Large-scale variation in single nucleotide polymorphism density within the laboratory axolotl (Ambystoma mexicanum).
Dev Dyn, 2021/06;250(6):822-837.
Timoshevskaya N[1], Voss SR[2, 3, 4], Labianca CN[5, 6], High CR[2, 3], Smith JJ[1]
Affiliations
PMID: 33001517DOI: 10.1002/dvdy.257
Impact factor: 2.842
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.
Keywords: SNPs; axolotl; genome; hybrid; salamander
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