Dataset Information

Mitochondrial genome of an Allegheny Woodrat (Neotoma magister).

ABSTRACT: The Allegheny woodrat (Neotoma magister) is endemic to the eastern United States. Population numbers have decreased rapidly over the last four decades due to habitat fragmentation, disease-related mortality, genetic isolation and inbreeding depression; however, effective management is hampered by limited genetic resources. To begin addressing this need, we sequenced and assembled the entire Allegheny woodrat mitochondrial genome. The genome assembly is 16,310 base pairs in length, with an overall base composition of 34% adenine, 27% thymine, 26% cytosine and 13% guanine. This resource will facilitate our understanding of woodrat population genetics and behavioral ecology.

SUBMITTER: Schofield M

PROVIDER: S-EPMC7800975 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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Publications

Mitochondrial genome of an Allegheny Woodrat (<i>Neotoma magister</i>).

Schofield Mandy M Duchamp Joseph J Larkin Jeffery L JL Smyser Timothy J TJ Doyle Jacqueline M JM

Mitochondrial DNA. Part B, Resources 20180222 1

The Allegheny woodrat (<i>Neotoma magister</i>) is endemic to the eastern United States. Population numbers have decreased rapidly over the last four decades due to habitat fragmentation, disease-related mortality, genetic isolation and inbreeding depression; however, effective management is hampered by limited genetic resources. To begin addressing this need, we sequenced and assembled the entire Allegheny woodrat mitochondrial genome. The genome assembly is 16,310 base pairs in length, with an ...[more]

PMID: 33490501

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Project description:Detoxification enzymes play a key role in plant-herbivore interactions, contributing to the on-going evolution of ecosystem functional diversity. Mammalian detoxification systems have been well studied by the medical and pharmacological industries to understand human drug metabolism; however, little is known of the mechanisms employed by wild herbivores to metabolize toxic plant secondary compounds. Using a wild rodent herbivore, the desert woodrat (Neotoma lepida), we investigated genomic structural variation, sequence variability, and expression patterns in a multigene subfamily involved in xenobiotic metabolism, cytochrome P450 2B (CYP2B). We hypothesized that differences in CYP2B expression and sequence diversity could explain differential abilities of woodrat populations to consume native plant toxins. Woodrats from two distinct populations were fed diets supplemented with either juniper (Juniperus osteosperma) or creosote bush (Larrea tridentata), plants consumed by woodrats in their respective desert habitats. We used Southern blot and quantitative PCR to determine that the genomic copy number of CYP2B in both populations was equivalent, and similar in number to known rodent copy number. We compared CYP2B expression patterns and sequence diversity using cloned hepatic CYP2B cDNA. The resulting sequences were very diverse, and clustered into four major clades by amino acid similarity. Sequences from the experimental treatments were distributed non-randomly across a CYP2B tree, indicating unique expression patterns from woodrats on different diets and from different habitats. Furthermore, within each major CYP2B clade, sequences shared a unique combination of amino acid residues at 13 sites throughout the protein known to be important for CYP2B enzyme function, implying differences in the function of each major CYP2B variant. This work is the most comprehensive investigation of the genetic diversity of a detoxification enzyme subfamily in a wild mammalian herbivore, and contributes an initial genetic framework to our understanding of how a wild herbivore responds to critical changes in its diet.

Dataset Information

Mitochondrial genome of an Allegheny Woodrat (Neotoma magister).

Publications

Mitochondrial genome of an Allegheny Woodrat (<i>Neotoma magister</i>).

Similar Datasets

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