CALMIM

The California Landfill Methane Inventory Model is a 1-dimensional soil gas transport and oxidation model that calculates annual landfill methane emissions based on the cover soil characteristics and annual climatic data for a given global location.

Agroecosystems & Environment

Data from: First Report of Squash vein yellowing virus in Watermelon in Guatemala

Watermelon (Citrullus lanatus) and other cucurbits are important crops grown in Guatemala for local consumption and export. Four samplings of crowns, peduncles, and/or leaves of symptomatic plants were made in March and April 2015. Total RNA was extracted from symptomatic plant tissue and tested by RT-PCR for SqVYV, CYSDV, PRSV, and/or begomoviruses. This is the first report of SqVYV infecting watermelon in Central America.

Plants and Crops

Data from: The Majority of Genotypes of the Virulence Gene inlA Are Intact among Natural Watershed Isolates of Listeria monocytogenes from the Central California Coast

Internalin A is an essential virulence gene involved in the uptake of the foodborne pathogen Listeria monocytogenes into host cells. It is intact in clinical strains and often truncated due to Premature Stop Codons (PMSCs) in isolates from processed foods and processing facilities. Less information is known about environmental isolates. We sequenced the inlA alleles and did Multi Locus Variable Number Tandem Repeat Analysis (MLVA) on 112 L. monocytogenes isolates from a 3-year period from naturally contaminated watersheds near a leafy green growing area in Central California.

Genomics and Genetics

Spatial Modeling for Resources Framework (SMRF)

Spatial Modeling for Resources Framework (SMRF) was developed at the USDA Agricultural Research Service (ARS) in Boise, ID, and was designed to increase the flexibility of taking measured weather data and distributing the point measurements across a watershed.

Agroecosystems & Environment

Data from: Chromosome-level genome assembly and transcriptome of the green alga Chromochloris zofingiensis illuminates astaxanthin production

For genome assembly of C. zofingiensis strain SAG 211–14, we used a hybrid approach blending short reads (Illumina), long reads (Pacific Biosciences of California), and whole-genome optical mapping (OpGen) (SI Appendix, SI Text and Datasets S1–S19, and refer to SI Appendix, Datasets Key). The combined power of these approaches yielded a high-quality haploid nuclear genome of C. zofingiensis of ∼58 Mbp distributed over 19 chromosomes (Fig. 2) in the tradition of model organism projects, as opposed to the fragmentary “gene-space” assemblies typical of modern projects using high-throughput methods and associated software. Approximately 99% of reads from the Illumina genomic libraries were accounted for, and nonplaceholder chromosomal sequence covers ∼94% of the optical map. Because no automated pipeline was found able to achieve the desired quality, methods are described in SI Appendix, SI Text.

Genomics and Genetics

Pacific Southwest Region (Region 5) Geospatial Data

The Pacific Southwest Region has geospatial datasets available for download from this website. These datasets are zipped personal or file geodatabases created using ESRI ArcGis 10.0 software. Additional descriptive information as well as data steward contact information, for each geodatabase, can be found under the metadata link.

Maps and Multimedia

Data from: Data from camera surveys identifying co-occurrence and occupancy linkages between fishers (Pekania pennanti), rodent prey, mesocarnivores, and larger predators in mixed-conifer forests

These data provide information on the frequency of fisher detections by camera traps, and single-season occupancy and local persistence of fishers in small patches of Sierra Nevada mixed-conifer forest habitats. The data are used to identify basic patterns of co-occurrence with fishers, and to evaluate the relative importance of presence of competing mesocarnivores, rodent prey, and predators for fisher occupancy of small, 1 km^2^ grid cells of forest habitat.

Animals and Livestock

Homalodisca vitripennis genome annotations v0.5.3

The Homalodisca vitripennis genome was recently sequenced and annotated as part of the i5k pilot project by the Baylor College of Medicine. This dataset presents the Homalodisca vitripennis genome v1.0. This assembly version is the pre-release version, prior to filtering and quality control by the National Center for Biotechnology Information's GenBank resource.

glassy-winged sharpshooter (Homalodisca vitripennis)

Homalodisca vitripennis Genome Assembly 1.0

The Baylor College of Medicine recently sequenced and annotated the Homalodisca vitripennis genome as part of the i5k pilot project. This dataset presents the Homalodisca vitripennis genome v1.0. This assembly version is the pre-release version, prior to filtering and quality control by the National Center for Biotechnology Information's GenBank resource.

glassy-winged sharpshooter (Homalodisca vitripennis)