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

Publisher: Oxford University Press Country of Publication: England NLM ID: 101566598 Publication Model: Print Cited Medium: Internet ISSN: 2160-1836 (Electronic) Linking ISSN: 21601836 NLM ISO Abbreviation: G3 (Bethesda) Subsets: MEDLINE

Publication: 2021- : [Oxford] : Oxford University Press
Original Publication: Bethesda, MD : Genetics Society of America, 2011-

Characidae*/genetics ; Chromosomes*/genetics ; Caves*; Animals ; Phylogeny ; Genome ; Genomics/methods ; Genetic Variation ; Quantitative Trait Loci ; Synteny ; Phenotype

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.)

Update of: bioRxiv. 2023 Nov 20:2023.11.16.567450. doi: 10.1101/2023.11.16.567450. (PMID: 38014157)

Bioinformatics. 2009 Jul 15;25(14):1754-60. (PMID: 19451168)
Nat Biotechnol. 2023 Oct;41(10):1474-1482. (PMID: 36797493)
Mol Ecol. 2018 Nov;27(22):4397-4416. (PMID: 30252986)
Nat Rev Genet. 2016 Jul;17(7):379-91. (PMID: 27087500)
Heredity (Edinb). 2005 Mar;94(3):280-94. (PMID: 15674378)
Cell Syst. 2016 Jul;3(1):99-101. (PMID: 27467250)
Evol Med Public Health. 2018 Aug 06;2018(1):186-189. (PMID: 30151194)
Methods Mol Biol. 2021;2324:35-48. (PMID: 34165707)
Science. 2021 Dec 17;374(6574):abg8871. (PMID: 34914532)
Nat Genet. 2016 Apr;48(4):427-37. (PMID: 26950095)
Curr Biol. 2021 Nov 8;31(21):4800-4809.e9. (PMID: 34496222)
Dev Biol. 2018 Sep 15;441(2):355-357. (PMID: 29684312)
Nature. 2022 Nov;611(7936):519-531. (PMID: 36261518)
Genome Biol. 2004;5(2):R12. (PMID: 14759262)
Cell Syst. 2018 Feb 28;6(2):256-258.e1. (PMID: 29428417)
Curr Biol. 2011 Apr 26;21(8):671-6. (PMID: 21474315)
G3 (Bethesda). 2023 Mar 9;13(3):. (PMID: 36626199)
Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. (PMID: 24259432)
Bioinformatics. 2015 Oct 1;31(19):3210-2. (PMID: 26059717)
J Exp Zool B Mol Dev Evol. 2020 Nov;334(7-8):397-404. (PMID: 32638529)
Nature. 2021 Apr;592(7856):737-746. (PMID: 33911273)
Elife. 2022 Sep 09;11:. (PMID: 36083267)
Genome Res. 2022 Mar;32(3):583-594. (PMID: 35082141)
Elife. 2020 Apr 21;9:. (PMID: 32314737)
G3 (Bethesda). 2023 Apr 11;13(4):. (PMID: 36905099)
Nat Commun. 2023 May 3;14(1):2557. (PMID: 37137902)
Genome Biol. 2019 Nov 14;20(1):238. (PMID: 31727128)
Nat Methods. 2021 Feb;18(2):170-175. (PMID: 33526886)
Database (Oxford). 2016 Jun 23;2016:. (PMID: 27337980)
Cell Rep. 2018 Nov 20;25(8):1997-2007.e7. (PMID: 30462998)
PLoS Comput Biol. 2019 Aug 21;15(8):e1007273. (PMID: 31433799)
PLoS Comput Biol. 2019 Jun 5;15(6):e1006994. (PMID: 31166948)
Nat Methods. 2020 Feb;17(2):155-158. (PMID: 31819265)
Bioinformatics. 2020 May 1;36(9):2896-2898. (PMID: 31971576)
Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):9668-73. (PMID: 26170297)
BMC Genomics. 2022 Feb 10;23(1):116. (PMID: 35144548)
Nat Commun. 2021 Mar 4;12(1):1447. (PMID: 33664263)
Bioinformatics. 2016 Oct 1;32(19):3021-3. (PMID: 27318204)
BMC Biol. 2020 Jan 28;18(1):11. (PMID: 31992286)

University of Missouri; 1923372 National Science Foundation; WT222155/Z/20/Z United Kingdom WT_ Wellcome Trust; United Kingdom WT_ Wellcome Trust; R24 OD011198 United States OD NIH HHS; 1R01GM127872-01 United States GF NIH HHS

Keywords: Astyanax mexicanus; cavefish; chromosome assembly

Date Created: 20240521 Date Completed: 20240807 Latest Revision: 20240809

20240809

PMC11304944

10.1093/g3journal/jkae103

38771704