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A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution

Author

Listed:
  • Wesley C. Warren

    (University of Missouri
    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
    University of Münster)

  • Edward S. Rice

    (University of Missouri)

  • Misty R. Riddle

    (Harvard Medical School
    University of Nevada)

  • Itzel Sifuentes-Romero

    (Florida Atlantic University)

  • Bethany A. Stanhope

    (Florida Atlantic University
    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
    KU Medical Center)

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.

Suggested Citation

  • 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 , 2021. "A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-21733-z
    DOI: 10.1038/s41467-021-21733-z
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    Cited by:

    1. Pau Balart-García & Leandro Aristide & Tessa M. Bradford & Perry G. Beasley-Hall & Slavko Polak & Steven J. B. Cooper & Rosa Fernández, 2023. "Parallel and convergent genomic changes underlie independent subterranean colonization across beetles," Nature Communications, Nature, vol. 14(1), pages 1-13, December.

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