Unlocking the genome of perch – From genes to ecology and back again

IF 1.6 3区 农林科学 Q3 FISHERIES
Anti Vasemägi, Mikhail Ozerov, Kristina Noreikiene, María-Eugenia López, Anna Gårdmark
{"title":"Unlocking the genome of perch – From genes to ecology and back again","authors":"Anti Vasemägi,&nbsp;Mikhail Ozerov,&nbsp;Kristina Noreikiene,&nbsp;María-Eugenia López,&nbsp;Anna Gårdmark","doi":"10.1111/eff.12713","DOIUrl":null,"url":null,"abstract":"<p>Eurasian perch <i>Perca fluviatilis</i> has been a popular model species for decades in the fields of aquatic ecology, community dynamics, behaviour, physiology and ecotoxicology. Yet, despite extensive research, the progress of integrating genomic perspective into existing ecological knowledge in perch has been relatively modest. Meanwhile, the emergence of high-throughput sequencing technologies has completely changed the methods for genetic variation assessment and conducting biodiversity and evolutionary research. During the last 5 years, three genome assemblies of <i>P. fluviatilis</i> have been generated, allowing substantial advancement of our understanding of the interactions between ecological and evolutionary processes at the whole-genome level. We review the past progress, current status and potential future impact of the genomic resources and tools for ecological research in Eurasian perch focusing on the utility of recent whole-genome assemblies. Furthermore, we demonstrate the power of genome-wide approaches and newly developed tools and outline recent cases where genomics have contributed to new ecological and evolutionary knowledge. We explore how the availability of reference assembly enables the efficient application of various statistical tools, and how genomic approaches can provide novel insights into resource polymorphism, host–parasite interactions and to genetic and phenotypic changes associated with climate change and harvesting-induced evolution. In summary, we call for increased integration of genomic tools into ecological research for perch, as well as for other fish species, which is likely to yield novel insights into processes linking the adaptation and plasticity to ecosystem functioning and environmental change.</p>","PeriodicalId":11422,"journal":{"name":"Ecology of Freshwater Fish","volume":null,"pages":null},"PeriodicalIF":1.6000,"publicationDate":"2023-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/eff.12713","citationCount":"4","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Ecology of Freshwater Fish","FirstCategoryId":"97","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1111/eff.12713","RegionNum":3,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"FISHERIES","Score":null,"Total":0}
引用次数: 4

Abstract

Eurasian perch Perca fluviatilis has been a popular model species for decades in the fields of aquatic ecology, community dynamics, behaviour, physiology and ecotoxicology. Yet, despite extensive research, the progress of integrating genomic perspective into existing ecological knowledge in perch has been relatively modest. Meanwhile, the emergence of high-throughput sequencing technologies has completely changed the methods for genetic variation assessment and conducting biodiversity and evolutionary research. During the last 5 years, three genome assemblies of P. fluviatilis have been generated, allowing substantial advancement of our understanding of the interactions between ecological and evolutionary processes at the whole-genome level. We review the past progress, current status and potential future impact of the genomic resources and tools for ecological research in Eurasian perch focusing on the utility of recent whole-genome assemblies. Furthermore, we demonstrate the power of genome-wide approaches and newly developed tools and outline recent cases where genomics have contributed to new ecological and evolutionary knowledge. We explore how the availability of reference assembly enables the efficient application of various statistical tools, and how genomic approaches can provide novel insights into resource polymorphism, host–parasite interactions and to genetic and phenotypic changes associated with climate change and harvesting-induced evolution. In summary, we call for increased integration of genomic tools into ecological research for perch, as well as for other fish species, which is likely to yield novel insights into processes linking the adaptation and plasticity to ecosystem functioning and environmental change.

Abstract Image

解开鲈鱼的基因组——从基因到生态再回来
几十年来,欧亚鲈在水生生态学、群落动力学、行为、生理学和生态毒理学等领域一直是一个受欢迎的模式物种。然而,尽管进行了广泛的研究,但将基因组观点整合到现有鲈鱼生态知识中的进展相对有限。同时,高通量测序技术的出现,彻底改变了遗传变异评估以及生物多样性和进化研究的方法。在过去的5年中,已经产生了三个河流假单胞虫的基因组组合,使我们在全基因组水平上对生态和进化过程之间相互作用的理解有了实质性的进展。本文综述了欧亚鲈鱼基因组资源和工具在生态学研究中的进展、现状和潜在的未来影响,重点介绍了最近全基因组组装的应用。此外,我们展示了全基因组方法和新开发的工具的力量,并概述了基因组学为新的生态和进化知识做出贡献的最新案例。我们探讨了参考汇编的可用性如何使各种统计工具的有效应用,以及基因组方法如何为资源多态性,宿主-寄生虫相互作用以及与气候变化和收获诱导的进化相关的遗传和表型变化提供新的见解。总之,我们呼吁将基因组工具更多地整合到鲈鱼以及其他鱼类的生态研究中,这可能会对生态系统功能和环境变化的适应和可塑性过程产生新的见解。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Ecology of Freshwater Fish
Ecology of Freshwater Fish 农林科学-海洋与淡水生物学
CiteScore
4.10
自引率
0.00%
发文量
45
审稿时长
12-24 weeks
期刊介绍: Ecology of Freshwater Fish publishes original contributions on all aspects of fish ecology in freshwater environments, including lakes, reservoirs, rivers, and streams. Manuscripts involving ecologically-oriented studies of behavior, conservation, development, genetics, life history, physiology, and host-parasite interactions are welcomed. Studies involving population ecology and community ecology are also of interest, as are evolutionary approaches including studies of population biology, evolutionary ecology, behavioral ecology, and historical ecology. Papers addressing the life stages of anadromous and catadromous species in estuaries and inshore coastal zones are considered if they contribute to the general understanding of freshwater fish ecology. Theoretical and modeling studies are suitable if they generate testable hypotheses, as are those with implications for fisheries. Manuscripts presenting analyses of published data are considered if they produce novel conclusions or syntheses. The journal publishes articles, fresh perspectives, and reviews and, occasionally, the proceedings of conferences and symposia.
×
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