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]
- Trinotate annotations for unigenes assembled from Schizaphis graminum (greenbug)xlb
::Note:: Data file is large and may take time to load.
MD5:Explore Data597.28 MB - Trinotate annotations of unigenes assembled from Sipha flava (yellow sugarcane aphid)xlb
::Note:: Data file is large and may take time to load.
MD5:Explore Data698.8 MB - Supplemental Data 1: Differential expression analysis of starvation and BCK60 sorghum treatments in S. graminum at 12 and 24 hoursxlsx
Reads were mapped back to the transcriptome assembly using bowtie2 and RSEM...
MD5:Explore Data339.15 KB - Supplemental Data 2. Differential expression analysis of starvation and BCK60 sorghum treatments in S. flava at 12 and 24 hoursxlsx
Reads were mapped back to the transcriptome assembly using bowtie2 and RSEM...
MD5:Explore Data140.21 KB - Supplemental Data 3. Differential expression analysis of Summer switchgrass and BCK60 sorghum treatments in S. graminum at 12 and 24 hoursxlsx
Reads were mapped back to the transcriptome assembly using bowtie2 and RSEM...
MD5:Explore Data170.91 KB - Supplemental Data 4. Differential expression analysis of Summer switchgrass and BCK60 sorghum treatments in S. flava at 12 and 24 hoursxlsx
Reads were mapped back to the transcriptome assembly using bowtie2 and RSEM...
MD5:Explore Data192.8 KB - Supplemental Data 5. Differential expression analysis of Kanlow switchgrass and BCK60 sorghum treatments in S. graminum t 12 and 24 hoursxlsx
Reads were mapped back to the transcriptome assembly using bowtie2 and RSEM...
MD5:Explore Data111.61 KB - Supplemental Data 6. Differential expression analysis of Kanlow switchgrass and BCK60 sorghum treatments in S. flava t 12 and 24 hoursxlsx
Reads were mapped back to the transcriptome assembly using bowtie2 and RSEM...
MD5:Explore Data108.75 KB
Field | Value |
---|---|
Tags | |
Modified | 2022-09-27 |
Release Date | 2018-09-21 |
Identifier | b9f0ad51-f40f-4171-839b-6a86b220323f |
Publisher | Ag Data Commons |
Spatial / Geographical Coverage Location | Lincoln, Nebraska |
License | |
Contact Name | Scully, Erin |
Contact Email | |
Public Access Level | Public |
Program Code | 005:040 - Department of Agriculture - National Research |
Bureau Code | 005:00 - Department of Agriculture |