Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery.

Autor: Warren WC; Department of Animal Sciences, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA.; Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA.; Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA., Rice ES; Department of Animal Sciences, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA.; Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA., X M; Department of Animal Sciences, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA.; Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA., Roback E; Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA., Keene A; Department of Biology, Texas A&M University, College Station, TX 77843, USA., Martin F; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Ogeh D; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Haggerty L; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK., Carroll RA; Department of Animal Sciences, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA.; Department of Surgery, University of Missouri, Bond Life Sciences Center, Columbia, MO 65211, USA., McGaugh S; Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA., Rohner N; Stowers Institute for Medical Research, Kansas City, MO 64110, USA.; Department of Molecular and Integrative Physiology, KU Medical Center, Kansas City, KS 66160, USA.
Jazyk: angličtina
Zdroj: G3 (Bethesda, Md.) [G3 (Bethesda)] 2024 Aug 07; Vol. 14 (8).
DOI: 10.1093/g3journal/jkae103
Abstrakt: The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment. Our assemblies represent the highest quality of sequence completeness with predicted protein-coding and noncoding gene metrics far surpassing prior resources and, to our knowledge, all long-read assembled teleost genomes, including zebrafish. Whole-genome synteny alignments show highly conserved gene order among cave forms in contrast to a higher number of chromosomal rearrangements when compared with other phylogenetically close or distant teleost species. By phylogenetically assessing gene orthology across distant branches of amniotes, we discover gene orthogroups unique to A. mexicanus. When compared with a representative surface fish genome, we find a rich amount of structural sequence diversity, defined here as the number and size of insertions and deletions as well as expanding and contracting repeats across cave forms. These new more complete genomic resources ensure higher trait resolution for comparative, functional, developmental, and genetic studies of drastic trait differences within a species.
Competing Interests: Conflicts of interest The author(s) declare no conflicts of interest.
(© The Author(s) 2024. Published by Oxford University Press on behalf of The Genetics Society of America.)
Databáze: MEDLINE
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