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Ag Data Commons migration begins October 18, 2023

The Ag Data Commons is migrating to a new platform – an institutional portal on Figshare. Starting October 18 the current system will be available for search and download only. Submissions will resume after the launch of our portal on Figshare in November. Stay tuned for details!

De novo transcriptome assembly of Schizaphis gramium Biotype I feeding on wheat

    Transcriptome was generated from pooled adult aphids that were fed on wheat plants containing the Dn4 and DN7 resistance gene as well as Yuma plants containing no resistant genes (Dn0). The assembly was generated using Trinity. All assembled transcripts, including those that were not predicted to encode ORFs, are included along with their corresponding functional annotations from Trinotate.

    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.

      GenSAS: A Web-Based Platform for Structural and Functional Annotation and Curation of Genomes

        The Genome Sequence Annotation Server (GenSAS) is an online platform that provides a pipeline for whole genome structural and functional annotation. Users can upload genome sequences and select from a variety of tools for repeat masking, prediction of gene models and other structural features as well as functional annotation tools. GenSAS integrates with JBrowse and Apollo to provide visualization and editing.