10.5061/DRYAD.25696
Malenke, Jael
University of Utah
Milash, Brett
University of Utah
Miller, Aaron
University of Utah
Dearing, Denise
University of Utah
Malenke, J. R.
University of Utah
Miller, A. W.
University of Utah
Dearing, M. D.
University of Utah
Data from: Transcriptome sequencing and microarray development for the
woodrat (Neotoma spp.): custom genetic tools for exploring herbivore
ecology
Dryad
dataset
2013
Species interactions
Neotoma lepida
Neotoma bryanti
2013-02-15T19:56:36Z
2013-02-15T19:56:36Z
en
https://doi.org/10.1111/1755-0998.12092
1890523 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
Massively parallel sequencing has enabled the creation of novel, in-depth
genetic tools for nonmodel, ecologically important organisms. We present
the de novo transcriptome sequencing, analysis and microarray development
for a vertebrate herbivore, the woodrat (Neotoma spp.). This genus is of
ecological and evolutionary interest, especially with respect to ingestion
and hepatic metabolism of potentially toxic plant secondary compounds. We
generated a liver transcriptome of the desert woodrat (Neotoma lepida)
using the Roche 454 platform. The assembled contigs were well annotated
using rodent references (99.7% annotation), and biotransformation function
was reflected in the gene ontology. The transcriptome was used to develop
a custom microarray (eArray, Agilent). We tested the microarray with three
experiments: one across species with similar habitat (thus, dietary)
niches, one across species with different habitat niches and one across
populations within a species. The resulting one-colour arrays had high
technical and biological quality. Probes designed from the woodrat
transcriptome performed significantly better than functionally similar
probes from the Norway rat (Rattus norvegicus). There were a multitude of
expression differences across the woodrat treatments, many of which
related to biotransformation processes and activities. The pattern and
function of the differences indicate shared ecological pressures, and not
merely phylogenetic distance, play an important role in shaping gene
expression profiles of woodrat species and populations. The quality and
functionality of the woodrat transcriptome and custom microarray suggest
these tools will be valuable for expanding the scope of herbivore biology,
as well as the exploration of conceptual topics in ecology.
qPCRvalid_Neo_arrayTable2_rattusVneo_allprobesTable2_matchedprobes_bothCompTable2_LRvsPS_Neoprobes