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Timoshevskaya N, Voss SR, Labianca CN, et al. Large-scale variation in single nucleotide polymorphism density within the laboratory axolotl (Ambystoma mexicanum). Dev Dyn. 2020;250(6):822-837doi: 10.1002/dvdy.257.
Timoshevskaya, N., Voss, S. R., Labianca, C. N., High, C. R., & Smith, J. J. (2021). Large-scale variation in single nucleotide polymorphism density within the laboratory axolotl (Ambystoma mexicanum). Developmental dynamics : an official publication of the American Association of Anatomists, 250(6), 822-837. https://doi.org/10.1002/dvdy.257
Timoshevskaya, Nataliya, et al. "Large-scale variation in single nucleotide polymorphism density within the laboratory axolotl (Ambystoma mexicanum)." Developmental dynamics : an official publication of the American Association of Anatomists vol. 250,6 (2021): 822-837. doi: https://doi.org/10.1002/dvdy.257
Timoshevskaya N, Voss SR, Labianca CN, High CR, Smith JJ. Large-scale variation in single nucleotide polymorphism density within the laboratory axolotl (Ambystoma mexicanum). Dev Dyn. 2021 Jun;250(6):822-837. doi: 10.1002/dvdy.257. Epub 2020 Oct 14. PMID: 33001517; PMCID: PMC8715502.
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Dev Dyn. 2021 Jun;250(6):822-837. doi: 10.1002/dvdy.257. Epub 2020 Oct 14.

Large-scale variation in single nucleotide polymorphism density within the laboratory axolotl (Ambystoma mexicanum).

Developmental dynamics : an official publication of the American Association of Anatomists

Nataliya Timoshevskaya, S Randal Voss, Caitlin N Labianca, Cassity R High, Jeramiah J Smith

Affiliations

  1. Department of Biology, University of Kentucky, Lexington, Kentucky, USA.
  2. Spinal Cord and Brain Injury Research Center, University of Kentucky, Lexington, Kentucky, USA.
  3. Department of Neuroscience, University of Kentucky, Lexington, Kentucky, USA.
  4. Ambystoma Genetic Stock Center, University of Kentucky, Lexington, Kentucky, USA.
  5. Paul Laurence Dunbar High School, Lexington, Kentucky, USA.
  6. Current Affiliation: Department of Biology, University of Rochester, Rochester, New York, USA.

PMID: 33001517 PMCID: PMC8715502 DOI: 10.1002/dvdy.257

Abstract

BACKGROUND: Recent efforts to assemble and analyze the Ambystoma mexicanum genome have dramatically improved the potential to develop molecular tools and pursue genome-wide analyses of genetic variation.

RESULTS: To better resolve the distribution and origins of genetic variation with A mexicanum, we compared DNA sequence data for two laboratory A mexicanum and one A tigrinum to identify 702 million high confidence polymorphisms distributed across the 32 Gb genome. While the wild-caught A tigrinum was generally more polymorphic in a genome-wide sense, several multi-megabase regions were identified from A mexicanum genomes that were actually more polymorphic than A tigrinum. Analysis of polymorphism and repeat content reveals that these regions likely originated from the intentional hybridization of A mexicanum and A tigrinum that was used to introduce the albino mutation into laboratory stocks.

CONCLUSIONS: Our findings show that axolotl genomes are variable with respect to introgressed DNA from a highly polymorphic species. It seems likely that other divergent regions will be discovered with additional sequencing of A mexicanum. This has practical implications for designing molecular probes and suggests a need to study A mexicanum phenotypic variation and genome evolution across the tiger salamander clade.

© 2020 Wiley Periodicals LLC.

Keywords: SNPs; axolotl; genome; hybrid; salamander

References

  1. Bioinformatics. 2009 Jul 15;25(14):1754-60 - PubMed
  2. Dev Biol. 2018 Jan 15;433(2):227-239 - PubMed
  3. Cold Spring Harb Protoc. 2009 Aug;2009(8):pdb.emo128 - PubMed
  4. Genetics. 2005 May;170(1):275-81 - PubMed
  5. Nature. 2018 Feb 1;554(7690):50-55 - PubMed
  6. Bioscience. 2015 Dec 1;65(12):1134-1140 - PubMed
  7. Bioinformatics. 2011 Nov 1;27(21):2987-93 - PubMed
  8. Sci Rep. 2018 Dec 14;8(1):17882 - PubMed
  9. Nat Commun. 2017 Dec 22;8(1):2286 - PubMed
  10. Sci Rep. 2015 Nov 10;5:16413 - PubMed
  11. Methods Mol Biol. 2015;1290:321-36 - PubMed
  12. Circulation. 2018 May 15;137(20):2152-2165 - PubMed
  13. Science. 1908 Jul 10;28(706):49-50 - PubMed
  14. Genomics. 2019 Dec;111(6):1216-1225 - PubMed
  15. Mol Syst Biol. 2011 Oct 11;7:539 - PubMed
  16. Can J Genet Cytol. 1985 Oct;27(5):510-4 - PubMed
  17. Dev Biol. 2017 Jun 15;426(2):143-154 - PubMed
  18. Sci Rep. 2017 Dec;7(1):6 - PubMed
  19. BMC Genomics. 2013 Jul 01;14:434 - PubMed
  20. Genome Res. 2010 Sep;20(9):1297-303 - PubMed
  21. Mol Biol Evol. 2012 Mar;29(3):985-93 - PubMed
  22. Sci Rep. 2019 May 1;9(1):6751 - PubMed
  23. Nucleic Acids Res. 2012 Aug;40(15):e115 - PubMed
  24. Fly (Austin). 2012 Apr-Jun;6(2):80-92 - PubMed
  25. Genome Res. 2002 Jun;12(6):996-1006 - PubMed
  26. Heredity (Edinb). 2009 Jun;102(6):542-8 - PubMed
  27. Front Endocrinol (Lausanne). 2019 Apr 02;10:194 - PubMed
  28. Genome Biol Evol. 2013;5(9):1716-30 - PubMed
  29. Genome Res. 2019 Feb;29(2):317-324 - PubMed
  30. Nucleic Acids Res. 2019 Jul 2;47(W1):W636-W641 - PubMed
  31. Cell Rep. 2017 Jan 17;18(3):762-776 - PubMed
  32. Curr Protoc Bioinformatics. 2014 Sep 08;47:11.12.1-34 - PubMed
  33. Regeneration (Oxf). 2015 Jun;2(3):120-136 - PubMed
  34. Proc Natl Acad Sci U S A. 1997 Dec 9;94(25):14185-9 - PubMed
  35. NPJ Regen Med. 2017 Nov 6;2:30 - PubMed
  36. Evolution. 1996 Feb;50(1):417-433 - PubMed
  37. Bioinformatics. 2009 Aug 15;25(16):2078-9 - PubMed
  38. Bioinformatics. 2014 Apr 1;30(7):1006-7 - PubMed
  39. BMC Genomics. 2005 Dec 16;6:181 - PubMed
  40. J Hered. 1967 May-Jun;58(3):95-101 - PubMed
  41. BMC Bioinformatics. 2009 Dec 15;10:421 - PubMed

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