,The ascomycete Neofusicoccum parvum, one of the causal agents of Botryosphaeria dieback, is a destructive wood‐infecting fungus and a serious threat to grape production worldwide. The capability to colonize woody tissue, combined with the secretion of phytotoxic compounds, is thought to underlie its pathogenicity and virulence. Here, we describe the repertoire of virulence factors and their transcriptional dynamics as the fungus feeds on different substrates and colonizes the woody stem. We assembled and annotated a highly contiguous genome using single‐molecule real‐time DNA sequencing. Transcriptome profiling by RNA sequencing determined the genome‐wide patterns of expression of virulence factors both in vitro (potato dextrose agar or medium amended with grape wood as substrate) and in planta. Pairwise statistical testing of differential expression, followed by co‐expression network analysis, revealed that physically clustered genes coding for putative virulence functions were induced depending on the substrate or stage of plant infection. Co‐expressed gene clusters were significantly enriched not only in genes associated with secondary metabolism, but also in those associated with cell wall degradation, suggesting that dynamic co‐regulation of transcriptional networks contributes to multiple aspects of N. parvum virulence. In most of the co‐expressed clusters, all genes shared at least a common motif in their promoter region, indicative of co‐regulation by the same transcription factor. Co‐expression analysis also identified chromatin regulators with correlated expression with inducible clusters of virulence factors, suggesting a complex, multi‐layered regulation of the virulence repertoire of N. parvum.,,

This data release includes metadata and tabular datasets that document (1) Austropuccina, Ceratocystis and Myrtaceae qPCR (quantitative polymerase chain reaction) DNA detections in Passive Environmental Samplers (PES), (2) wind speed, wind gust speed, and wind direction measurements collected at two sites in the Kahuku Unit of Hawai'i Volcanoes National Park (HAVO) where paired PES were located, (3) localities, sites and elevations where PES were located, and (4) Genbank accession numbers for Austropuccinia and Ceratocystis DNA sequences amplified from samples collected in a subset of PES. These raw data were analyzed and reported in the manuscript "Environmental Monitoring for Invasive Fungal Pathogens of ʽŌhiʽa (Metrosideros polymorpha) on the Island of Hawaiʽi".

Data includes head smut infection level (caused by the fungal pathogen, Ustilago bullata) on cheatgrass (Bromus tectorum) and cheatgrass cover for plots measured annually during the first four years after the 2015 Soda wildfire. Additional landscape and weather covariates that are hypothesized to influence infection and host density are included.

Rapid ʽŌhiʽa Death (ROD) currently threatens ōhiʽa lehua (Metrosideros polymorpha) on Hawaiʽi Island. First identified in Puna in 2014, the disease has now spread island wide. Besides direct sampling of trees, environmental sampling could serve as an easier and broader strategy to detect Ceratocystis spp., the fungi causing Rapid Ohia Death (ROD). Envrionmental sampling could also help monitor the effect of felling ROD infected trees. We developed Passive and Active Environmental Samplers for collecting airborne particulates and deployed them at a property in Puna, where both C. lukuohia, and C. huliohia had been detected, and where the land owner practiced the management method of felling infected trees. We set up 2 Active Environmental Samplers (modified mosquito traps connected to a battery that uses a fan to continuously draw in air) and 3 Passive Environmental Samplers (uses a vane to move in the direction of the wind without the use of electricity) from July 12th to October 25th, 2016. The Active Traps contained one slide (1 replicate) each, while the Passive Traps contained 4 slides (4 replicates) each. Wind and precipitation data from a National Oceanic and Atmospheric Agency (NOAA) weather station at the Hilo airport was used in analysis. The dataset contains a list of sampling weeks, their start and end dates, and whether or not tree felling occurred during that week.

Rapid ʽŌhiʽa Death (ROD) currently threatens ōhiʽa lehua (Metrosideros polymorpha) on Hawaiʽi Island. First identified in Puna in 2014, the disease has now spread island wide. Besides direct sampling of trees, environmental sampling could serve as an easier and broader strategy to detect Ceratocystis spp., the fungi causing ROD. Environmental sampling could also help monitor the effect of felling ROD infected trees. We developed Passive and Active Environmental Samplers and deployed them at a property in Puna, where both C. lukuohia, and C. huliohia had been detected, and where the land owner practiced the management method of felling infected trees. We set up 2 Active Environmental Samplers (modified mosquito traps connected to a battery that uses a fan to continuously draw in air) and 3 Passive Environmental Samplers (uses a vane to move in the direction of the wind without the use of electricity) from July 12th to October 25th, 2016. The Active Samplers contained one slide (1 replicate) each, while the Passive Samplers contained 4 slides (4 replicates) each. Samplers were located in the lawn (2 Active, 1 Passive), next to a rainwater catchment tank (1 Passive), and next to a small shed (1 Passive). The dataset contains a list of sampling weeks and their start and end dates, and quantitative polymerase chain reaction (qPCR) results for individual slides that were collected from Active and Passive Samplers located at the Lawn, Tank and Shed sites. Samples were tested twice for Ceratocystis lukuohia, Ceratocystis huliohia, and Metrosideros polymorpha DNA after extraction with a Machery Nagel Plant II Extraction Kit and again after DNA was concentrated by ethanol precipitation. Positive qPCR test results are presented as quantitation cycle (Cq) in which fluorescence is detected for Ceratocystis lukuohia, Ceratocystis huliohia, and Metrosideros polymorpha DNA for each individual slide and number of replicates that were positive out of three for C. lukuohia and C. huliohia and out of six for M. polymorpha. Lines that are blank in columns for Cq values reflect negative test results. When Cq values have more than one replicate for a test, the reported Cq value represents the average of all positive replicates.

Swiss needle cast foliar retention metrics. This dataset is associated with the following publication: Lan, Y., D.C. Shaw, E. Lee, and P. Beedlow. Distribution of a foliage disease fungus within canopies of mature Douglas-fir in western Oregon. Frontiers in Forests and Global Change. Frontiers, Lausanne, SWITZERLAND, 5: 743039, (2022).

##This checklist database is a collection of reports from 16 sources referenced in the "data_set" parameter. They consist of: 1. bishop museum: Data from the Bishop museum fungal database 2. board report: From National Agricultural Pest Information System (NAPIS) board reports 3. [bugwood](https://www.bugwood.org/plantdiseases.cfm): Widely prevalent Fungi, Bacteria, and Virues in Hawaii from bugwood database 4. CAPS survey data: Cooperative Agriculture Pest Survey databases (negative data) 5. [crop knowledge master](http://www.extento.hawaii.edu/kbase/crop/cropmenu.htm): crop knowledge master website 6. CTAHR New Pest reports: Collected by Dr. Michael Melzer 7. [Don Gardner](http://www.hear.org/pph/database/#dongardnerlegacydatabase): Data from Don Gardner’s legacy database 8. First report: First reports found from literature search of scientific journals (Google Scholar, Web of Science, PubMed) 9. [GBIF](https://www.gbif.org/): Global Biodiversity Information Facility 10. [hawaii checklist](https://scholarspace.manoa.hawaii.edu/items/43c51984-f009-40ff-851c-107f0269a6d5): The “2009 Checklist of Plant Diseases in Hawaii” 11. Hawaii NPDN data: National Plant Diagnostic Data from Hawaii (detections from Hawaii and dignosed at labs in AZ, FL, HI, NC, NY, OR, SC, and WI). 12. [HDOA new pest advisory](https://hdoa.hawaii.gov/pi/ppc/new-pest-advisories/): Hawaii Department of Agriculture new pest advisory 13. miscellaneous: personal literature search 14. NAPIS data: National Agricultural Pest Information System database 15. [UH extension articles](https://www.ctahr.hawaii.edu/site/PubList.aspx?key=Plant%20Disease): University of Hawaii extension articles 16. USDA_confirmations: USDA National Agricultural Statistics Service This is a compile of detections and not negative data. The exception would be the CAPS data, in which negative data would represent the entire state. Negative CAPS data are represented by zero values in the island columns. ##The database consist of 23 columns. Below is a discription of each column. Number of unique values are in parentheses. 1. host_family (186): Scientific family name of plant host 2. host_genus (675): Scientific genus name of plant host 3. host_species (839): Scientific species name of plant host 4. host_scientific_name (1361): Scientfic binomial noenclature of plant host 5. host_common_name (921): Plant host common name from [Forest & Kim Starr](http://www.starrenvironmental.com/images/) and USDA PLANTS Database 6. pathogen_genus (3378): Scientific genus name of plant pathogen genus name of plant pathogen 7. pathogen_species (3397): Scientific species name of plant pathogen 8. pathogen_scientific_name (7007): Scientfic binomial noenclature of pathogen host 9. pathogen_group (16): Seperates organisms in pathogen name columns into nematode, entomopathogenic fungi, saprophytic fungi, bacteria, amoeba, unknown, virus, fungi, and parasitic plant 10. pathogen_status (2): Consit of sources that determine organism in pathogen name columns as a plant-pathogen or not (manual research, hawaii checklist pathogen, fungus-host database pathogen, based on name - for viruses only, and NPDN database pathogen) 11. data_set (16): Source of report (details above) 12. status: The status of pathogen present in Hawaii (absent or present) 13. year: Date of report (117 years) 14. Hawaii: Presence of pathogen in the island of Hawaii (1=present, 0=absent, blank=unknown) 15. Maui: Presence of pathogen in the island of Maui (1=present, 0=absent, blank=unknown) 16. Lanai: Presence of pathogen in the island of Lanai (1=present, 0=absent, blank=unknown) 17. Molokai: Presence of pathogen in the island of Molokai (1=present, 0=absent, blank=unknown) 18. Oahu: Presence of pathogen in the island of Oahu (1=present, 0=absent, blank=unknown) 19. Kauai: Presence of pathogen in the island of Kauai (1=present, 0=absent, blank=unknown) 20. Kahoolawe: Presence of pathogen in the island of Kahoolawe (1=present, 0=absent, blank=unknown)

The exotic grass-fire cycle is degrading semiarid rangelands, such as the vast areas of shrub-steppe in North America now invaded by fire-promoting cheatgrass. Chemical- or bio-herbicides are sprayed onto soils to inhibit the invaders, but information on chemical- or bio-herbicide effects on plant communities is limited. We asked how the plant community responded to the bioherbicide Pseudomonas fluorescens strain ACK55 (Battalion Pro®) in comparison to the separate and combined effects of the most conventional pre-emergent chemical herbicide, imazapic (Plateau®), in two cheatgrass-invaded sagebrush-steppe sites. Plant community responses are compared with soil microbial community responses in the Larger Work, and soil microbial data are available in GenBank. Plant community responses are compared with soil microbial community responses in the Larger Work, and soil microbial sequence data were deposited to the NCBI Short Read Archive (BioProject PRJNA1254875).

,Ramularia crupinae is a foliar and stem blighting fungal pathogen specific to the invasive rangeland weed common crupina (Crupina vulgaris). This fungal plant pathogen was recently approved by the Animal and Plant Health Inspection Service (APHIS) as the first biological control agent for the management of common crupina in the western United States. The genome assembly for R. crupinae 00-010 (https://mycocosm.jgi.doe.gov/Ramcr1/Ramcr1.info.html) contains 18 contigs totaling 37.9 Mb, and was annotated using the JGI fungal annotation pipeline. The information contained within this Ag Data Commons dataset provides an updated R. crupinae chromosome-level genome assembly. These data are freely available for research purposes.,Resources in this dataset:,