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 Hillier, Zhilian Hu, Alex C. Keene, Alexander Kenzior, Johanna E. Kowalko, Chad Tomlinson, Milinn Kremitzki, Madeleine E. Lemieux, Tina Graves-Lindsay, Suzanne E. McGaugh, Jeffrey T. Miller, Mathilda T. M. Mommersteeg, Rachel L. Moran, Robert Peuß, Edward S. Rice, Misty R. Riddle, Itzel Sifuentes-Romero, Bethany A. Stanhope, Clifford J. Tabin, Sunishka Thakur, Yoshiyuki Yamamoto and Nicolas Rohner ()
Additional contact information
Wesley C. Warren: University of Missouri
Tyler E. Boggs: University of Cincinnati
Richard Borowsky: New York University
Brian M. Carlson: Northern Kentucky University
Estephany Ferrufino: Florida Atlantic University
Joshua B. Gross: University of Cincinnati
LaDeana Hillier: University of Washington
Zhilian Hu: University of Oxford
Alex C. Keene: Florida Atlantic University
Alexander Kenzior: Stowers Institute for Medical Research
Johanna E. Kowalko: Florida Atlantic University
Chad Tomlinson: Washington University
Milinn Kremitzki: Washington University
Madeleine E. Lemieux: Bioinfo
Tina Graves-Lindsay: Washington University
Suzanne E. McGaugh: University of Minnesota
Jeffrey T. Miller: University of Minnesota
Mathilda T. M. Mommersteeg: University of Oxford
Rachel L. Moran: University of Minnesota
Robert Peuß: Stowers Institute for Medical Research
Edward S. Rice: University of Missouri
Misty R. Riddle: Harvard Medical School
Itzel Sifuentes-Romero: Florida Atlantic University
Bethany A. Stanhope: Florida Atlantic University
Clifford J. Tabin: Harvard Medical School
Sunishka Thakur: Florida Atlantic University
Yoshiyuki Yamamoto: University College London
Nicolas Rohner: Stowers Institute for Medical Research

Nature Communications, 2021, vol. 12, issue 1, 1-12

Abstract: 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.

Date: 2021
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DOI: 10.1038/s41467-021-21733-z

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