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

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 popula...

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Autores principales: Wilder, Aryn P, Dudchenko, Olga, Curry, Caitlin, Korody, Marisa, Turbek, Sheela P, Daly, Mark, Misuraca, Ann, Wang, Gaojianyong, Khan, Ruqayya, Weisz, David, Fronczek, Julie, Aiden, Erez Lieberman, Houck, Marlys L, Shier, Debra M, Ryder, Oliver A, Steiner, Cynthia C
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9348616/
https://www.ncbi.nlm.nih.gov/pubmed/35894178
http://dx.doi.org/10.1093/gbe/evac122
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author Wilder, Aryn P
Dudchenko, Olga
Curry, Caitlin
Korody, Marisa
Turbek, Sheela P
Daly, Mark
Misuraca, Ann
Wang, Gaojianyong
Khan, Ruqayya
Weisz, David
Fronczek, Julie
Aiden, Erez Lieberman
Houck, Marlys L
Shier, Debra M
Ryder, Oliver A
Steiner, Cynthia C
author_facet Wilder, Aryn P
Dudchenko, Olga
Curry, Caitlin
Korody, Marisa
Turbek, Sheela P
Daly, Mark
Misuraca, Ann
Wang, Gaojianyong
Khan, Ruqayya
Weisz, David
Fronczek, Julie
Aiden, Erez Lieberman
Houck, Marlys L
Shier, Debra M
Ryder, Oliver A
Steiner, Cynthia C
author_sort Wilder, Aryn P
collection PubMed
description 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 N(e) 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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spelling pubmed-93486162022-08-04 A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population Wilder, Aryn P Dudchenko, Olga Curry, Caitlin Korody, Marisa Turbek, Sheela P Daly, Mark Misuraca, Ann Wang, Gaojianyong Khan, Ruqayya Weisz, David Fronczek, Julie Aiden, Erez Lieberman Houck, Marlys L Shier, Debra M Ryder, Oliver A Steiner, Cynthia C Genome Biol Evol Letter 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 N(e) 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. Oxford University Press 2022-07-27 /pmc/articles/PMC9348616/ /pubmed/35894178 http://dx.doi.org/10.1093/gbe/evac122 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution. https://creativecommons.org/licenses/by/4.0/This 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.
spellingShingle Letter
Wilder, Aryn P
Dudchenko, Olga
Curry, Caitlin
Korody, Marisa
Turbek, Sheela P
Daly, Mark
Misuraca, Ann
Wang, Gaojianyong
Khan, Ruqayya
Weisz, David
Fronczek, Julie
Aiden, Erez Lieberman
Houck, Marlys L
Shier, Debra M
Ryder, Oliver A
Steiner, Cynthia C
A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population
title A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population
title_full A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population
title_fullStr A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population
title_full_unstemmed A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population
title_short A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population
title_sort chromosome-length reference genome for the endangered pacific pocket mouse reveals recent inbreeding in a historically large population
topic Letter
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9348616/
https://www.ncbi.nlm.nih.gov/pubmed/35894178
http://dx.doi.org/10.1093/gbe/evac122
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