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Transcriptome sequencing and microarray development for the woodrat (Neotoma spp.): custom genetic tools for exploring herbivore ecology

ABSTRACT: Transcriptome sequencing and microarray development for the woodrat (Neotoma spp.): custom genetic tools for exploring herbivore ecology

PROVIDER: PRJNA188188 | ENA |

REPOSITORIES: ENA

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Transcriptome sequencing and microarray development for the woodrat (Neotoma spp.): custom genetic tools for exploring herbivore ecology

Project description: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) with 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). To compare the effect of native diet/habitat and phylogenetic similarity, we performed 3 experiments with the Neotoma probes only: one across species with similar habitat niches (N. lepida versus N. bryanti, Palm Springs), one across species with different habitat niches (N. lepida versus N. bryanti, Caspers Wilderness), and one across populations within a species (N. bryant Palm Springs versus Caspers Wilderness). The resulting one-color 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). Biotransformation processes and functions were highly represented in the results. Comparisons between ecologically similar woodrat species revealed fewer gene expression differences than ecologically different woodrat species. The conspecific comparison had overall fewest differences.

2013-07-30 | GSE43941 | GEO

Transcriptome sequencing and microarray development for the woodrat (Neotoma spp.): custom genetic tools for exploring herbivore ecology

2013-07-30 | E-GEOD-43941 | biostudies-arrayexpress

Temperature-mediated changes in hepatic gene expression of a mammalian herbivore (Neotoma lepida)

Project description:The effects of ambient temperature and dietary plant toxins on differential gene expression in the liver were compared in herbivorous rodents (woodrats, genus Neotoma) using microarrays custom-designed for woodrats. Expression profiles revealed a greater number of up-egulated genes at 22C comapred to a thermoneutral temperature (27C). Genes and pathways up-regulated at 22C were related to growth and biosynthesis, suggesting the liver could be in a building state at this temperature. Conversely, genes associated with gluconeogenesis, apoptosis and protein misfolding, which likely reflected a more stressed state for the liver. Taken together, these results highlighted the important role of temperature on gene expression profiles in the desert woodrat. As crucial players in many ecosystems, understanding how herbivorous mammals will respond to climate change is imperative to accurately predict repercussions and aid in conservation efforts.

2017-05-02 | GSE80595 | GEO

Neotoma floridana isolate:mNeoFlo1

Project description:Neotoma floridana (Eastern woodrat) genome, mNeoFlo1, haplotype 1

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Neotoma floridana isolate:mNeoFlo1

Project description:Neotoma floridana (Eastern woodrat) genome, mNeoFlo1, haplotype 2

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Neotoma lepida

Project description:Temperature-mediated changes in hepatic gene expression of a mammalian herbivore (Neotoma lepida)

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