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

1 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

Funding Information:
National Institute of General Medical Sciences, Grant/Award Number: R35GM130349; National Institutes of Health, Grant/Award Number: R24OD010435; U.S. Department of Defense, Grant/Award Number: W911NF1110475; National Science Foundation, Grant/Award Number: DBI‐0951484 Funding information

Funding Information:
This work was funded by grants from the National Institutes of Health (NIH) (R24OD010435) to S. Randal Voss, (5R35GM130349) to Jeramiah J. Smith and Department of Defence (DOD) (W911NF1110475) to S. Randal Voss. Animals used in this study were provided by the Ambystoma Genetic Stock Center, which is currently funded by the NIH (P40OD019794) and previously by the National Science Foundation (NSF) (DBI‐0951484) to S. Randal Voss. The contents of this paper are solely the responsibility of the authors and do not necessarily represent the official views of NIH, DOD, or NSF. Partial computational support was provided by The University of Kentucky High Performance Computing complex.

Publisher Copyright:
© 2020 Wiley Periodicals LLC


  • SNPs
  • axolotl
  • genome
  • hybrid
  • salamander

ASJC Scopus subject areas

  • Developmental Biology


Dive into the research topics of 'Large-scale variation in single nucleotide polymorphism density within the laboratory axolotl (Ambystoma mexicanum)'. Together they form a unique fingerprint.

Cite this