10.5061/DRYAD.T3J7M
Horn, Rebekah L.
Trent University
Ramaraj, Thiruvarangan
National Center for Genome Resources
Devitt, Nicholas P.
National Center for Genome Resources
Schilkey, Faye D.
National Center for Genome Resources
Cowley, David E.
New Mexico State University
Data from: De novo assembly of a tadpole shrimp (Triops newberryi)
transcriptome and preliminary differential gene expression analysis
Dryad
dataset
2016
Gene regulation
RNA-sequencing
Crustaceans
Triops newberryi
Branchiopod
2016-06-13T15:46:48Z
2016-06-13T15:46:48Z
en
https://doi.org/10.1111/1755-0998.12555
4867626 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Next-generation sequencing techniques, such as RNA sequencing, have
provided a wealth of genomic information for nonmodel species.
Transcriptomic information can be used to quantify the patterns of gene
expression, which can identify how environmental differences invoke
organismal stress responses and provide a gauge in predicting species
adaptability. In our study, we used RNA sequencing to characterize the
first transcriptome from a naupliar tadpole shrimp (Triops newberryi) to
identify the genes expressed during the early life history stages and
which could be important for future genomic studies. RNA was extracted
from naupliar T. newberryi that were reared in a laboratory-controlled
setting and in two different water types, a native and a non-native
condition. A total of six replicates, three per condition, were sequenced
with the Illumina Hi-Seq 2000 achieving 365 M 50-nt reads. High-quality
reads were produced and de novo assembly was used to construct a T.
newberryi transcriptome that was approximately 24.8 M base pairs. More
than 10 000 peptides were predicted from the assembly, and genes were
sorted into gene ontology categories. The use of different water
conditions allowed for a preliminary differential gene expression analysis
in order to compare the changes in gene expression between conditions.
There were 299 differentially expressed genes between water conditions
that might serve as a focal point for future genomic studies of Triops
acclimation to different environments. The Triops transcriptome could
serve as vital genomic information for additional studies on Branchiopod
crustaceans.
Triops newberryi transcriptome annotationsAn excel file containing all of
the functional characterizations from the different annotation databases
including, Swiss-Prot, Pfam-A, TIGRFAM, SUPERFAMILY.Horn_etal_Tnewberryi
Transcriptome Annotations.xlsxedgeR R-scriptAn R file including the code
used to run the differential expression analysis in the package
edgeR.edgR_RScript.RTriops newberry transcriptome read countsAn excel file
containing the raw read counts for the contigs identified by the
annotations as coding sequences. These read counts are the input for the
edgeR package to perform differential gene expression analysis.Tnewberry
Transcriptome Cds Read Counts.xlsxTriops newberryi CateGOrizer resultsAn
excel file containing the results from the program CateGOrizer. The file
indicates the GO class id, term and how many contigs were classified under
a specific GO term. This raw data was used to make Figure 1 in the Horn et
al. manuscript.Triops newberryi CateGOrizer Results.xlsx
Southern New Mexico
United States of America