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Wilder AP, Dudchenko O, Curry C, Korody M, Turbek SP, Daly M, Misuraca A, Gaojianyong WANG, Khan R, Weisz D, Fronczek J, Aiden EL, Houck ML, Shier DM, Ryder OA, Steiner CC. A chromosome-length reference genome for the endangered Pacific pocket mouse reveals recent inbreeding in a historically large population. Genome Biol Evol 2022; 14:6650481. [PMID: 35894178 PMCID: PMC9348616 DOI: 10.1093/gbe/evac122] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2022] [Indexed: 11/16/2022] Open
Abstract
High-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.
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Affiliation(s)
- Aryn P Wilder
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA.,Center for Theoretical Biological Physics and Department of Computer Science, Rice University, USA
| | - Caitlin Curry
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Marisa Korody
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Sheela P Turbek
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA.,Ecology and Evolutionary Biology, University of Colorado, Boulder, USA
| | | | - Ann Misuraca
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - W A N G Gaojianyong
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
| | - Julie Fronczek
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA.,Center for Theoretical Biological Physics and Department of Computer Science, Rice University, USA.,UWA School of Agriculture and Environment, The University of Western Australia, Australia.,Broad Institute of MIT and Harvard, USA.,Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, China
| | - Marlys L Houck
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Debra M Shier
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA.,Department of Ecology & Evolutionary Biology, University of California Los Angeles, USA
| | - Oliver A Ryder
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
| | - Cynthia C Steiner
- Conservation Science Wildlife Health, San Diego Zoo Wildlife Alliance, USA
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Wilder AP, Navarro AY, King SND, Miller WB, Thomas SM, Steiner CC, Ryder OA, Shier DM. Fitness costs associated with ancestry to isolated populations of an endangered species. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01272-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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McKnight ML. MITOCHONDRIAL DNA PHYLOGEOGRAPHY OFPEROGNATHUS AMPLUSANDPEROGNATHUS LONGIMEMBRIS(RODENTIA: HETEROMYIDAE): A POSSIBLE MAMMALIAN RING SPECIES. Evolution 2017; 49:816-826. [DOI: 10.1111/j.1558-5646.1995.tb02318.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/1994] [Accepted: 08/01/1994] [Indexed: 11/29/2022]
Affiliation(s)
- Mark L. McKnight
- Section of Evolution and Ecology; Center for Population Biology, University of California; Davis California 95616
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