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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.

[Note: Supplemental files 1-6 added 2/5/2019]

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)
Koch, Kyle G.
(ORCID)
Palmer, Nathan A.
(Scopus Author ID)
Geib, Scott M.
(ORCID)
Sarath, Gautam
(ORCID)
Heng-Moss, Tiffany M.
(Scopus Author ID)
Bradshaw, Jeffery D.
(Scopus Author ID)
Product Type
Genome/Genetics Data
Spatial / Geographical Coverage Location
Lincoln, Nebraska
Equipment or Software Used
Trinity
Trinotate
Intended Use
This dataset was generated to understand the transcriptional responses of two generalist aphids (Schizaphis graminum and Sipha flava) to different switchgrass cultivars using RNA-Seq.
Use Limitations
For this experiment, aphids were reared on either switchgrass (cv Kanlow and Summer) or sorghum (BCK60). In addition, RNA-Seq data from starved aphids was also included in the comparison. Because our study included only a limited set of experimental conditions, the gene inventory of our transcriptome assembly is only representative of the genes that were expressed under these conditions.
Publisher
Ag Data Commons
Contact Name
Scully, Erin
Contact Email
Erin.Scully@ars.usda.gov
Public Access Level
Public
Primary Article

Koch, K., Scully, E., Palmer, N., Geib, S., Sarath, G., Heng-Moss, T., & Bradshaw, J. (expected 2019). Divergent Switchgrass Cultivars modify Cereal Aphid Transcriptomes. (submitted to Journal Of Economic Entomology).

License
U.S. Public Domain
Funding Source(s)
National Institute of Food and Agriculture
2011-67009-30096
Agricultural Research Service
042-21000-030-00D
Dataset DOI (digital object identifier)
10.15482/USDA.ADC/1471686
Program Code
005:040 - Department of Agriculture - National Research
Bureau Code
005:00 - Department of Agriculture
ARIS Log Number
356 432
Modified Date
2019-02-05
Release Date
2018-09-11
Ag Data Commons Keywords: 
  • Genomics & Genetics
  • Transcriptome
  • Genomics & Genetics
State or Territory: 
Nebraska
National Agricultural Library Thesaurus Term: 
unigenes
Schizaphis graminum
Sipha flava
transcriptome
adults
Aphidoidea
Panicum virgatum
data collection
databases
signal peptide
prediction
gene ontology
transcription (genetics)
cultivars
sequence analysis
rearing
inventories
summer
Sorghum bicolor
biotic stress
abiotic stress
User-supplied Tags: 
switchgrass
Kanlow
Summer
de novo transcriptome
RNA-Seq
Sorghum bicolor
Panicum virgatum
BCK60
biotic stress
abiotic stress
NP215
NP304
ISO Topic(s): 
biota

Suggested Citations:

(original article) Koch, K., Scully, E., Palmer, N., Geib, S., Sarath, G., Heng-Moss, T., & Bradshaw, J. (expected 2019). Divergent Switchgrass Cultivars modify Cereal Aphid Transcriptomes. (submitted to Journal Of Economic Entomology).

(dataset) Scully, Erin D.; Koch, Kyle G.; Palmer, Nathan A.; Geib, Scott M.; Sarath, Gautam; Heng-Moss, Tiffany M.; Bradshaw, Jeffery D. (2018). Annotations of Unigenes Assembled from Schizaphis graminum and Sipha flava. Ag Data Commons. http://dx.doi.org/10.15482/USDA.ADC/1471686