Data from: A comparative survey of the frequency and distribution of polymorphism in the genome of Xenopus tropicalis

Naturally occurring DNA sequence variation within a species underlies
evolutionary adaptation and can give rise to phenotypic changes that
provide novel insight into biological questions. This variation exists in
laboratory populations just as in wild populations and, in addition to
being a source of useful alleles for genetic studies, can impact efforts
to identify induced mutations in sequence-based genetic screens. The
Western clawed frog Xenopus tropicalis (X. tropicalis) has been adopted as
a model system for studying the genetic control of embryonic development
and a variety of other areas of research. Its diploid genome has been
extensively sequenced and efforts are underway to isolate mutants by
phenotype- and genotype-based approaches. Here, we describe a study of
genetic polymorphism in laboratory strains of X. tropicalis. Polymorphism
was detected in the coding and non-coding regions of developmental genes
distributed widely across the genome. Laboratory strains exhibit
unexpectedly high frequencies of genetic polymorphism, with alleles
carrying a variety of synonymous and non-synonymous codon substitutions
and nucleotide insertions/deletions. Inter-strain comparisons of
polymorphism uncover a high proportion of shared alleles between Nigerian
and Ivory Coast strains, in spite of their distinct geographical origins.
These observations will likely influence the design of future
sequence-based mutation screens, particularly those using DNA
mismatch-based detection methods which can be disrupted by the presence of
naturally occurring sequence variants. The existence of a significant
reservoir of alleles also suggests that existing laboratory stocks may be
a useful source of novel alleles for mapping and functional studies.