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

PMID: 33001517 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

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Publication Types

• Journal Article
• Research Support, N.I.H., Extramural
• Research Support, U.S. Gov't, Non-P.H.S.

Grant support

• R35 GM130349/GM/NIGMS NIH HHS/United States
• R24 OD010435/OD/NIH HHS/United States
• P40 OD019794/OD/NIH HHS/United States