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Transcriptome sequencing and microarray development for the woodrat (Neotoma spp.): custom genetic tools for
J R Malenke1, B Milash, A W Miller
1Department of Biology, University of Utah, Salt Lake City, UT 84112, USA. malenke@biology.utah.edu
Molecular Ecology Resources
|March 19, 2013
Summary
We developed new genetic tools for woodrats (Neotoma spp.) by sequencing their transcriptome. These tools revealed that ecological pressures, not just evolutionary distance, shape gene expression in these important herbivores.
Area of Science:
- Genomics
- Ecology
- Evolutionary Biology
Background:
- Nonmodel organisms, like woodrats (Neotoma spp.), are ecologically important but lack in-depth genetic tools.
- Understanding how herbivores metabolize plant toxins is crucial for ecology and evolution.
Purpose of the Study:
- To develop novel genetic tools (transcriptome and microarray) for woodrats.
- To investigate gene expression differences in woodrats across species and populations.
- To explore the role of ecological pressures versus phylogenetic distance in shaping gene expression.
Main Methods:
- De novo transcriptome sequencing of the desert woodrat (Neotoma lepida) liver using Roche 454.
- Development and testing of a custom microarray (Agilent) with woodrat-specific probes.
- Analysis of gene expression patterns across different woodrat species and populations.
Main Results:
- High-quality, well-annotated woodrat transcriptome and functional microarray were developed.
- Woodrat-specific probes performed better than those from Norway rats (Rattus norvegicus).
- Significant gene expression differences were observed, particularly in biotransformation processes, linked to ecological pressures.
Conclusions:
- The developed transcriptome and microarray are valuable tools for studying herbivore biology and ecology.
- Ecological pressures significantly influence woodrat gene expression, alongside evolutionary history.
- These findings advance our understanding of adaptation in ecologically important herbivores.
