The Aquatic eDNAtlas Project: Lab Results Map - USFS RMRS

The eDNA samples in the eDNAtlas database describe species occurrence locations and were collected by the U.S. Forest Service and numerous agencies that have partnered with the National Genomics Center for Wildlife and Fish Conservation (NGC) throughout the United States. The eDNAtlas is accessed via an interactive ArcGIS Online (AGOL) map that allows users to view and download sample site information and lab results of species occurrence for the U.S. The results are primarily based on samples analyzed at the National Genomics Center for Wildlife and Fish Conservation (NGC) and associated with geospatial attributes created by the Boise Spatial Streams Group (BSSG).

Genomics and Genetics

Data from: Range size, local abundance and effect inform species descriptions at scales relevant for local conservation practice

This study describes how metrics defining invasions may be more broadly applied to both native and invasive species in vegetation management, supporting their relevance to local scales of species conservation and management. A sample monitoring dataset is used to compare range size, local abundance and effect as well as summary calculations of landscape penetration (range size × local abundance) and impact (landscape penetration × effect) for native and invasive species in the mixed-grass plant community of western North Dakota, USA.

Agroecosystems & Environment

Data from: Data for the calculation of an indicator of the comprehensiveness of conservation of useful wild plants

The datasets and code presented in this Data in Brief article are related to the research article entitled "Comprehensiveness of conservation of useful wild plants: an operational indicator for biodiversity and sustainable development targets". These data facilitate indicator assessments and serve as a baseline against which future calculations of the indicator can be measured. The data can also contribute to other species distribution modeling, ecological research, and conservation analysis purposes.

Plants and Crops

Data from: The downed and dead wood inventory of forests in the United States

The Forest Inventory and Analysis program of the United States (US) Forest Service has conducted an annual downed dead wood (DDW) inventory on all coterminous US forest land since 2002 (~1 plot per 38,850 ha), with a sample intensification occurring since 2012 (~1 plot per 19,425 ha). The data are organized according to DDW components and by sampling information which can all be linked to a multitude of auxiliary information in the national database.

Agroecosystems & Environment

The Triticeae Toolbox

The Triticeae Toolbox (T3) webportal hosts data generated by the Triticeae Coordinated Agricultural Project (CAP), funded by the National Institute for Food and Agriculture (NIFA) of the United States Department of Agriculture (USDA). T3 contains SNP, phenotypic, and pedigree data from wheat and barley germplasm in the Triticeae CAP integrating rapidly expanding DNA marker and sequence data with traditional phenotypic data.

Ag Data Commons

De novo transcriptome assembly and annotations for wheat curl mite (Aceria tosichella)

To study the impact of wheat streak mosaic virus on global gene expression in wheat curl mite, we generated a de novo transcriptome assembly using 50 x 50 paired end reads from the Illumina HiSeq 2500. Reads were assembled using Trinity (version 2.0.6) and contigs greater than 200 nt were retained. All assembled transcripts were annotated using the Trinotate pipeline using blastp searches against the Swiss-prot/Uni-Prot database, blastx searches against the Swiss-prot/Uni-Prot databases, HMM searches against the Pfam-A database, blastp searches against the non-redundant protein database, and signalP and tmHMM predictions. To reduce noise from low abundance transcripts not well supported by the data, we filtered the assembly to retain only those transcripts with TPM values >=0.5.

Genomics and Genetics