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Inbreeding Ratio and Genetic Relationships among Strains of the Western Clawed Frog, Xenopus tropicalis.

Igawa T, Watanabe A, Suzuki A, Kashiwagi A, Kashiwagi K, Noble A, Guille M, Simpson DE, Horb ME, Fujii T, Sumida M - PLoS ONE (2015)

Bottom Line: It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s.Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains.Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts.

View Article: PubMed Central - PubMed

Affiliation: Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.

ABSTRACT
The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains has not yet been clarified, and establishment of inbred strains has not yet been achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima University has maintained stocks of multiple X. tropicalis strains and conducted consecutive breeding as part of the National BioResource Project. In the present study we investigated the inbreeding ratio and genetic relationship of four inbred strains at IAB, as well as stocks from other institutions, using highly polymorphic microsatellite markers and mitochondrial haplotypes. Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains. The Ivory Coast strains clearly differed from the Nigerian strains genetically, and three subgroups were identified within both the Nigerian and Ivory Coast strains. It is noteworthy that the Ivory Coast strains have an evolutionary divergent genetic background. Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts.

No MeSH data available.


Neighbor joining trees and comparison of the control region structures of mitochondrial genomes.(A) Neighbor joining trees of the strains based on genetic distances (DA) of SSLP data (left) and p-distance of mitochondrial haplotypes (2,328 nucleotide sites) (right). Numbers on branches indicate percent bootstrap probability (>50%). The values for SSLP tree are given in order for DA/DPS. (B) Comparison of the control region structures of mitochondrial genomes. Structures of the control region and alignments of identified putative origin of H-strand replication (OH), conserved sequence blocks (CSB-1-3), and repeat motifs are shown. (C) Neighbor joining tree of the strains and wild individuals based on p-distance of mitochondrial haplotypes (1,109 nucleotide sites).
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pone.0133963.g004: Neighbor joining trees and comparison of the control region structures of mitochondrial genomes.(A) Neighbor joining trees of the strains based on genetic distances (DA) of SSLP data (left) and p-distance of mitochondrial haplotypes (2,328 nucleotide sites) (right). Numbers on branches indicate percent bootstrap probability (>50%). The values for SSLP tree are given in order for DA/DPS. (B) Comparison of the control region structures of mitochondrial genomes. Structures of the control region and alignments of identified putative origin of H-strand replication (OH), conserved sequence blocks (CSB-1-3), and repeat motifs are shown. (C) Neighbor joining tree of the strains and wild individuals based on p-distance of mitochondrial haplotypes (1,109 nucleotide sites).

Mentions: These divergent patterns in the genotypic data of SSLP and the haplotypes of mitochondrial DNA were basically reflected in the phylogenetic trees based on these data. For the phylogenetic trees based on genetic distance matrixes of SSLP genotypic data, both DA and Dps showed similar results with higher bootstrap values, thus we show only the tree based on DA, with bootstrap values in both DA and Dps (Fig 4A). In this tree, the two major strain groups were firstly diverged with high bootstrap values (100% in both DA and Dps). Within the Nigerian group, NH (IAB) was the first to diverge, followed by a split into two groups: one consisting of Golden (IAB), N (Gurdon Inst.) and N (NASCO), and the other consisting of NA (IAB), N (NXR), Cambridge (EXRC) and Superman (NXR). Although this grouping was clearly supported with relatively higher bootstrap values (> 70%), the relationships within the latter group were ambiguous with mostly lower bootstrap values around 50% or less. N (Gurdon Inst.) and N (NASCO) in particular were genetically almost identical, showing the smallest values of 0.137 and 0.271 for DA and Dps, respectively (Table 2). Within the Ivory Coast group, IC (IAB) was clearly diverged from the two TGA blue strains with high bootstrap values (100% in both DA and Dps). The phylogenetic tree of mitochondrial DNA haplotypes of all twelve strains was constructed based on 2,328 nucleotide sites after elimination of ambiguous and gap sites (Fig 4B). Although this tree is somewhat similar to SSLP tree, the IC (IAB) was the first to diverge when the midpoint of the tree length was rooted, reflecting the large difference in the nucleotide sequence of its haplotype. However the bootstrap support of a clade consisting of IC (EXRC) and TGA blue haplotypes was not so high (= 65%), and thus the evolutionary relationships of these haplotypes are still unclear. We also conducted analyses adding three haplotypes from three wild populations deposited in the DNA database. Another tree was constructed based on 1,109 nucleotide sites after the elimination of missing sequence and ambiguous sites in these additional data. In this tree, the relationships among strains were basically the same as the above tree. Interestingly, the haplotype of the individual from Uyere, Nigeria was found to be identical to that of IC (EXRC), while the haplotypes of the individuals from Adiapodoum, Ivory Coast and Free town, Sierra Leone were not grouped with any others and shown to be diverged at an intermediate position between IC (IAB) and the other Ivory Coast strains.


Inbreeding Ratio and Genetic Relationships among Strains of the Western Clawed Frog, Xenopus tropicalis.

Igawa T, Watanabe A, Suzuki A, Kashiwagi A, Kashiwagi K, Noble A, Guille M, Simpson DE, Horb ME, Fujii T, Sumida M - PLoS ONE (2015)

Neighbor joining trees and comparison of the control region structures of mitochondrial genomes.(A) Neighbor joining trees of the strains based on genetic distances (DA) of SSLP data (left) and p-distance of mitochondrial haplotypes (2,328 nucleotide sites) (right). Numbers on branches indicate percent bootstrap probability (>50%). The values for SSLP tree are given in order for DA/DPS. (B) Comparison of the control region structures of mitochondrial genomes. Structures of the control region and alignments of identified putative origin of H-strand replication (OH), conserved sequence blocks (CSB-1-3), and repeat motifs are shown. (C) Neighbor joining tree of the strains and wild individuals based on p-distance of mitochondrial haplotypes (1,109 nucleotide sites).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4519292&req=5

pone.0133963.g004: Neighbor joining trees and comparison of the control region structures of mitochondrial genomes.(A) Neighbor joining trees of the strains based on genetic distances (DA) of SSLP data (left) and p-distance of mitochondrial haplotypes (2,328 nucleotide sites) (right). Numbers on branches indicate percent bootstrap probability (>50%). The values for SSLP tree are given in order for DA/DPS. (B) Comparison of the control region structures of mitochondrial genomes. Structures of the control region and alignments of identified putative origin of H-strand replication (OH), conserved sequence blocks (CSB-1-3), and repeat motifs are shown. (C) Neighbor joining tree of the strains and wild individuals based on p-distance of mitochondrial haplotypes (1,109 nucleotide sites).
Mentions: These divergent patterns in the genotypic data of SSLP and the haplotypes of mitochondrial DNA were basically reflected in the phylogenetic trees based on these data. For the phylogenetic trees based on genetic distance matrixes of SSLP genotypic data, both DA and Dps showed similar results with higher bootstrap values, thus we show only the tree based on DA, with bootstrap values in both DA and Dps (Fig 4A). In this tree, the two major strain groups were firstly diverged with high bootstrap values (100% in both DA and Dps). Within the Nigerian group, NH (IAB) was the first to diverge, followed by a split into two groups: one consisting of Golden (IAB), N (Gurdon Inst.) and N (NASCO), and the other consisting of NA (IAB), N (NXR), Cambridge (EXRC) and Superman (NXR). Although this grouping was clearly supported with relatively higher bootstrap values (> 70%), the relationships within the latter group were ambiguous with mostly lower bootstrap values around 50% or less. N (Gurdon Inst.) and N (NASCO) in particular were genetically almost identical, showing the smallest values of 0.137 and 0.271 for DA and Dps, respectively (Table 2). Within the Ivory Coast group, IC (IAB) was clearly diverged from the two TGA blue strains with high bootstrap values (100% in both DA and Dps). The phylogenetic tree of mitochondrial DNA haplotypes of all twelve strains was constructed based on 2,328 nucleotide sites after elimination of ambiguous and gap sites (Fig 4B). Although this tree is somewhat similar to SSLP tree, the IC (IAB) was the first to diverge when the midpoint of the tree length was rooted, reflecting the large difference in the nucleotide sequence of its haplotype. However the bootstrap support of a clade consisting of IC (EXRC) and TGA blue haplotypes was not so high (= 65%), and thus the evolutionary relationships of these haplotypes are still unclear. We also conducted analyses adding three haplotypes from three wild populations deposited in the DNA database. Another tree was constructed based on 1,109 nucleotide sites after the elimination of missing sequence and ambiguous sites in these additional data. In this tree, the relationships among strains were basically the same as the above tree. Interestingly, the haplotype of the individual from Uyere, Nigeria was found to be identical to that of IC (EXRC), while the haplotypes of the individuals from Adiapodoum, Ivory Coast and Free town, Sierra Leone were not grouped with any others and shown to be diverged at an intermediate position between IC (IAB) and the other Ivory Coast strains.

Bottom Line: It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s.Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains.Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts.

View Article: PubMed Central - PubMed

Affiliation: Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.

ABSTRACT
The Western clawed frog, Xenopus tropicalis, is a highly promising model amphibian, especially in developmental and physiological research, and as a tool for understanding disease. It was originally found in the West African rainforest belt, and was introduced to the research community in the 1990s. The major strains thus far known include the Nigerian and Ivory Coast strains. However, due to its short history as an experimental animal, the genetic relationship among the various strains has not yet been clarified, and establishment of inbred strains has not yet been achieved. Since 2003 the Institute for Amphibian Biology (IAB), Hiroshima University has maintained stocks of multiple X. tropicalis strains and conducted consecutive breeding as part of the National BioResource Project. In the present study we investigated the inbreeding ratio and genetic relationship of four inbred strains at IAB, as well as stocks from other institutions, using highly polymorphic microsatellite markers and mitochondrial haplotypes. Our results show successive reduction of heterozygosity in the genome of the IAB inbred strains. The Ivory Coast strains clearly differed from the Nigerian strains genetically, and three subgroups were identified within both the Nigerian and Ivory Coast strains. It is noteworthy that the Ivory Coast strains have an evolutionary divergent genetic background. Our results serve as a guide for the most effective use of X. tropicalis strains, and the long-term maintenance of multiple strains will contribute to further research efforts.

No MeSH data available.