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Medaka: a promising model animal for comparative population genomics.

Matsumoto Y, Oota H, Asaoka Y, Nishina H, Watanabe K, Bujnicki JM, Oda S, Kawamura S, Mitani H - BMC Res Notes (2009)

Bottom Line: Medaka (Oryzias latipes) and its congeneric species, tiny fresh-water teleosts distributed broadly in East and Southeast Asia, meet these criteria.We found medaka SNPs for which the same sites in human orthologs are known to be highly differentiated among the HapMap populations.These results indicate that medaka is a promising model system for comparative population genomics exploring the functional and adaptive significance of allelic differentiations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan. miraihe08@brain.riken.jp

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus

Nucleotide (upper) and amino acid (lower) sequence alignments of THEA2. Hd-rR is the inbred strain derived from the southern Japanese population for which the complete genome sequence has been determined [11]. All three (Hd-rR, Northern Japanese and East Korea) are Oryzias latipes. The others are closely related species.
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Figure 2: Nucleotide (upper) and amino acid (lower) sequence alignments of THEA2. Hd-rR is the inbred strain derived from the southern Japanese population for which the complete genome sequence has been determined [11]. All three (Hd-rR, Northern Japanese and East Korea) are Oryzias latipes. The others are closely related species.

Mentions: Of the 11 genes, we found that medaka THEA2 (BFIT2) contained a nonsynonymous SNP at the exactly same site where a high Fst is observed in humans (rs1702003 in exon 6: see the HapMap database; Fig. 2). THEA2 is known to be a temperature responsive gene, and it is expressed in brown adipose tissue (BAT) in response to cold stress in mice [18]. The genotype frequencies at rs1702003 are 98.3% G/G and 1.7% G/A in Europeans and 100% A/A in East Asians and Africans. This could suggest that the European-specific allele of the cold-inducible gene is an adaptation of Europeans to the cold environment around 40,000 years ago when early modern humans expanded to Europe. Interestingly, only Philippine medaka (Oryzias luzonensis), inhabiting a warmer environment, has a different allele from the other Oryzias species. While in situ hybridization showed THEA2 is expressed ubiquitously in medaka embryos, RT-PCR indicated greater THEA2 expression in the brown tissue homologous to mammalian BAT than in the other tissues in adult medaka (data not shown). In the structural predictions for the THEA2, we found that the two SNPs indicated for the human and medaka proteins are located at the junction between the Acyl-CoA hydrolase structural domains in a loop predicted to be highly flexible. There, a G-D (in humans) or L-P change (in medaka) is likely to affect the dynamics of the protein chain and influence (1) the interaction between domains and/or (2) the transmission of conformational changes. We speculate that the amino acid change that affects protein flexibility may be related to temperature adaptation.


Medaka: a promising model animal for comparative population genomics.

Matsumoto Y, Oota H, Asaoka Y, Nishina H, Watanabe K, Bujnicki JM, Oda S, Kawamura S, Mitani H - BMC Res Notes (2009)

Nucleotide (upper) and amino acid (lower) sequence alignments of THEA2. Hd-rR is the inbred strain derived from the southern Japanese population for which the complete genome sequence has been determined [11]. All three (Hd-rR, Northern Japanese and East Korea) are Oryzias latipes. The others are closely related species.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2683866&req=5

Figure 2: Nucleotide (upper) and amino acid (lower) sequence alignments of THEA2. Hd-rR is the inbred strain derived from the southern Japanese population for which the complete genome sequence has been determined [11]. All three (Hd-rR, Northern Japanese and East Korea) are Oryzias latipes. The others are closely related species.
Mentions: Of the 11 genes, we found that medaka THEA2 (BFIT2) contained a nonsynonymous SNP at the exactly same site where a high Fst is observed in humans (rs1702003 in exon 6: see the HapMap database; Fig. 2). THEA2 is known to be a temperature responsive gene, and it is expressed in brown adipose tissue (BAT) in response to cold stress in mice [18]. The genotype frequencies at rs1702003 are 98.3% G/G and 1.7% G/A in Europeans and 100% A/A in East Asians and Africans. This could suggest that the European-specific allele of the cold-inducible gene is an adaptation of Europeans to the cold environment around 40,000 years ago when early modern humans expanded to Europe. Interestingly, only Philippine medaka (Oryzias luzonensis), inhabiting a warmer environment, has a different allele from the other Oryzias species. While in situ hybridization showed THEA2 is expressed ubiquitously in medaka embryos, RT-PCR indicated greater THEA2 expression in the brown tissue homologous to mammalian BAT than in the other tissues in adult medaka (data not shown). In the structural predictions for the THEA2, we found that the two SNPs indicated for the human and medaka proteins are located at the junction between the Acyl-CoA hydrolase structural domains in a loop predicted to be highly flexible. There, a G-D (in humans) or L-P change (in medaka) is likely to affect the dynamics of the protein chain and influence (1) the interaction between domains and/or (2) the transmission of conformational changes. We speculate that the amino acid change that affects protein flexibility may be related to temperature adaptation.

Bottom Line: Medaka (Oryzias latipes) and its congeneric species, tiny fresh-water teleosts distributed broadly in East and Southeast Asia, meet these criteria.We found medaka SNPs for which the same sites in human orthologs are known to be highly differentiated among the HapMap populations.These results indicate that medaka is a promising model system for comparative population genomics exploring the functional and adaptive significance of allelic differentiations.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan. miraihe08@brain.riken.jp

ABSTRACT

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.

No MeSH data available.


Related in: MedlinePlus