A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution
Wesley C. Warren,Tyler E. Boggs,Richard Borowsky,Brian M. Carlson,Estephany Ferrufino,Joshua B. Gross,LaDeana W. Hillier,Zhilian Hu,Alex C. Keene,Alexander Kenzior,Johanna E. Kowalko,Chad Tomlinson,Milinn Kremitzki,Madeleine E. Lemieux,Tina A. Graves-Lindsay,Suzanne E. McGaugh,Jeffrey T. Miller,Mathilda T.M. Mommersteeg,Rachel L. Moran,Robert Peuß,Robert Peuß,Edward S. Rice,Misty R. Riddle,Misty R. Riddle,Itzel Sifuentes-Romero,Bethany A. Stanhope,Clifford J. Tabin,Sunishka Thakur,Yoshiyuki Yamamoto,Nicolas Rohner,Nicolas Rohner +30 more
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TLDR
In this paper, a high-resolution, chromosome-level surface fish genome was presented, enabling the first genome-wide comparison between surface fish and cavefish populations, using this resource, they performed quantitative trait locus (QTL) mapping analyses and found new candidate genes for eye loss such as dusp26.Abstract:
Identifying the genetic factors that underlie complex traits is central to understanding the mechanistic underpinnings of evolution. Cave-dwelling Astyanax mexicanus populations are well adapted to subterranean life and many populations appear to have evolved troglomorphic traits independently, while the surface-dwelling populations can be used as a proxy for the ancestral form. Here we present a high-resolution, chromosome-level surface fish genome, enabling the first genome-wide comparison between surface fish and cavefish populations. Using this resource, we performed quantitative trait locus (QTL) mapping analyses and found new candidate genes for eye loss such as dusp26. We used CRISPR gene editing in A. mexicanus to confirm the essential role of a gene within an eye size QTL, rx3, in eye formation. We also generated the first genome-wide evaluation of deletion variability across cavefish populations to gain insight into this potential source of cave adaptation. The surface fish genome reference now provides a more complete resource for comparative, functional and genetic studies of drastic trait differences within a species.read more
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Sexual Dimorphism in Aggression: Sex-Specific Fighting Strategies Across Species.
TL;DR: Aggressive behavior is thought to have evolved as a strategy for gaining access to resources such as territory, food, and potential mates in both invertebrate and vertebrate species as discussed by the authors.
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Fish models for investigating nutritional regulation of embryonic development.
Misty R. Riddle,Chi-Kuo Hu +1 more
TL;DR: In this paper, the authors discuss the reasons that teleost fishes are powerful models to understand nutritional control of development and highlight three species that are particularly valuable for future investigations: the zebrafish, Danio rerio, the African Killifish, Nothobranchius furzeri, and the Mexican tetra, Astyanax mexicanus.
Journal ArticleDOI
Hybridization underlies localized trait evolution in cavefish
TL;DR: This article investigated the impact of hybridization on complex trait evolution in the Mexican tetra Astyanax mexicanus and found that hybridization between cave and surface populations may contribute to localized variation in traits associated with cave evolution, including pigmentation, eye development, and sleep.
Journal ArticleDOI
Genome-wide analysis of cis-regulatory changes underlying metabolic adaptation of cavefish
Jaya Krishnan,Chris Seidel,Ning Zhang,Narendra Pratap Singh,Jake VanCampen,Robert Peuß,Shaolei Xiong,Alexander Kenzior,Hua Li,Joan W. Conaway,Nicolas Rohner +10 more
TL;DR: This article performed genome-wide epigenetic profiling in the liver tissues of Astyanax and found that many of the identified cis-regulatory elements (CREs) have genetically diverged and have differential chromatin features between surface and cave morphotypes, while retaining remarkably similar regulatory signatures between independently derived cave populations.
Journal ArticleDOI
Genome-wide analysis of cis-regulatory changes underlying metabolic adaptation of cavefish
Jaya Krishnan,Chris Seidel,Ning Zhang,Narendra Pratap Singh,Jake VanCampen,Robert Peuß,Shaolei Xiong,Alexander Kenzior,Hua Li,Joan W. Conaway,Nicolas Rohner +10 more
TL;DR: This paper performed genome-wide epigenetic profiling in the liver tissues of Astyanax and found that many of the identified cis-regulatory elements (CREs) have genetically diverged and have differential chromatin features between surface and cave morphotypes, while retaining remarkably similar regulatory signatures between independently derived cave populations.
References
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