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Medaka: a promising model animal for comparative population genomics

BACKGROUND: Within-species genome diversity has been best studied in humans. The international HapMap project has revealed a tremendous amount of single-nucleotide polymorphisms (SNPs) among humans, many of which show signals of positive selection during human evolution. In most of the cases, howeve...

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Autores principales: Matsumoto, Yoshifumi, Oota, Hiroki, Asaoka, Yoichi, Nishina, Hiroshi, Watanabe, Koji, Bujnicki, Janusz M, Oda, Shoji, Kawamura, Shoji, Mitani, Hiroshi
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683866/
https://www.ncbi.nlm.nih.gov/pubmed/19426554
http://dx.doi.org/10.1186/1756-0500-2-88
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author Matsumoto, Yoshifumi
Oota, Hiroki
Asaoka, Yoichi
Nishina, Hiroshi
Watanabe, Koji
Bujnicki, Janusz M
Oda, Shoji
Kawamura, Shoji
Mitani, Hiroshi
author_facet Matsumoto, Yoshifumi
Oota, Hiroki
Asaoka, Yoichi
Nishina, Hiroshi
Watanabe, Koji
Bujnicki, Janusz M
Oda, Shoji
Kawamura, Shoji
Mitani, Hiroshi
author_sort Matsumoto, Yoshifumi
collection PubMed
description BACKGROUND: Within-species genome diversity has been best studied in humans. The international HapMap project has revealed a tremendous amount of single-nucleotide polymorphisms (SNPs) among humans, many of which show signals of positive selection during human evolution. In most of the cases, however, functional differences between the alleles remain experimentally unverified due to the inherent difficulty of human genetic studies. It would therefore be highly useful to have a vertebrate model with the following characteristics: (1) high within-species genetic diversity, (2) a variety of gene-manipulation protocols already developed, and (3) a completely sequenced genome. Medaka (Oryzias latipes) and its congeneric species, tiny fresh-water teleosts distributed broadly in East and Southeast Asia, meet these criteria. FINDINGS: Using Oryzias species from 27 local populations, we conducted a simple screening of nonsynonymous SNPs for 11 genes with apparent orthology between medaka and humans. We found medaka SNPs for which the same sites in human orthologs are known to be highly differentiated among the HapMap populations. Importantly, some of these SNPs show signals of positive selection. CONCLUSION: These results indicate that medaka is a promising model system for comparative population genomics exploring the functional and adaptive significance of allelic differentiations.
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spelling pubmed-26838662009-05-19 Medaka: a promising model animal for comparative population genomics Matsumoto, Yoshifumi Oota, Hiroki Asaoka, Yoichi Nishina, Hiroshi Watanabe, Koji Bujnicki, Janusz M Oda, Shoji Kawamura, Shoji Mitani, Hiroshi BMC Res Notes Short Report BACKGROUND: Within-species genome diversity has been best studied in humans. The international HapMap project has revealed a tremendous amount of single-nucleotide polymorphisms (SNPs) among humans, many of which show signals of positive selection during human evolution. In most of the cases, however, functional differences between the alleles remain experimentally unverified due to the inherent difficulty of human genetic studies. It would therefore be highly useful to have a vertebrate model with the following characteristics: (1) high within-species genetic diversity, (2) a variety of gene-manipulation protocols already developed, and (3) a completely sequenced genome. Medaka (Oryzias latipes) and its congeneric species, tiny fresh-water teleosts distributed broadly in East and Southeast Asia, meet these criteria. FINDINGS: Using Oryzias species from 27 local populations, we conducted a simple screening of nonsynonymous SNPs for 11 genes with apparent orthology between medaka and humans. We found medaka SNPs for which the same sites in human orthologs are known to be highly differentiated among the HapMap populations. Importantly, some of these SNPs show signals of positive selection. CONCLUSION: These results indicate that medaka is a promising model system for comparative population genomics exploring the functional and adaptive significance of allelic differentiations. BioMed Central 2009-05-10 /pmc/articles/PMC2683866/ /pubmed/19426554 http://dx.doi.org/10.1186/1756-0500-2-88 Text en Copyright © 2009 Oota et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Short Report
Matsumoto, Yoshifumi
Oota, Hiroki
Asaoka, Yoichi
Nishina, Hiroshi
Watanabe, Koji
Bujnicki, Janusz M
Oda, Shoji
Kawamura, Shoji
Mitani, Hiroshi
Medaka: a promising model animal for comparative population genomics
title Medaka: a promising model animal for comparative population genomics
title_full Medaka: a promising model animal for comparative population genomics
title_fullStr Medaka: a promising model animal for comparative population genomics
title_full_unstemmed Medaka: a promising model animal for comparative population genomics
title_short Medaka: a promising model animal for comparative population genomics
title_sort medaka: a promising model animal for comparative population genomics
topic Short Report
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2683866/
https://www.ncbi.nlm.nih.gov/pubmed/19426554
http://dx.doi.org/10.1186/1756-0500-2-88
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