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.
- Nucleotide coding regions for final transcriptome assembly for wheat curl mitetxt
Nucleotide sequences corresponding to coding regions from the final...
- Protein predictions for final transcriptome assembly (wheat curl mite)txt
Protein coding regions were predicted using Transdecoder. ORFs were...
- Trinotate annotations for final Trinity assembly (wheat curl mite)xlb
Trinotate results for final wheat curl mite transcritpome assembly. Blastp...
- Final trinity transcriptome assembly for wheat curl mitetxt
Transcripts less than 200 nt and transcripts with TPM values less than 0.5...
- Protein predictions for raw trinity transcriptome assembly (wheat curl mite)txt
Putative coding regions were predicted using Transdecoder. Default...
- Trinotate annotations for raw Trinity assemblyxlb
Trinotate results for raw wheat curl mite transcriptome assembly
- Blastp results versus non-redundant protein databasetxt
Blastp results for protein coding unigenes from raw Trinity transcriptome...
- Raw Trinity Assemblytxt
Raw trinity assembly obtained from wheat curl mite using 50 x 50 Illumina...
Dataset InfoThese fields are compatible with DCAT, an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web.
|Equipment or Software Used|
The dataset was generated to compare the transcriptional responses of wheat curl mites exposed to wheat streak mosaic viruses with control mites. The purpose of this study was to gain a better understanding of how wheat streak mosaic virus alters reproduction and development of wheat curl mite.
The transcriptome assembly was generated from pools of mites feeding on virus infected plants or control plants that had been inoculated with water. Thus, this assembly will only contain genes that are expressed by mites during these conditions and may not necessarily represent a complete inventory of genes coded by wheat curl mite.
Ag Data Commons
|Public Access Level|
Agricultural Research Service
National Institute of Food and Agriculture
|Dataset DOI (digital object identifier)|
005:040 - Department of Agriculture - National Research
005:18 - Agricultural Research Service
|ARIS Log Number|
- Genomics & Genetics
- Genomics & Genetics