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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
PubMed
Summary
This summary is machine-generated.

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.

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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.