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

Annotations of Unigenes Assembled from Schizaphis graminum and Sipha flava

Transcriptomes were assembled de novo from pools of adult aphids that were feeding on sorghum and switchgrass. Reads from all replicates were pooled, normalized in silico to 25X coverage, and assembled using Trinity. Only the most abundant isoform for each unigene was retained for annotation and unigenes with transcripts per million mapped reads (TPM) less than 0.5 were removed from the dataset. The remaining unigenes were annotated using Trinotate with BLASTP comparisons against the Swiss-Prot/UniProt database. In addition, Pfam-A assignments were computed using hmmer, signal peptide predictions were performed using SignalP, and transmembrane domain predictions were performed using tmHMM. Gene ontology (GO assignments) were retrieved from Trinotate using the highest scoring BLASTp matches as queries.

Genomics and Genetics

USDA/ARS Kimberly, ID - Furrow Infiltration and Erosion Data, 1998 to 2016

The data are derived from the field monitoring of irrigated furrows from 1998 to 2016 at the research farm of the USDA/ARS-Northwest Irrigation and Water Research Laboratory in Kimberly, Idaho, USA (south-central Idaho). For each monitored furrow, irrigation inflow rates, outflow rates, and sediment concentrations were recorded periodically during the irrigation. A gated pipe conveyed irrigation water across the plots at the head, or inflow-end, of the furrows and adjustable spigots supplied water to each irrigated furrow.

Agroecosystems & Environment

Data from: The assembled transcriptome of the adult horn fly, Haematobia irritans

To better understand the adult horn fly, Haematobia irritans irritans, and the development of resistance in natural populations, an Illumina paired-end read HiSeq and GAII approach was used to determine the transcriptomes of untreated control adult females, untreated control adult males, permethrin-treated surviving adult males and permethrin + piperonyl butoxide-treated killed adult males from a Louisiana population of horn flies with a moderate level of pyrethroid resistance.

Genomics and Genetics


myPhyloDB is an open-source software package aimed at developing a user-friendly web-interface for accessing and analyzing all of your laboratory's microbial ecology data (currently supported project types: soil, air, water, microbial, and human-associated). The storage and handling capabilities of myPhyloDB archives users' raw sequencing files, and allows for easy selection of any combination of projects/samples from all of your projects using the built-in SQL database. The data processing capabilities of myPhyloDB are also flexible enough to allow the upload, storage, and analysis of pre-processed data or raw (454 or Illumina) data files using the built-in versions of Mothur and R.

Agroecosystems & Environment

Compilation of climate data from heterogeneous networks across the Hawaiian Islands

This paper provides: (1) a summary of the available climate data in Hawai‘i including a detailed description of the various meteorological observation networks and data accessibility, and (2) a quality-controlled meteorological dataset across the Hawaiian Islands for the 25-year period 1990-2014. The dataset draws on observations from 471 climate stations and includes rainfall, maximum and minimum surface air temperature, relative humidity, wind speed, downward shortwave and longwave radiation data.

Agroecosystems & Environment