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Transcriptome sequencing and microarray development for the woodrat ( N eotoma spp .): custom genetic tools for exploring herbivore ecology
Author(s) -
Malenke J. R.,
Milash B.,
Miller A. W.,
Dearing M. D.
Publication year - 2013
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12092
Subject(s) - transcriptome , biology , de novo transcriptome assembly , dna microarray , microarray , computational biology , adaptation (eye) , evolutionary biology , ecology , gene , genetics , gene expression , neuroscience
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 ( N eotoma 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 ( N eotoma lepida ) using the R oche 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 (e A rray, A gilent). 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 N orway rat ( R attus 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.