通过全基因组重测序鉴定北美梭鱼基因变异的丧失和祖先的性别决定系统。

IF 2.1 3区 生物学 Q3 GENETICS & HEREDITY
Hollie A Johnson, Eric B Rondeau, Ben J G Sutherland, David R Minkley, Jong S Leong, Joanne Whitehead, Cody A Despins, Brent E Gowen, Brian J Collyard, Christopher M Whipps, John M Farrell, Ben F Koop
{"title":"通过全基因组重测序鉴定北美梭鱼基因变异的丧失和祖先的性别决定系统。","authors":"Hollie A Johnson, Eric B Rondeau, Ben J G Sutherland, David R Minkley, Jong S Leong, Joanne Whitehead, Cody A Despins, Brent E Gowen, Brian J Collyard, Christopher M Whipps, John M Farrell, Ben F Koop","doi":"10.1093/g3journal/jkae183","DOIUrl":null,"url":null,"abstract":"<p><p>The northern pike Esox lucius is a freshwater fish with low genetic diversity but ecological success throughout the Northern Hemisphere. Here, we generate an annotated chromosome-level genome assembly of 941 Mbp in length with 25 chromosome-length scaffolds. We then genotype 47 northern pike from Alaska through New Jersey at a genome-wide scale and characterize a striking decrease in genetic diversity along the sampling range. Individuals west of the North American Continental Divide have substantially higher diversity than those to the east (e.g. Interior Alaska and St. Lawrence River have on average 181 and 64K heterozygous SNPs per individual, or a heterozygous SNP every 5.2 and 14.6 kbp, respectively). Individuals clustered within each population with strong support, with numerous private alleles observed within each population. Evidence for recent population expansion was observed for a Manitoba hatchery and the St. Lawrence population (Tajima's D = -1.07 and -1.30, respectively). Several chromosomes have large regions with elevated diversity, including LG24, which holds amhby, the ancestral sex determining gene. As expected amhby was largely male-specific in Alaska and the Yukon and absent southeast to these populations, but we document some amhby(-) males in Alaska and amhby(+) males in the Columbia River, providing evidence for a patchwork of presence of this system in the western region. These results support the theory that northern pike recolonized North America from refugia in Alaska and expanded following deglaciation from west to east, with probable founder effects resulting in loss of both neutral and functional diversity (e.g. amhby).</p>","PeriodicalId":12468,"journal":{"name":"G3: Genes|Genomes|Genetics","volume":" ","pages":""},"PeriodicalIF":2.1000,"publicationDate":"2024-10-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457062/pdf/","citationCount":"0","resultStr":"{\"title\":\"Loss of genetic variation and ancestral sex determination system in North American northern pike characterized by whole-genome resequencing.\",\"authors\":\"Hollie A Johnson, Eric B Rondeau, Ben J G Sutherland, David R Minkley, Jong S Leong, Joanne Whitehead, Cody A Despins, Brent E Gowen, Brian J Collyard, Christopher M Whipps, John M Farrell, Ben F Koop\",\"doi\":\"10.1093/g3journal/jkae183\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The northern pike Esox lucius is a freshwater fish with low genetic diversity but ecological success throughout the Northern Hemisphere. Here, we generate an annotated chromosome-level genome assembly of 941 Mbp in length with 25 chromosome-length scaffolds. We then genotype 47 northern pike from Alaska through New Jersey at a genome-wide scale and characterize a striking decrease in genetic diversity along the sampling range. Individuals west of the North American Continental Divide have substantially higher diversity than those to the east (e.g. Interior Alaska and St. Lawrence River have on average 181 and 64K heterozygous SNPs per individual, or a heterozygous SNP every 5.2 and 14.6 kbp, respectively). Individuals clustered within each population with strong support, with numerous private alleles observed within each population. Evidence for recent population expansion was observed for a Manitoba hatchery and the St. Lawrence population (Tajima's D = -1.07 and -1.30, respectively). Several chromosomes have large regions with elevated diversity, including LG24, which holds amhby, the ancestral sex determining gene. As expected amhby was largely male-specific in Alaska and the Yukon and absent southeast to these populations, but we document some amhby(-) males in Alaska and amhby(+) males in the Columbia River, providing evidence for a patchwork of presence of this system in the western region. These results support the theory that northern pike recolonized North America from refugia in Alaska and expanded following deglaciation from west to east, with probable founder effects resulting in loss of both neutral and functional diversity (e.g. amhby).</p>\",\"PeriodicalId\":12468,\"journal\":{\"name\":\"G3: Genes|Genomes|Genetics\",\"volume\":\" \",\"pages\":\"\"},\"PeriodicalIF\":2.1000,\"publicationDate\":\"2024-10-07\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11457062/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"G3: Genes|Genomes|Genetics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1093/g3journal/jkae183\",\"RegionNum\":3,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"G3: Genes|Genomes|Genetics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1093/g3journal/jkae183","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0

摘要

北梭子鱼(Esox lucius)是一种淡水鱼,遗传多样性较低,但在整个北半球的生态环境中都很成功。在这里,我们生成了一个长度为 941 Mbp 的染色体级基因组注释装配,其中包含 25 个染色体长度的支架。然后,我们在全基因组范围内对从阿拉斯加到新泽西的 47 条梭子鱼进行了基因分型,结果表明沿取样范围遗传多样性显著下降。北美大陆分水岭以西的个体比东部的个体具有更高的多样性(例如,阿拉斯加内陆和圣劳伦斯河平均每个个体有 181K 和 64K 个杂合 SNP,即每 5.2 kbp 和 14.6 kbp 分别有一个杂合 SNP)。每个种群中的个体都有很强的聚类支持,每个种群中都观察到许多私有等位基因。在马尼托巴孵化场和圣劳伦斯种群(Tajima's D = -1.07 和 -1.30)观察到近期种群扩张的证据。有几条染色体上的大片区域具有较高的多样性,其中包括 LG24,该区域含有祖先的性别决定基因 amhby。不出所料,amhby 在阿拉斯加和育空地区主要是男性特异性的,而在这些种群的东南部则不存在,但我们记录了阿拉斯加的一些 amhby(-)雄性和哥伦比亚河的 amhby(+)雄性,为该系统在西部地区的零星存在提供了证据。这些结果支持这样一种理论,即北部梭子鱼从阿拉斯加的避难所重新移居北美,并在降冰期之后从西向东扩展,可能的创始人效应导致了中性和功能多样性(如amhby)的丧失。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Loss of genetic variation and ancestral sex determination system in North American northern pike characterized by whole-genome resequencing.

The northern pike Esox lucius is a freshwater fish with low genetic diversity but ecological success throughout the Northern Hemisphere. Here, we generate an annotated chromosome-level genome assembly of 941 Mbp in length with 25 chromosome-length scaffolds. We then genotype 47 northern pike from Alaska through New Jersey at a genome-wide scale and characterize a striking decrease in genetic diversity along the sampling range. Individuals west of the North American Continental Divide have substantially higher diversity than those to the east (e.g. Interior Alaska and St. Lawrence River have on average 181 and 64K heterozygous SNPs per individual, or a heterozygous SNP every 5.2 and 14.6 kbp, respectively). Individuals clustered within each population with strong support, with numerous private alleles observed within each population. Evidence for recent population expansion was observed for a Manitoba hatchery and the St. Lawrence population (Tajima's D = -1.07 and -1.30, respectively). Several chromosomes have large regions with elevated diversity, including LG24, which holds amhby, the ancestral sex determining gene. As expected amhby was largely male-specific in Alaska and the Yukon and absent southeast to these populations, but we document some amhby(-) males in Alaska and amhby(+) males in the Columbia River, providing evidence for a patchwork of presence of this system in the western region. These results support the theory that northern pike recolonized North America from refugia in Alaska and expanded following deglaciation from west to east, with probable founder effects resulting in loss of both neutral and functional diversity (e.g. amhby).

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
G3: Genes|Genomes|Genetics
G3: Genes|Genomes|Genetics GENETICS & HEREDITY-
CiteScore
5.10
自引率
3.80%
发文量
305
审稿时长
3-8 weeks
期刊介绍: G3: Genes, Genomes, Genetics provides a forum for the publication of high‐quality foundational research, particularly research that generates useful genetic and genomic information such as genome maps, single gene studies, genome‐wide association and QTL studies, as well as genome reports, mutant screens, and advances in methods and technology. The Editorial Board of G3 believes that rapid dissemination of these data is the necessary foundation for analysis that leads to mechanistic insights. G3, published by the Genetics Society of America, meets the critical and growing need of the genetics community for rapid review and publication of important results in all areas of genetics. G3 offers the opportunity to publish the puzzling finding or to present unpublished results that may not have been submitted for review and publication due to a perceived lack of a potential high-impact finding. G3 has earned the DOAJ Seal, which is a mark of certification for open access journals, awarded by DOAJ to journals that achieve a high level of openness, adhere to Best Practice and high publishing standards.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信