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opencc-by-4.0May 2024View details →

Transcriptome data of the analysis of two isolates of the tomato pathogen Cladosporium fulvum during host interaction

This dataset contains sequences of assembled transcripts from isolates Race 5 and Race 4 of the tomato pathogen Cladosporium fulvum during interaction with its host. transcripts: Assembled transcripts in FASTA and GTF fomats. The GTF files have coordinates of the transcripts in the reference genomes of isolates Race 5 (GCA_020509005.2) and Race 4 (GCA_035196885.1). The other FASTA files include the predicted open reading frames (ORFs) in the transcripts. The nucleotide coding sequence and translated amino acid sequences of the ORFs are in separated FASTA files. In the file names isolate Race 5 is indicated with '*R5*', and isolate Race 4 is indicated with '*R4*'. Description of the files is shown below: <ul> <li><code>representatives_R4_diff_introns.fasta</code>: full-length transcript sequences from isolate Race 4.</li> <li><code>representatives_R5_diff_introns.fasta</code>: full-length transcript sequences from isolate Race 5.</li> <li><code>representatives_R4_diff_introns.gtf</code>: coordinates of the transcripts from isolate Race 4 in the genome of Race 4.</li> <li><code>representatives_R5_diff_introns.gtf</code>: coordinates of the transcripts from isolate Race 5 in the genome of Race 5.</li> <li><code>representatives_orfs_aa_R4_diff_introns.fasta:</code> predicted protein sequences encoded in the transcripts from isolate Race 4.</li> <li><code>representatives_orfs_aa_R5_diff_introns.fasta</code>: predicted protein sequences encoded in the transcripts from isolate Race 5.</li> <li><code>representatives_orfs_cds_R4_diff_introns.fasta</code>: predicted coding sequences in the transcripts from isolate Race 4.</li> <li><code>representatives_orfs_cds_R5_diff_introns.fasta</code>: predicted coding sequences in the transcripts from isolate Race 5.</li> </ul> expression: Contains tab-separated files with the expression values (transcripts per million - TPM) of the transcripts from isolates Race 5 and Race 4 at specific time points (2, 4, 6, 8, 10, 12, and 14 dpi) during interaction with tomato. TPM values were estimated with the alignment-free method Salmon.

opencc-by-4.0Jun 2024View details →

Comparative analyses of compatible and incompatible host-pathogen interactions provide insight into divergent host specialization of closely related pathogens

The following animations accompany the manuscript "Comparative analyses of compatible and incompatible host-pathogen interactions provide insight into divergent host specialization of closely related pathogens". These animations are of confocal microscopy images of wheat leaves infected with isolates of Zymoseptoria pseudodarliae and Z. ardabiliae, at two infection stages (early and late), scrolling through different planes of focus into the wheat leaf. Two isolates of Zymoseptoria pseudodarliae (Zp13 and Zp72) and three isolates of Zymoseptoria ardabiliae (Za17, Za48, and Za94) on wheat, were screened in this study. Each isolate is expressing GFP in order to visualise hyphae. Z. pseudodarliae and Z. ardabiliae are avirulent on wheat, and infections do not pentrate beyond the stomata and into the wheat tissue. These differ from previously obtained images of Z. tritici (virulent on wheat), which penetrate into the wheat tissue (<a href="https://doi.org/10.1002/ece3.4724">https://doi.org/10.1002/ece3.4724</a>).

opencc-by-4.0Jul 2024View details →

Deformed Wing Virus interacts with host's arginine kinase to enhance viral replication in honey bees

Dataset used to plot the figures presented in the manuscript "Deformed Wing Virus interacts with host’s arginine kinase to enhance viral replication in honey bees".   Abstract Deformed wing virus (DWV) is a major bee pathogen that is actively transmitted by the parasitic mite Varroa destructor and plays a primary role in winter Apis mellifera colony losses. Despite intense investigation of this essential pollinator species, driven by its unique environmental and economic importance, the mechanisms underlying the molecular interactions between DWV and honey bees are still poorly understood. Here we report on a group of honey bee proteins, identified by mass spectrometry, that specifically co-immunoprecipitate with DWV virus particles. Most of the proteins identified are involved in fundamental metabolic pathways. Here we focused on Arginine kinase (ArgK), a conserved protein playing multiple roles both in physiological and pathological processes. We found that ArgK RNA levels positively correlate with DWV load in field-collected honey-bee larvae and adults and significantly increase in larvae and adults upon DWV injection in controlled laboratory conditions, indicating that the ArgK gene was upregulated by DWV infection. Silencing ArgK gene expression in vitro, using RNAi, resulted in reduced DWV viral load, thus demonstrating that ArgK function promotes the progression of DWV infection, likely altering the delicate balance between metabolism and immunity.  In summary, these data indicate that successful DWV infection relies on transcriptional regulation and active recruitment of host ArgK by this viral pathogen. Therefore, our findings open novel perspectives on the potential control of DWV pathogenicity by targeting its interaction with specific host proteins.

opennotspecifiedMar 2015View details →

Figure 1 in Interaction between Tephritidae (Insecta, Diptera) and plants of the family Asteraceae: new host and distribution records for the state of Rio Grande do Sul, Brazil

Figure 1. Localities in Rio Grande do Sul, Brazil, where the fauna of Tephritidae (Dip* tera) from capitula of Asteraceae was sampled.

opencc-by-4.0Sep 2024View details →

Comparative analyses of compatible and incompatible host-pathogen interactions provide insight into divergent host specialization of closely related pathogens

Supplementary Animations   Animation S1. Directed growth of Z. pseudotritici Zp13 hyphae towards wheat stomata 7 dpi. Tomographic animation of confocal image z-stack showing spore germination, filament development, and penetration of wheat stomata by hyphae of Z. pseudotritici isolate Zp13 at 7 dpi. Nuclei and wheat cells displayed in purple and fungal structures in green. Scale bar = 50 µm.   Animation S2. Directed growth of Z. ardabiliae Za17 hyphae towards wheat stomata 17 dpi. Tomographic animation of confocal image z-stack showing spore germination, filament development, and penetration of wheat stomata by hyphae of Z. ardabiliae isolate Za17 at 17 dpi. Nuclei and wheat cells displayed in purple and fungal structures in green. Scale bar = 25 µm.   Animation S3. Z. pseudotritici Zp13 hyphae penetrate wheat stoma 14 dpi. Tomographic animation of confocal image z-stack showing penetration of wheat stoma by two hyphae of Z. pseudotritici isolate Zp13 at 14 dpi. Nuclei and wheat cells displayed in purple and fungal structures in green. Scale bar = 20 µm.   Animation S4. Z. ardabiliae Za94 hyphae penetrate wheat stoma 8 dpi. Tomographic animation of confocal image z-stack showing penetration of wheat stoma by two hyphae of Z. ardabiliae isolate Za94 at 8 dpi. Nuclei and wheat cells displayed in purple and fungal structures in green. Reference transmitted images in grey. Scale bar = 25 µm.   Animation S5. Z. pseudotritici Zp72 hypha arrested between guard cells 10 dpi. Tomographic animation of confocal image z-stack showing infecting hypha of Z. pseudotritici isolate Zp72 that is arrested at wheat stomatal guard cells at 10 dpi. Nuclei and wheat cells displayed in purple and fungal structures in green. Reference transmitted images in grey. Scale bar = 25 µm.   Animation S6. Z. ardabiliae Za94 hyphae arrested between guard cells 17 dpi. Tomographic animation of confocal image z-stack showing infecting hyphae of Z. ardabiliae isolate Za94 that are arrested between wheat stomatal guard cells at 17 dpi. Nuclei and wheat cells displayed in purple and fungal structures in green. Scale bar = 25 µm.   Animation S7. Z. ardabiliae Za48 hypha arrested in sub-stomatal cavity 8 dpi. Tomographic animation of confocal image z-stack showing infecting hypha of Z. ardabiliae isolate Za48 that is arrested in a wheat sub-stomatal cavity at 8 dpi. Nuclei and wheat cells displayed in purple and fungal structures in green. Reference transmitted images in grey. Scale bar = 25 µm.   Animation S8. Z. pseudotritici Zp13 hypha arrested in sub-stomatal cavity 17 dpi. Tomographic animation of confocal image z-stack showing infecting hypha of Z. pseudotritici isolate Zp13 that is arrested in a wheat sub-stomatal cavity at 17 dpi. Nuclei and wheat cells displayed in purple and fungal structures in green. Scale bar = 25 µm.

opencc-by-4.0Sep 2024View details →

Data and Scripts for "Timing matters in Macrophage / CD4+ T cell interactions: An agent-based model comparing Mycobacterium tuberculosis host-pathogen interactions between latently infected and naïve individuals"

This contains the data and graphing scripts necessary to recreate all figures in the paper "Timing matters in Macrophage / CD4+ T cell interactions: An agent-based model comparing Mycobacterium tuberculosis host-pathogen interactions between latently infected and naïve individuals". Supplemental Material for the paper is also provided here. Please refer to the README.md for instructions on how to use. The model can be found at: https://github.itap.purdue.edu/ElsjePienaarGroup/LTBINaiveinvitroModel/ along with the uncalibrated parameter files and scripts to run on HPCs.

opencc-zeroDec 2015View details →

Data from: The many dimensions of diet breadth: phytochemical, genetic, behavioral, and physiological perspectives on the interaction between a native herbivore and an exotic host

From the perspective of an herbivorous insect, conspecific host plants are not identical, and intraspecific variation in host nutritional quality or defensive capacity might mediate spatially variable outcomes in plant-insect interactions. Here we explore this possibility in the context of an ongoing host breadth expansion of a native butterfly (the Melissa blue, Lycaeides melissa) onto an exotic host plant (alfalfa, Medicago sativa). We examine variation among seven alfalfa populations that differed in terms of colonization by L. melissa; specifically, we examined variation in phytochemistry, foliar protein, and plant population genetic structure, as well as responses of caterpillars and adult butterflies to foliage from the same populations. Regional patterns of alfalfa colonization by L. melissa were well predicted by phytochemical variation, and colonized patches of alfalfa showed a similar level of inter-individual phytochemical diversity. However, phytochemical variation was a poor predictor of larval performance, despite the fact that survival and weight gain differed dramatically among caterpillars reared on plants from different alfalfa populations. Moreover, we observed a mismatch between alfalfa supporting the best larval performance and alfalfa favored by ovipositing females. Thus, the axes of plant variation that mediate interactions with L. melissa depend upon herbivore life history stage, which raises important issues for our understanding of adaptation to novel resources by an organism with a complex life history.

opencc-zeroDec 2015View details →

Data from: Tree phylogenetic diversity promotes host–parasitoid interactions

Evidence from grassland experiments suggests that a plant community's phylogenetic diversity (PD) is a strong predictor of ecosystem processes, even stronger than species richness per se. This has, however, never been extended to species-rich forests and host–parasitoid interactions. We used cavity-nesting Hymenoptera and their parasitoids collected in a subtropical forest as a model system to test whether hosts, parasitoids, and their interactions are influenced by tree PD and a comprehensive set of environmental variables, including tree species richness. Parasitism rate and parasitoid abundance were positively correlated with tree PD. All variables describing parasitoids decreased with elevation, and were, except parasitism rate, dependent on host abundance. Quantitative descriptors of host–parasitoid networks were independent of the environment. Our study indicates that host–parasitoid interactions in species-rich forests are related to the PD of the tree community, which influences parasitism rates through parasitoid abundance. We show that effects of tree community PD are much stronger than effects of tree species richness, can cascade to high trophic levels, and promote trophic interactions. As during habitat modification phylogenetic information is usually lost non-randomly, even species-rich habitats may not be able to continuously provide the ecosystem process parasitism if the evolutionarily most distinct plant lineages vanish.

opencc-zeroJun 2019View details →

Data from: Transcriptomics of host-specific interactions in natural populations of the parasitic plant purple witchweed (Striga hermonthica)

Host-specific interactions can maintain genetic and phenotypic diversity in parasites that attack multiple host species. Host diversity, in turn, may promote parasite diversity by selection for genetic divergence or plastic responses to host type. The parasitic weed purple witchweed [Striga hermonthica (Delile) Benth.] causes devastating crop losses in sub-Saharan Africa and is capable of infesting a wide range of grass hosts. Despite some evidence for host adaptation and host-by-Striga genotype interactions, little is known about intraspecific Striga genomic diversity. Here we present a study of transcriptomic diversity in populations of S. hermonthica growing on different hosts (maize [Zea mays L.] vs. grain sorghum [Sorghum bicolor (L.) Moench]). We examined gene expression variation and differences in allelic frequency in expressed genes of aboveground tissues from populations in western Nigeria parasitizing each host. Despite low levels of host-based genome-wide differentiation, we identified a set of parasite transcripts specifically associated with each host. Parasite genes in several different functional categories implicated as important in host–parasite interactions differed in expression level and allele on different hosts, including genes involved in nutrient transport, defense and pathogenesis, and plant hormone response. Overall, we provide a set of candidate transcripts that demonstrate host-specific interactions in vegetative tissues of the emerged parasite S. hermonthica. Our study shows how signals of host-specific processes can be detected aboveground, expanding the focus of host–parasite interactions beyond the haustorial connection.

opencc-zeroDec 2016View details →

Data from: Experimental assemblage of novel plant-herbivore interactions: ecological host shifts after 40 million years of isolation

Geographic isolation is the first step in insect herbivore diet specialization. Such specialization is postulated to increase insect fitness, but may simultaneously reduce insect ability to colonize novel hosts. During the Paleocene-Eocene, plants from the order Zingiberales became isolated either in the Paleotropics or in the Neotropics. During the Cretaceous, rolled-leaf beetles diversified in the Neotropics concurrently with neotropical Zingiberales. Using a community of Costa Rican rolled-leaf beetles and their Zingiberales host plants as study system, we explored if previous geographic isolation precludes insects to expand their diets to exotic hosts. We recorded interactions between rolled-leaf beetles and native Zingiberales by combining DNA barcodes and field records for 7450 beetles feeding on 3202 host plants. To determine phylogenetic patterns of diet expansions, we set 20 field plots including five exotic Zingiberales, recording beetles feeding on these exotic hosts. In the laboratory, using both native and exotic host plants, we reared a subset of insect species that had expanded their diets to the exotic plants. The original plant-herbivore community comprised 24 beetle species feeding on 35 native hosts, representing 103 plant-herbivore interactions. After exotic host plant introduction, 20% of the beetle species expanded their diets to exotic Zingiberales. Insects only established on exotic hosts that belong to the same plant family as their native hosts. Laboratory experiments show that beetles are able to complete development on these novel hosts. In conclusion, rolled-leaf beetles are pre-adapted to expand their diets to novel host plants even after millions of years of geographic isolation.

opencc-zeroAug 2021View details →

Data from: Local adaptation and rapid evolution of aphids in response to genetic interactions with their cottonwood hosts

Several studies have demonstrated the ecological consequences of genetic variation within a single plant species. For example, these studies show that individual plant genotypes support unique composition of the plants' associated arthropod community. By contrast, fewer studies have explored how plant genetic variation may influence evolutionary dynamics in the plant's associated species. Here, we examine how aphids respond evolutionarily to genetic variation in their host plant. We conducted two experiments to examine local adaptation and rapid evolution of the free-feeding aphid Chaitophorus populicola across genetic variants of its host plant, Populus angustifolia. To test for local adaptation, we collected tree cuttings and aphid colonies from three sites along an elevation / climate gradient and conducted a reciprocal transplant experiment. In general, home aphids (aphid transplanted onto trees from the same site) produced 1.7-3.4 times as many offspring as foreign aphids (aphids transplanted onto trees from different sites). To test for rapid evolution, we used 4 clonally replicated aphid genotypes and transplanted each onto 5 clonally replicated P. angustifolia genotypes. Each tree genotype started with the same aphid genotype composition. After 21 days (~two aphid generations), aphid genotype composition changed (i.e. aphids evolved) and some tree genotypes supported unique evolutionary trajectories of aphids. These results suggest that plant evolution in response to human perturbation, such as climate change and invasive species will also result in evolutionary responses in strongly interacting species that could cascade to affect whole communities.

opencc-zeroSep 2021View details →

The effects of novel leaf litter deposition on competitive, predator–prey and host–parasite interactions of American toad larvae

Wetland plant communities are changing rapidly due to a wide range of human activities. The deposition of leaf litter from novel plant communities can alter both the chemical and physical habitat of aquatic ecosystems. Lesser understood are the ecological consequences of novel leaf litter inputs in aquatic communities. Towards this goal, we used two plant invasion scenarios (comparing native black huckleberry to exotic autumn olive and native swamp loosestrife to exotic purple loosestrife) to simulate a shift in wetland plant communities. In this study, we investigated the effects of novel leaf litter leachates on three aquatic ecological interactions: intraspecific competition, predation, and parasitism. We examined how leaf litter leachates influence the interactions of American toad larvae (Anaxyrus americanus) with their conspecifics, a dragonfly predator (Anax spp.) and a trematode parasite (Echinostomatidae). We found that leaf litter type influenced competitive interactions only for the huckleberry versus autumn olive comparison. We did not detect any effects of leaf litter type on predator-prey interactions. Finally, litter type strongly influenced host-parasite interactions for both leaf litter comparisons, altering host susceptibility, parasite survival and net infection rates. These results highlight the breadth of potential ecological repercussions of shifting wetland plant communities for native ecosystems.

FIGURE 3 in Using DNA barcoding to identify host-parasite interactions between cryptic species of goby (Coryphopterus: Gobiidae, Perciformes) and parasitic copepods (Pharodes tortugensis: Chondracanthidae, Cyclopoida)

FIGURE 3. Maximum likelihood tree derived from COI sequences of our copepod samples (labeled as P. tortugensis) plus voucher sequences from related copepods in the suborder Ergasilida (see Table 5 for a list). Sequences of copepods confamilial to P. tortugenis (Chondracanthidae) are labelled to species (and shaded blue in the online colour version), and members other taxa are labeled to family (and shaded pink in the colour online version). Support values for bipartitions are indicated, and divergence represented by dark blue scale bar = 3 %.

FIGURE 1 in Using DNA barcoding to identify host-parasite interactions between cryptic species of goby (Coryphopterus: Gobiidae, Perciformes) and parasitic copepods (Pharodes tortugensis: Chondracanthidae, Cyclopoida)

FIGURE 1. Maximum likelihood tree derived from COI sequences of our goby samples plus voucher sequences from all Coryphopterus species except C. punctipectophorus. Voucher sequences are identified by GenBank sequence ID. Sequences from several other goby species are included as outgroups (not all are identified in the figure; see Table 4 for a list). Support values for bipartitions are indicated, and divergence represented by scale bar = 6%.

FIGURE 2 in Using DNA barcoding to identify host-parasite interactions between cryptic species of goby (Coryphopterus: Gobiidae, Perciformes) and parasitic copepods (Pharodes tortugensis: Chondracanthidae, Cyclopoida)

FIGURE 2. Differences in body depth between goby species. A boxplot of body depth (as a % of body length in SL) for the three gobies, with sample sizes in parentheses. For the boxplot: box boundaries represent 25th and 75th percentiles respectively; line inside box indicates the median, lower and upper error lines indicate 10th and 90th percentiles respectively, and circles show data falling outside 10th and 90th percentiles.

opencc-by-4.0Apr 2023View details →

A cryptic host-parasitoid interaction reduces the impact of heatwaves on host populations

This is a dataset accompanying the preprint of the same title. The experiment investigated how parasitoid infection affects the heat tolerance of host populations, and how this interactive effect is modulated by the availability of nutrients (dietary yeast).   Abstract: Laboratory measures of thermal performances are widely used to predict the response of populations to climate change. However, such approaches rarely account for numerous stressors that organisms experience alongside a changing climate, such as interactions with consumers and food resources. Trophic interactions such as predation have been shown to stabilise prey populations during heatwaves. Parasitism not only greatly influences the demography as predation does, but also the physiological states of hosts. The extent to which parasitoid infection modifies the tolerance of host populations has not been addressed empirically. We hypothesised that parasitism would in contrast lower the heat tolerance of hosts, and that this negative effect would be more pronounced when nutrition was limited due to conflicts in resource allocation to different defensive processes. We, therefore, examined the independent and joint effects of an extreme temperature event, parasitism, and nutrition on the survival of three Drosophila hosts. Dietary yeast (a primary source of protein) had contrasting impacts on the ability of populations to withstand high temperatures and parasitoid infection. Past exposure to parasitoids stabilized host populations against heatwaves, regardless of their underlying susceptibility to parasitism. Particularly, parasitoid infection occurring on unsuitable hosts (no parasitoids successfully emerge from these hosts) also reduced the extent to which host abundances were decreased by heatwaves. Our results emphasize the context-dependency of heat tolerance which is crucial for predicting consumer-resource dynamics under climate change.

opencc-by-4.0Apr 2023View details →

Structure Databases: Analysis and Augmentation of Guest-Host Interaction Energy Models as CHA and AEI Zeolite Crystallization Phase Predictors

Structures and energies associated with the paper: Analysis and Augmentation of Guest-Host Interaction Energy Models as CHA and AEI Zeolite Crystallization Phase Predictors

opencc-by-4.0Jun 2023View details →

Aggressive interactions among white-tailed deer and their impact on the use of 4-poster devices for host-targeted tick control

Spreadsheet of data transcribed from images of deer and non-target wildlife with coded behaviors used in the manuscript "Aggressive interactions among white-tailed deer and their impact on the use of 4-poster devices for host-targeted tick control". Data involves cameras placed at three sites in Maryland 2016-2017.

Fig. 5 in Correlational nutritional relationships and interactions between expansive holoparasite Orobanche laxissima and woody hosts on metal-rich soils

Fig. 5. General habit of parasite, its hosts and habitats: A-C – Orobanche laxissima (Orobanchaceae) parasitizes Punica granatum (Lythraceae) in Sighnaghi, B – flowering P. granatum, D-F – O. laxissima parasitizes Fraxinus angustifolia (Oleaceae) near Antoki, E F. angustifolia leaves. Photo by R. Piwowarczyk.