Abstract
BackgroundSpecies adaptation to laboratory conditions is a special case of domestication that has modified model organisms phenotypically and genetically. The characterisation of these changes is crucial to understand how this variation can affect the outcome of biological experiments. Yet despite the wide use of laboratory animals in biological research, knowledge of the genetic diversity within and between different strains and populations of some animal models is still scarce. This is particularly the case of the Mexican axolotl, which has been bred in captivity since 1864.ResultsUsing gene expression data from nine different projects, nucleotide sequence variants were characterised, and distinctive genetic background of the experimental specimens was uncovered. This study provides a catalogue of thousands of nucleotide variants along predicted protein-coding genes, while identifying genome-wide differences between pigment phenotypes in laboratory populations.ConclusionsAwareness of the genetic variation could guide a better experimental design while helping to develop molecular tools for monitoring genetic diversity and studying gene functions in laboratory axolotls. Overall, this study highlights the cross-taxa utility that transcriptomic data might have to assess the genetic variation of the experimental specimens, which might help to shorten the journey towards reproducible research.
Highlights
Species adaptation to laboratory conditions is a special case of domestication that has modified model organisms phenotypically and genetically
The variants were categorized into two groups: i) insertions and deletions of bases (INDELs, 128,504, 21.94%), and ii) single nucleotide variants (3289 multiallelic and 453,973 bi-allelic variants, 0.56 and 77.5%, respectively)
While the complex history of contemporary laboratory populations has been previously described [17, 19], very little is known about existing levels of genetic variation
Summary
Species adaptation to laboratory conditions is a special case of domestication that has modified model organisms phenotypically and genetically. The characterisation of these changes is crucial to understand how this variation can affect the outcome of biological experiments. Despite the wide use of laboratory animals in biological research, knowledge of the genetic diversity within and between different strains and populations of some animal models is still scarce. This is the case of the Mexican axolotl, which has been bred in captivity since 1864. Through the years of captive breeding, animal import, genetic drift, and non-random mating, the genetic structure of captive populations can be altered increasing the differences both between wild and domesticated animals, and among different captive populations [4, 7, 8]
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