen-free and pathogen-exposed environments. We found that manipulating maternal presence changed the expression of 154 genes, including several metabolism and growth-related genes, and that this change depended on pathogen presence. Specifically, localization and cell transporter genes were downregulated in maternal absence without pathogens but upregulated with pathogens. At least one immunity gene (pathogenesis-related protein 5) was affected by pathogen exposure regardless of maternal presence. Overall, our findings explicate how offspring adjust to parental deprivation on a molecular level and reveal that such adjustments heavily depend on pathogens in the environment. This emphasizes the central role of pathogens in family life evolution.

Bioaccumulation and biomagnification of hexabromocyclododecane (HBCDD) in insect-dominated food webs from a former e-waste recycling site in South China.

Hexabromocyclododecane (HBCDD) has frequently been detected in wildlife. However, there is limited research on its bioaccumulation and biomagnification in insect-dominated aquatic and terrestrial food webs. This study investigated the occurrence of HBCDD in insects and their predators collected from a former e-waste contaminated pond and its surrounding region. The concentrations of Æ©HBCDD (sum concentrations of α-, ß-, and γ-HBCDDs) ranged from nd to 179 ng g-1 lipid weight. α-HBCDD was the predominant diastereoisomer in all biotic samples, and the contribution of α-HBCDD was higher in predators than in prey insects. A significantly positive linear relationship was found between Æ©HBCDD concentrations (lipid weight) and trophic levels based on δ15N in aquatic organisms (p < 0.05), while trophic dilution was observed in the terrestrial food web. This result indicates an opposite trophic transfer tendency of HBCDD in terrestrial and aquatic ecosystems. The biomagnification factor (BMF) for α-HBCDD was higher in terrestrial birds (2.03) than in frogs (0.29), toads (0.85), and lizards (0.63). This may be due to differences between poikilotherms and homeotherms in terrestrial ecosystems.

Transgene Stacking as Effective Tool for Enhanced Disease Resistance in Plants.

Introduction of more than one gene into crop plants simultaneously or sequentially, called transgene stacking, has been a more effective strategy for conferring higher and durable insect and disease resistance in transgenic plants than single-gene technology. Transgenes can be stacked against one or more pathogens or for traits such as herbicide tolerance or anthocyanin pigmentation. Polygenic agronomic traits can be improved by multiple gene transformation. The most widely engineered stacked traits are insect resistance and herbicide tolerance as these traits may lead to lesser use of pesticides, higher yield, and efficient control of weeds. In this review, we summarize transgene stacking of two or more transgenes into crops for different agronomic traits, potential applications of gene stacking, its limitations and future prospects.

Let's talk about sexes: sex-related N-glycosylation in ecologically important invertebrates.

Parasitic helminths and pest insects are organisms with great ecological importance, having direct or indirect detrimental effects on people's lives worldwide. Several reports in literature indicate that the glycan repertoire of parasites plays important roles in host-parasite interactions and modulation and evasion of the host immune system, while insect glycans are essential for their survival, growth and development. Although glycosylation is the result of a highly conserved machinery, differences between species and between different stages of one organism's life cycle occur. This review provides insight into recent glycomics studies both for helminths and insects, focussing on sex differences and the role of carbohydrate structures in reproduction. Information on the differential N-glycosylation process between males and females can generate a better understanding of the biology and physiology of these economic important organisms, and can contribute to the discovery of novel anti-fecundity vaccine candidates and drug targets, as well as in the elaboration of innovative pest management strategies.

Ability of near-infrared spectroscopy for non-destructive detection of internal insect infestation in fruits: Meta-analysis of spectral ranges and optical measurement modes.

The feasibility of utilizing near-infrared (NIR) spectroscopy has been recently assessed for rapid and non-destructive detection of internal insect infestation in some fruits. Based on the findings, this technology can be used for on/in-line inspection of the fruits in terms of insect infestation if suitable instrument is selected for accurate spectral measurements and system development. The spectral range and optical measurement mode are two of the most important factors which can affect the accuracy of the spectral measurements and detection models. The aim of this study is meta-analysis of these factors' effects on the ability of NIR-based spectroscopy for non-destructive detection of hidden insect infestation in fruits. Eight studies (65 observations) were extracted based on the criteria of this study. Overall, utilizing NIR-based spectroscopy led to 13.98% error (95% CI = 10.69-17.27%) for non-destructive detection of hidden insect infestation in fruits. Spectral ranges of Vis/SWNIR (above 300 up to 1100 nm), NIR (above 780 up to 2500 nm), and Vis/NIR (above 300 up to 2500 nm) showed errors of 21.71% (95% CI = 16.56-26.86%), 13.30% (95% CI = 5.24-21.36%), and 13.65% (95% CI = 5.9-21.4%), respectively. It was noted that wavelengths above 1100 nm (NIR region) are more useful to detect insect infestation in fruit. Results also indicated that optical measurement modes of interactance, reflectance, and transmittance had errors of 6.66% (95% CI = 4.18-9.14%), 15.73% (95% CI = 10.99-20.47%), and 16.04% (95% CI = 7.26-24.82%), respectively. This meta-analysis suggests that utilizing interactance mode for spectra measurement in NIR-based spectroscopy can increase the accuracy of discrimination of insect infested fruits especially when the spectral range of the spectrometer is Vis/SWNIR. Moreover, it should be selected a spectrometer with the wavelength range of NIR or Vis/NIR when using reflectance or transmittance mode is necessary for developing an in/on-line system to detect insect infestation in fruits.

Gas exchange, biomass and non-structural carbohydrates dynamics in vines under combined drought and biotic stress.

BACKGROUND: Intensity of drought stress and pest attacks is forecasted to increase in the near future posing a serious threat to natural and agricultural ecosystems. Knowledge on potential effects of a combined abiotic-biotic stress on whole-plant physiology is lacking. We monitored the water status and carbon metabolism of a vine rootstock with or without scion subjected to water shortening and/or infestation with the sucking insect phylloxera (Daktulosphaira vitifoliae Fitch). We measured non-structural carbohydrates and biomass of different plant organs to assess the stress-induced responses at the root, stem, and leaf level. Effects of watering on root infestation were also addressed. RESULTS: Higher root infestation was observed in drought-stressed plants compared to well-watered. The drought had a significant impact on most of the measured functional traits. Phylloxera further influenced vines water and carbon metabolism and enforced the sink strength of the roots by stimulating photosynthates translocation. The insect induced carbon depletion, reprogramed vine development, while preventing biomass compensation. A synergic effect of biotic-abiotic stress could be detected in several physiological and morphological traits. CONCLUSIONS: Our results indicate that events of water shortage favour insects' feeding damage and increase the abundance of root nodosities. Root phylloxera infestation imposes a considerable stress to the plants which might exacerbate the negative effects of drought.