Ag Data Commons
4 files

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

posted on 2024-02-15, 20:20 authored by Erin ScullyErin Scully, Lina Aguirre Rojas, Laramy Enders, Alicia E. Timm, Deepak K. Sihna, Charles Michael Smith

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.

Resources in this dataset:

  • Resource Title: De novo transcriptome assembly of Schizaphis graminum Biotype I.

    File Name: Trinity.fasta_.txt

    Resource Description: Reads were assembled using Trinity version 2.3.2. All transcripts greater than 200 nt were retained in this version of the assembly.

    Resource Software Recommended: Notepad++,url:

  • Resource Title: Filtered Transcriptome Assembly of Schizaphis graminum.

    File Name: GreenbugFilteredTrinity.transdecoder.mRNA.fasta_.txt

    Resource Description: Only transcripts with transcripts per million mapped reads values (TPM) >=0.05 and transcripts whose expression levels represented >=10% of their dominant isoform were retained for differential expression.

    Resource Software Recommended: Notepad++,url:

  • Resource Title: Trinotate results for Schizaphis graminum transcriptome assembly.

    File Name: Greenbug_trinotate_annotation_report.xls

    Resource Description: Trinotate was used to obtain highest scoring blastp matches to annotated proteins curated in the swiss-prot, detect Pfam domains, obtain gene ontology annotations, and obtain KEGG annotations.

    Resource Software Recommended: Microsoft Excel,url:

  • Resource Title: Protein coding translations of Schizaphis graminum assembly.

    File Name:

    Resource Description: TransDecoder was used to predict open reading frames in the final transcriptome assembly.

    Resource Software Recommended: Notepad++,url:




Data contact name

Scully, Erin

Data contact email


Ag Data Commons


  • Not specified

Geographic Coverage


ISO Topic Category

  • biota

National Agricultural Library Thesaurus terms

transcriptome; biotypes; wheat; imagos; Triticum; resistance genes; open reading frames; gene expression regulation; Schizaphis graminum; proteins; gene ontology; Aphidoidea

OMB Bureau Code

  • 005:18 - Agricultural Research Service

OMB Program Code

  • 005:040 - National Research

Primary article PubAg Handle

Pending citation

  • No

Public Access Level

  • Public

Preferred dataset citation

Scully, Erin D.; Aguirre Rojas, Lina; Enders, Laramy; Timm, Alicia E.; Sihna, Deepak K.; Smith, Charles Michael (2020). De novo transcriptome assembly of Schizaphis gramium Biotype I feeding on wheat. Ag Data Commons.