AgBase

AgBase Version 2.0 is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products including gene ontology annotations. Its long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. AgBase uses controlled vocabularies developed by the Gene Ontology (GO) Consortium to describe molecular function, biological process, and cellular component for genes and gene products in agricultural species.

Genomics and Genetics

Data from: A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System

A 2.3 Gb de novo genome assembly of a field-collected adult female Spotted Lanternfly (Lycorma delicatula) using a single PacBio SMRT Cell is provided. Supporting files for the manuscript "A High-Quality Genome Assembly from a Single, Field-collected Spotted Lanternfly (Lycorma delicatula) using the PacBio Sequel II System", include several intermediate versions of the assembly (raw output from Falcon, raw output from Falcon unzip, etc.) as well as the final assembly primary contigs and haplotigs (for the regions of the genome that were phased).

SLF-spotted lanternfly (Lycorma delicatula); adult winged. Photo: Stephen Ausmus, ARS Image Gallery

Cligen

Cligen is a stochastic weather generator which produces daily estimates of precipitation, temperature, dewpoint, wind, and solar radiation for a single geographic point, using monthly parameters (means, SD's, skewness, etc.) derived from the historic measurements. Unlike other climate generators, it produces individual storm parameter estimates, including time to peak, peak intensity, and storm duration, which are required to run the WEPP and the WEPS soil erosion models.

Agroecosystems & Environment

Data from: Cultivar resistance to common scab disease of potato is dependent on the pathogen species

All data from the paper "Cultivar resistance to common scab disease of potato is dependent on the pathogen species." Three separate datasets are included:
1.A csv file with the disease severity of three common scab pathogens across 55 different potato cultivars in a greenhouse pot assay (Figures 2-5 in the associated paper). The included R script was used with this data to perform the ANOVA for the data from the greenhouse pot assay (Table 2 in the associated paper). This script can be used in R for any similar dataset to calculate the significance and percent of total variation for any number of user-defined fixed effects.
2. A zipped file with all of the qPCR data for the expression of the txtAB genes (Figure 6 in the associated paper).
3. An Excel file with the HPLC data for making the thaxtomin detection standard curve and quantifying the amount of thaxtomin in the test sample.

Plants and Crops

Oncopeltus fasciatus hybrid genome assembly 1.0

The milkweed bug, Oncopeltus fasciatus, was sequenced as part of the i5k pilot project from Baylor College of Medicine (Illumina data). To augment those resources, we present here a hybrid genome assembly with low coverage PacBio data, assembled with PBJelly: the Oncopeltus fasciatus Hybrid Genome Assembly v1.0.

insects 5000 program

Data from: Genome of the small hive beetle (Aethina tumida, Coleoptera: Nitidulidae), a worldwide parasite of social bee colonies, provides insights into detoxification and herbivory

The small hive beetle (Aethina tumida, ATUMI) is an invasive parasite of bee colonies. ATUMI feeds on both fruits and bee nest products, facilitating its spread and increasing its impact on honey bees and other pollinators. The ATUMI genome has been sequenced and annotated, providing the first genomic resources for this species and for the Nitidulidae.

Genomics and Genetics

Data from: Draft genome of the rice coral Montipora capitata obtained from linked-read sequencing

THIS DATA HAS BEEN UPDATED: PLEASE SEE http://dx.doi.org/10.15482/USDA.ADC/1503958 FOR THE UPDATED VERSION. Gene models for protein-coding genes in the genome of the rice coral Montipora capitata, Hawaii Island. Annotation was performed with Augustus v3.3.1, using RNA-seq data as extrinsic evidence. Gene structures (.gff), coding sequences (_cds.fas), and amino acid sequences (_aa.fas) are provided.

Genomics and Genetics