A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population

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dc.citation.articleNumberevac122en_US
dc.citation.issueNumber8en_US
dc.citation.journalTitleGenome Biology and Evolutionen_US
dc.citation.volumeNumber14en_US
dc.contributor.authorWilder, Aryn Pen_US
dc.contributor.authorDudchenko, Olgaen_US
dc.contributor.authorCurry, Caitlinen_US
dc.contributor.authorKorody, Marisaen_US
dc.contributor.authorTurbek, Sheela Pen_US
dc.contributor.authorDaly, Marken_US
dc.contributor.authorMisuraca, Annen_US
dc.contributor.authorWang, Gaojianyongen_US
dc.contributor.authorKhan, Ruqayyaen_US
dc.contributor.authorWeisz, Daviden_US
dc.contributor.authorFronczek, Julieen_US
dc.contributor.authorAiden, Erez Liebermanen_US
dc.contributor.authorHouck, Marlys Len_US
dc.contributor.authorShier, Debra Men_US
dc.contributor.authorRyder, Oliver Aen_US
dc.contributor.authorSteiner, Cynthia Cen_US
dc.contributor.orgCenter for Theoretical Biological Physicsen_US
dc.date.accessioned2022-09-01T14:18:20Zen_US
dc.date.available2022-09-01T14:18:20Zen_US
dc.date.issued2022en_US
dc.description.abstractHigh-quality reference genomes are fundamental tools for understanding population history, and can provide estimates of genetic and demographic parameters relevant to the conservation of biodiversity. The federally endangered Pacific pocket mouse (PPM), which persists in three small, isolated populations in southern California, is a promising model for studying how demographic history shapes genetic diversity, and how diversity in turn may influence extinction risk. To facilitate these studies in PPM, we combined PacBio HiFi long reads with Omni-C and Hi-C data to generate a de novo genome assembly, and annotated the genome using RNAseq. The assembly comprised 28 chromosome-length scaffolds (N50 = 72.6 MB) and the complete mitochondrial genome, and included a long heterochromatic region on chromosome 18 not represented in the previously available short-read assembly. Heterozygosity was highly variable across the genome of the reference individual, with 18% of windows falling in runs of homozygosity (ROH) >1 MB, and nearly 9% in tracts spanning >5 MB. Yet outside of ROH, heterozygosity was relatively high (0.0027), and historical Ne estimates were large. These patterns of genetic variation suggest recent inbreeding in a formerly large population. Currently the most contiguous assembly for a heteromyid rodent, this reference genome provides insight into the past and recent demographic history of the population, and will be a critical tool for management and future studies of outbreeding depression, inbreeding depression, and genetic load.en_US
dc.identifier.citationWilder, Aryn P, Dudchenko, Olga, Curry, Caitlin, et al.. "A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population." <i>Genome Biology and Evolution,</i> 14, no. 8 (2022) Oxford University Press: https://doi.org/10.1093/gbe/evac122.en_US
dc.identifier.digitalevac122en_US
dc.identifier.doihttps://doi.org/10.1093/gbe/evac122en_US
dc.identifier.urihttps://hdl.handle.net/1911/113165en_US
dc.language.isoengen_US
dc.publisherOxford University Pressen_US
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.titleA Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Populationen_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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