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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.

Dataset Info

These fields are compatible with DCAT, an RDF vocabulary designed to facilitate interoperability between data catalogs published on the Web.
FieldValue
Authors
Scully, Erin D.
(ORCID)
Gupta, Adarsh K.
(ORCID)
Palmer, Nathan A.
(Scopus Author ID)
Geib, Scott M.
(ORCID)
Sarath, Gautam
(ORCID)
Hein, Gary L.
(ORCID)
Tatineni, Satyanarayana
(ORCID)
Product Type
Genome/Genetics Data
Equipment or Software Used
Trinity
Trinotate
blastp
Intended Use
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.
Use Limitations
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.
Publisher
Ag Data Commons
Contact Name
Scully, Erin
Contact Email
Erin.Scully@ars.usda.gov
Public Access Level
Public
License
U.S. Public Domain
Funding Source(s)
Agricultural Research Service
5440-21000-033-00D
National Institute of Food and Agriculture
2013-68004-20358
Dataset DOI (digital object identifier)
10.15482/USDA.ADC/1471685
Program Code
005:040 - Department of Agriculture - National Research
Bureau Code
005:18 - Agricultural Research Service
ARIS Log Number
357 669
Modified Date
2018-12-11
Release Date
2018-09-18
Ag Data Commons Keywords: 
  • Genomics & Genetics
  • Genomics & Genetics
  • Transcriptome
State or Territory: 
Kansas
Nebraska
National Agricultural Library Thesaurus Term: 
transcriptome
Aceria tosichella
Wheat streak mosaic virus
gene expression
databases
prediction
wheat
open reading frames
unigenes
data collection
transcription (genetics)
reproduction
mites
plant diseases and disorders
plant viruses
viruses
inventories
sequence analysis
Eriophyidae
User-supplied Tags: 
de novo transcriptome
Aceria tosichella
Trinity
Transdecoder
mites
wheat streak mosaic virus
RNA-Seq
Eriophyidae
NP304
np301
ISO Topic(s): 
biota

Suggested Citation:

(dataset) Scully, Erin D.; Gupta, Adarsh K.; Palmer, Nathan A.; Geib, Scott M.; Sarath, Gautam; Hein, Gary L.; Tatineni, Satyanarayana (2018). De novo transcriptome assembly and annotations for wheat curl mite (Aceria tosichella). Ag Data Commons. http://dx.doi.org/10.15482/USDA.ADC/1471685