Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
10
datasets available to search
ShareScore release 0.9.0
Dataset results
10 results for “Potyvirus”
Viral reference genomes to disentangle the recombinant phylogenetic history of the potyviruses
<p>Potyviruses are a large genus of plant-infecting RNA viruses in the family Potyviridae. Due to their rapid diversification and frequent recombination, reconstructing the phylogenetic history of the potyviruses has proven difficult. Phylogenies reconstructed from different protein-coding regions of the viral genome often reveal conflicing or discordant relationships. But the extent to which discordance is due to interspecific recombination versus phylogenetic noise or errors in reconstruction is unclear. </p> <p>To explore the recombinant history of the potyviruses, we assembled a dataset containing referece genomes for 131 species of potyviruses. High-quality, full-length reference genomes for all species were obtained form NCBI GenBank. Viral genomes were carefully aligned at the codon-level and screened for recombination. The full alignment was then partitioned into several sub-alignments between each detected recombination event, such that each sub-aligment corresponds to a non-recombinant block (NRB) free of detected recombination events. Local phylogenetic trees for each NRB were then reconstructed to explore how phylogenetic relationships varied across different regions of the potyvirus genome. </p> <p>We then used our program Espalier to disentangle the phylogenetic history of the potyviruses. Espalier reconciles and removes discordances between phylogenetic trees that are likely attributable to phylogenetic error while retaining recombination events that are strongly supported by the sequence data. Applying Espalier to the potyviruses revealed that most phylogenetic discordace between local trees is likely attributable to phylogenetic noise. Removing the discordance attributable to phylogenetic error allows us to much more clearly visualize the phylogenetic history of the potyviruses.</p>
Viral reference genomes to disentangle the recombinant phylogenetic history of the potyviruses
Open the record for dataset details and reuse information.
Data from: Outcomes of co-infection by two potyviruses: implications for the evolution of manipulative strategies
Recent studies have documented effects of plant-viruses on host plants that appear to enhance transmission by insect vectors. But, almost no empirical work has explored the implications of such apparent manipulation for interactions among co-infecting pathogens. We examined single and mixed infections of two potyviruses, Watermelon mosaic virus (WMV) and Zucchini yellow mosaic virus (ZYMV), that frequently co-occur in cucurbitaceae populations and share the same aphid vectors. We found that ZYMV isolates replicated at similar rates in single and mixed infections, while WMV strains accumulated to signficantly lower levels in the presence of ZYMV. Furthermore, ZYMV induced changes in leaf colour and volatile emissions that enhanced aphid (Aphis gossypii) recruitment to infected plants. In contrast, WMV did not elicit strong effects on plant-aphid interactions. Nevertheless, WMV was still readily transmitted from mixed infections, despite fairing poorly in in-plant competition. These findings suggest that pathogen effects on host-vector interactions may well influence competition among co-infecting pathogens. For example, if non-manipulative pathogens benefit from the increased vector traffic elicited by manipulative competitors, their costs of competition may be mitigated to some extent. Conversely, the benefits of manipulation may be limited by free-rider effects in systems where there is strong competition among pathogens for host resources and/or access to vectors.
Data from: Outcomes of co-infection by two potyviruses: implications for the evolution of manipulative strategies
Open the record for dataset details and reuse information.
Analysis of transcriptional response to mutated Potyvirus Potato virus A that induces necrotic symptoms.
GEO Series GSE42833. Nicotiana tabacum. 8 samples. Type: Expression profiling by array.
Viral fitness correlates with the magnitude and direction of the perturbation induced in the host's transcriptome: the tobacco etch potyvirus - tobacco case study.
GEO Series GSE99838. Nicotiana tabacum. 26 samples. Type: Expression profiling by array.
Transcript profiling of different Arabidopsis thaliana ecotypes in response to Tobacco etch potyvirus infection
GEO Series GSE37269. Arabidopsis thaliana. 53 samples. Type: Expression profiling by array.
potyvirus-Transcriptional analysis of Arabidopsis thaliana infected by a potyvirus.
GEO Series GSE8875. Arabidopsis thaliana. 12 samples. Type: Expression profiling by array.
potyvirus effect-Transcriptionnal response to potyviruses infection in Arabidopsis
GEO Series GSE10707. Arabidopsis thaliana. 12 samples. Type: Expression profiling by array.
arabidopsis ecotypes-Transcriptionnal response to potyviruses infection in Arabidopsis
GEO Series GSE10711. Arabidopsis thaliana. 12 samples. Type: Expression profiling by array.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.