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

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

Research output: Contribution to journalArticlepeer-review

2 Scopus citations


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.

Original languageEnglish
Pages (from-to)822-837
Number of pages16
JournalDevelopmental Dynamics
Issue number6
StatePublished - Jun 2021

Bibliographical note

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© 2020 Wiley Periodicals LLC


  • SNPs
  • axolotl
  • genome
  • hybrid
  • salamander

ASJC Scopus subject areas

  • Developmental Biology


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