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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 o...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2011
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150332/ https://www.ncbi.nlm.nih.gov/pubmed/21829622 http://dx.doi.org/10.1371/journal.pone.0022392 |
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author | Showell, Chris Carruthers, Samantha Hall, Amanda Pardo-Manuel de Villena, Fernando Stemple, Derek Conlon, Frank L. |
author_facet | Showell, Chris Carruthers, Samantha Hall, Amanda Pardo-Manuel de Villena, Fernando Stemple, Derek Conlon, Frank L. |
author_sort | Showell, Chris |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-3150332 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-31503322011-08-09 A Comparative Survey of the Frequency and Distribution of Polymorphism in the Genome of Xenopus tropicalis Showell, Chris Carruthers, Samantha Hall, Amanda Pardo-Manuel de Villena, Fernando Stemple, Derek Conlon, Frank L. PLoS One Research Article 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. Public Library of Science 2011-08-04 /pmc/articles/PMC3150332/ /pubmed/21829622 http://dx.doi.org/10.1371/journal.pone.0022392 Text en Showell et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Showell, Chris Carruthers, Samantha Hall, Amanda Pardo-Manuel de Villena, Fernando Stemple, Derek Conlon, Frank L. A Comparative Survey of the Frequency and Distribution of Polymorphism in the Genome of Xenopus tropicalis |
title | A Comparative Survey of the Frequency and Distribution of Polymorphism in the Genome of Xenopus tropicalis
|
title_full | A Comparative Survey of the Frequency and Distribution of Polymorphism in the Genome of Xenopus tropicalis
|
title_fullStr | A Comparative Survey of the Frequency and Distribution of Polymorphism in the Genome of Xenopus tropicalis
|
title_full_unstemmed | A Comparative Survey of the Frequency and Distribution of Polymorphism in the Genome of Xenopus tropicalis
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title_short | A Comparative Survey of the Frequency and Distribution of Polymorphism in the Genome of Xenopus tropicalis
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title_sort | comparative survey of the frequency and distribution of polymorphism in the genome of xenopus tropicalis |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150332/ https://www.ncbi.nlm.nih.gov/pubmed/21829622 http://dx.doi.org/10.1371/journal.pone.0022392 |
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