A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of "Genetic Purging" and Genomic Stability

doi:10.3390/genes13071270

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

	A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of "Genetic Purging" and Genomic Stability
	Mohr, David W.1; Gaughran, Stephen J.2; Paschall, Justin 1; Naguib, Ahmed 3; Pang, Andy Wing Chun 3; Dudchenko, Olga 4,5; Aiden, Erez Lieberman4,5,6,7,8 ; Church, Deanna M.9; Scott, Alan F.1
	2022-07-01
发表期刊	GENES (IF:2.8[JCR-2023],3.3[5-Year])
EISSN	2073-4425
卷号	13 期号:7
发表状态	已发表
DOI	10.3390/genes13071270
摘要	The Hawaiian monk seal (HMS) is the single extant species of tropical earless seals of the genus Neomonachus. The species survived a severe bottleneck in the late 19th century and experienced subsequent population declines until becoming the subject of a NOAA-led species recovery effort beginning in 1976 when the population was fewer than 1000 animals. Like other recovering species, the Hawaiian monk seal has been reported to have reduced genetic heterogeneity due to the bottleneck and subsequent inbreeding. Here, we report a chromosomal reference assembly for a male animal produced using a variety of methods. The final assembly consisted of 16 autosomes, an X, and portions of the Y chromosomes. We compared variants in this animal to other HMS and to a frequently sequenced human sample, confirming about 12% of the variation seen in man. To confirm that the reference animal was representative of the HMS, we compared his sequence to that of 10 other individuals and noted similarly low variation in all. Variation in the major histocompatibility (MHC) genes was nearly absent compared to the orthologous human loci. Demographic analysis predicts that Hawaiian monk seals have had a long history of small populations preceding the bottleneck, and their current low levels of heterozygosity may indicate specialization to a stable environment. When we compared our reference assembly to that of other species, we observed significant conservation of chromosomal architecture with other pinnipeds, especially other phocids. This reference should be a useful tool for future evolutionary studies as well as the long-term management of this species.
关键词	Hawaiian monk seal pinniped endangered species genetic purging genome assembly chromosome evolution
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收录类别	SCI ; SCIE
语种	英语
资助项目	Welch Foundation[Q-1866] ; McNair Medical Institute ScUS-Israel Binational Science Foundation Award[2019276] ; Behavioral Plasticity Research Institute (NSF)[DBI-2021795] ; NSF Physics Frontiers Center Award[NSF PHY-2019745] ; NIH CEGS["RM1HG011016-01A1","UM1HG009375"]
WOS研究方向	Genetics & Heredity
WOS类目	Genetics & Heredity
WOS记录号	WOS:000833207700001
出版者	MDPI
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/214782
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	Scott, Alan F.
作者单位	1.Johns Hopkins Univ, Dept Genet Med, Sch Med, Baltimore, MD 21287 USA 2.Princeton Univ, Dept Ecol & Evolutionary Biol, Princeton, NJ 08544 USA 3.Bionano Genom Inc, 9640 Towne Ctr Dr,Suite 100, San Diego, CA 92121 USA 4.Baylor Coll Med, Ctr Genome Architecture, Dept Mol & Human Genet, Houston, TX 77030 USA 5.Rice Univ, Ctr Theoret Biol Phys, Houston, TX 77030 USA 6.Univ Western Australia, UWA Sch Agr & Environm, Crawley, WA 6009, Australia 7.Broad Inst MIT & Harvard, Cambridge, MA 02139 USA 8.ShanghaiTech Univ, Shanghai Inst Adv Immunochem Studies, Shanghai 201210, Peoples R China 9.Inscripta, 5500 Cent Ave, Boulder, CO 80301 USA
推荐引用方式 GB/T 7714	Mohr, David W.,Gaughran, Stephen J.,Paschall, Justin,et al. A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of "Genetic Purging" and Genomic Stability[J]. GENES,2022,13(7).
APA	Mohr, David W..,Gaughran, Stephen J..,Paschall, Justin.,Naguib, Ahmed.,Pang, Andy Wing Chun.,...&Scott, Alan F..(2022).A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of "Genetic Purging" and Genomic Stability.GENES,13(7).
MLA	Mohr, David W.,et al."A Chromosome-Length Assembly of the Hawaiian Monk Seal (Neomonachus schauinslandi): A History of "Genetic Purging" and Genomic Stability".GENES 13.7(2022).