非模式物种的基因组学革命:鲑鱼的预测与现实。

IF 3.9 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Samuel A May, Samuel W Rosenbaum, Devon E Pearse, Marty Kardos, Craig R Primmer, Diana S Baetscher, Robin S Waples
{"title":"非模式物种的基因组学革命:鲑鱼的预测与现实。","authors":"Samuel A May, Samuel W Rosenbaum, Devon E Pearse, Marty Kardos, Craig R Primmer, Diana S Baetscher, Robin S Waples","doi":"10.1111/mec.17758","DOIUrl":null,"url":null,"abstract":"<p><p>The increasing feasibility of whole-genome sequencing has been highly anticipated, promising to transform our understanding of the biology of nonmodel species. Notably, dramatic cost reductions beginning around 2007 with the advent of high-throughput sequencing inspired publications heralding the 'genomics revolution', with predictions about its future impacts. Although such predictions served as useful guideposts, value is added when statements are evaluated with the benefit of hindsight. Here, we review 10 key predictions made early in the genomics revolution, highlighting those realised while identifying challenges limiting others. We focus on predictions concerning applied aspects of genomics and examples involving salmonid species which, due to their socioeconomic and ecological significance, have been frontrunners in applications of genomics in nonmodel species. Predicted outcomes included enhanced analytical power, deeper insights into the genetic basis of phenotype and fitness variation, disease management and breeding program advancements. Although many predictions have materialised, several expectations remain unmet due to technological, analytical and knowledge barriers. Additionally, largely unforeseen advancements, including the identification and management applicability of large-effect loci, close-kin mark-recapture, environmental DNA and gene editing have added under-anticipated value. Finally, emerging innovations in artificial intelligence and bioinformatics offer promising new directions. This retrospective evaluation of the impacts of the genomic revolution offers insights into the future of genomics for nonmodel species.</p>","PeriodicalId":210,"journal":{"name":"Molecular Ecology","volume":" ","pages":"e17758"},"PeriodicalIF":3.9000,"publicationDate":"2025-04-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids.\",\"authors\":\"Samuel A May, Samuel W Rosenbaum, Devon E Pearse, Marty Kardos, Craig R Primmer, Diana S Baetscher, Robin S Waples\",\"doi\":\"10.1111/mec.17758\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>The increasing feasibility of whole-genome sequencing has been highly anticipated, promising to transform our understanding of the biology of nonmodel species. Notably, dramatic cost reductions beginning around 2007 with the advent of high-throughput sequencing inspired publications heralding the 'genomics revolution', with predictions about its future impacts. Although such predictions served as useful guideposts, value is added when statements are evaluated with the benefit of hindsight. Here, we review 10 key predictions made early in the genomics revolution, highlighting those realised while identifying challenges limiting others. We focus on predictions concerning applied aspects of genomics and examples involving salmonid species which, due to their socioeconomic and ecological significance, have been frontrunners in applications of genomics in nonmodel species. Predicted outcomes included enhanced analytical power, deeper insights into the genetic basis of phenotype and fitness variation, disease management and breeding program advancements. Although many predictions have materialised, several expectations remain unmet due to technological, analytical and knowledge barriers. Additionally, largely unforeseen advancements, including the identification and management applicability of large-effect loci, close-kin mark-recapture, environmental DNA and gene editing have added under-anticipated value. Finally, emerging innovations in artificial intelligence and bioinformatics offer promising new directions. This retrospective evaluation of the impacts of the genomic revolution offers insights into the future of genomics for nonmodel species.</p>\",\"PeriodicalId\":210,\"journal\":{\"name\":\"Molecular Ecology\",\"volume\":\" \",\"pages\":\"e17758\"},\"PeriodicalIF\":3.9000,\"publicationDate\":\"2025-04-18\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Molecular Ecology\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1111/mec.17758\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Ecology","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1111/mec.17758","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

全基因组测序的可行性已经被寄予厚望,有望改变我们对非模式物种生物学的理解。值得注意的是,从2007年左右开始,随着高通量测序的出现,成本大幅降低,激发了预示“基因组学革命”的出版物,并预测了其未来的影响。尽管这些预测起到了有用的指导作用,但当事后对陈述进行评估时,价值就会增加。在这里,我们回顾了基因组学革命早期做出的10个关键预测,重点介绍了那些已经实现的预测,同时指出了限制其他预测的挑战。我们关注基因组学的应用方面的预测和涉及鲑鱼物种的例子,由于它们的社会经济和生态意义,它们已经成为基因组学在非模式物种应用中的领跑者。预测结果包括提高分析能力,更深入地了解表型和适应度变异的遗传基础,疾病管理和育种计划的进展。尽管许多预测已经实现,但由于技术、分析和知识方面的障碍,一些期望仍未实现。此外,在很大程度上未预见到的进步,包括大效应位点的识别和管理适用性、近亲属标记重获、环境DNA和基因编辑,都增加了未被预期的价值。最后,人工智能和生物信息学的新兴创新提供了有希望的新方向。这对基因组革命影响的回顾性评估为非模式物种基因组学的未来提供了见解。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
The Genomics Revolution in Nonmodel Species: Predictions vs. Reality for Salmonids.

The increasing feasibility of whole-genome sequencing has been highly anticipated, promising to transform our understanding of the biology of nonmodel species. Notably, dramatic cost reductions beginning around 2007 with the advent of high-throughput sequencing inspired publications heralding the 'genomics revolution', with predictions about its future impacts. Although such predictions served as useful guideposts, value is added when statements are evaluated with the benefit of hindsight. Here, we review 10 key predictions made early in the genomics revolution, highlighting those realised while identifying challenges limiting others. We focus on predictions concerning applied aspects of genomics and examples involving salmonid species which, due to their socioeconomic and ecological significance, have been frontrunners in applications of genomics in nonmodel species. Predicted outcomes included enhanced analytical power, deeper insights into the genetic basis of phenotype and fitness variation, disease management and breeding program advancements. Although many predictions have materialised, several expectations remain unmet due to technological, analytical and knowledge barriers. Additionally, largely unforeseen advancements, including the identification and management applicability of large-effect loci, close-kin mark-recapture, environmental DNA and gene editing have added under-anticipated value. Finally, emerging innovations in artificial intelligence and bioinformatics offer promising new directions. This retrospective evaluation of the impacts of the genomic revolution offers insights into the future of genomics for nonmodel species.

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
Molecular Ecology
Molecular Ecology 生物-进化生物学
CiteScore
8.40
自引率
10.20%
发文量
472
审稿时长
1 months
期刊介绍: Molecular Ecology publishes papers that utilize molecular genetic techniques to address consequential questions in ecology, evolution, behaviour and conservation. Studies may employ neutral markers for inference about ecological and evolutionary processes or examine ecologically important genes and their products directly. We discourage papers that are primarily descriptive and are relevant only to the taxon being studied. Papers reporting on molecular marker development, molecular diagnostics, barcoding, or DNA taxonomy, or technical methods should be re-directed to our sister journal, Molecular Ecology Resources. Likewise, papers with a strongly applied focus should be submitted to Evolutionary Applications. Research areas of interest to Molecular Ecology include: * population structure and phylogeography * reproductive strategies * relatedness and kin selection * sex allocation * population genetic theory * analytical methods development * conservation genetics * speciation genetics * microbial biodiversity * evolutionary dynamics of QTLs * ecological interactions * molecular adaptation and environmental genomics * impact of genetically modified organisms
×
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:604180095
Book学术官方微信