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

doi:10.1093/gbe/evac122

KMS > 免疫化学研究所 > 特聘教授组 > Roger D. Kornberg组

	A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population
	Wilder, Aryn P.1; Dudchenko, Olga 2,3,4; Curry, Caitlin 1; Korody, Marisa 1; Turbek, Sheela P.1,5; Daly, Mark 6; Misuraca, Ann 1; Wang, Gaojianyong 7; Khan, Ruqayya 2; Weisz, David 2; Fronczek, Julie 1; Aiden, Erez Lieberman2,3,4,8,9,10 ; Houck, Marlys L.1; Shier, Debra M.11; Ryder, Oliver A.1; Steiner, Cynthia C.1
	2022-08-03
发表期刊	GENOME BIOLOGY AND EVOLUTION (IF:3.2[JCR-2023],3.2[5-Year])
ISSN	1759-6653
卷号	14 期号:8
发表状态	已发表
DOI	10.1093/gbe/evac122
摘要	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.
关键词	runs of homozygosity effective population size HiFi chromosome conformation capture mitochondrial genome
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收录类别	SCI ; SCIE
语种	英语
资助项目	Morris Animal Foundation[D19ZO-082] ; Welch Foundation[Q-1866] ; National Institutes of Health["UM1HG009375","RM1HG011016-01A1"] ; US-Israel Binational Science Foundation[2019276] ; National Science Foundation["NSF DBI-2021795","NSF PHY-2019745","NSF DEB 1928891"]
WOS研究方向	Evolutionary Biology ; Genetics & Heredity
WOS类目	Evolutionary Biology ; Genetics & Heredity
WOS记录号	WOS:000835868400002
出版者	OXFORD UNIV PRESS
引用统计	正在获取...
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/219675
专题	免疫化学研究所_特聘教授组_结构生物化学实验室
通讯作者	Wilder, Aryn P.
作者单位	1.San Diego Zoo Wildlife Alliance, Conservat Sci Wildlife Hlth, Escondido, CA 92101 USA 2.Baylor Coll Med, Dept Mol & Human Genet, Ctr Genome Architecture, Houston, TX 77030 USA 3.Rice Univ, Ctr Theoret Biol Phys, Houston, TX 77005 USA 4.Rice Univ, Dept Comp Sci, Houston, TX 77005 USA 5.Univ Colorado, Ecol & Evolutionary Biol, Boulder, CO 80309 USA 6.Dovetail Genom, Scotts Valley, CA USA 7.Max Planck Inst Mol Genet, Dept Genome Regulat, Berlin, Germany 8.Univ Western Australia, UWA Sch Agr & Environm, Crawley, Australia 9.Broad Inst MIT & Harvard, Cambridge, MA 02142 USA 10.ShanghaiTech, Shanghai Inst Adv Immunochem Studies, Shanghai, Peoples R China 11.Univ Calif Los Angeles, Dept Ecol & Evolutionary Biol, Los Angeles, CA USA
推荐引用方式 GB/T 7714	Wilder, 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[J]. GENOME BIOLOGY AND EVOLUTION,2022,14(8).
APA	Wilder, Aryn P..,Dudchenko, Olga.,Curry, Caitlin.,Korody, Marisa.,Turbek, Sheela P..,...&Steiner, Cynthia C..(2022).A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population.GENOME BIOLOGY AND EVOLUTION,14(8).
MLA	Wilder, Aryn P.,et al."A Chromosome-Length Reference Genome for the Endangered Pacific Pocket Mouse Reveals Recent Inbreeding in a Historically Large Population".GENOME BIOLOGY AND EVOLUTION 14.8(2022).