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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.
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???displayArticle.pmcLink???PMC3150332 ???displayArticle.link???PLoS One ???displayArticle.grants???[+]
Fig 2. X. tropicalis strain phylogeny.
A consensus, unrooted, neighbor-joining tree representing the phylogenetic relationships between 55 sequenced individuals is shown. The UNC Nigerian F5 strain is represented by four individuals, the genotyped parents of the group 1 and group 2 animals previously analyzed. The Ivory Coast F8 and commercial Nigerian F5 individuals are labeled IC1-22 and N1-29 respectively. The bootstrap values are shown alongside the branches, indicating the number of times the partition of the individuals into the two sets separated by the branch occurred amongst the 100 trees on which the consensus tree is based.
Figure 1. Overview of shared and unique polymorphism amongst sequenced strains.This Venn diagram summarizes the pattern of shared and unique polymorphism between the UNC Nigerian F5, commercial Nigerian F5 and Ivory Coast F8 inbred frogs genotyped for 28 polymorphisms in 12 polymorphic genes.
Figure 2. X. tropicalis strain phylogeny.A consensus, unrooted, neighbor-joining tree representing the phylogenetic relationships between 55 sequenced individuals is shown. The UNC Nigerian F5 strain is represented by four individuals, the genotyped parents of the group 1 and group 2 animals previously analyzed. The Ivory Coast F8 and commercial Nigerian F5 individuals are labeled IC1-22 and N1-29 respectively. The bootstrap values are shown alongside the branches, indicating the number of times the partition of the individuals into the two sets separated by the branch occurred amongst the 100 trees on which the consensus tree is based.
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