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Lee SH, Wang CY, Li IJ, Abe G, Ota KG. Exploring the origin of a unique mutant allele in twin-tail goldfish using CRISPR/Cas9 mutants. Sci Rep 2024; 14:8716. [PMID: 38622170 PMCID: PMC11018756 DOI: 10.1038/s41598-024-58448-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 03/29/2024] [Indexed: 04/17/2024] Open
Abstract
Artificial selection has been widely applied to genetically fix rare phenotypic features in ornamental domesticated animals. For many of these animals, the mutated loci and alleles underlying rare phenotypes are known. However, few studies have explored whether these rare genetic mutations might have been fixed due to competition among related mutated alleles or if the fixation occurred due to contingent stochastic events. Here, we performed genetic crossing with twin-tail ornamental goldfish and CRISPR/Cas9-mutated goldfish to investigate why only a single mutated allele-chdS with a E127X stop codon (also called chdAE127X)-gives rise to the twin-tail phenotype in the modern domesticated goldfish population. Two closely related chdS mutants were generated with CRISPR/Cas9 and compared with the E127X allele in F2 and F3 generations. Both of the CRISPR/Cas9-generated alleles were equivalent to the E127X allele in terms of penetrance/expressivity of the twin-tail phenotype and viability of carriers. These findings indicate that multiple truncating mutations could have produced viable twin-tail goldfish. Therefore, the absence of polymorphic alleles for the twin-tail phenotype in modern goldfish likely stems from stochastic elimination or a lack of competing alleles in the common ancestor. Our study is the first experimental comparison of a singular domestication-derived allele with CRISPR/Cas9-generated alleles to understand how genetic fixation of a unique genotype and phenotype may have occurred. Thus, our work may provide a conceptual framework for future investigations of rare evolutionary events in domesticated animals.
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Affiliation(s)
- Shu-Hua Lee
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
| | - Chen-Yi Wang
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
| | - Ing-Jia Li
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
| | - Gembu Abe
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
- Division of Developmental Biology, Department of Functional Morphology, Faculty of Medicine, School of Life Science, Tottori University, Nishi-cho 86, Yonago, 683-8503, Japan
| | - Kinya G Ota
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan.
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Abe G, Lee SH, Li IJ, Ota KG. An alternative evolutionary pathway for the twin-tail goldfish via szl gene mutation. J Exp Zool B Mol Dev Evol 2019; 330:234-241. [PMID: 29947476 PMCID: PMC6033011 DOI: 10.1002/jez.b.22811] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Revised: 05/18/2018] [Accepted: 05/23/2018] [Indexed: 12/22/2022]
Abstract
The twin‐tail of ornamental goldfish provides unique evolutionary evidence that the highly conserved midline localization of axial skeleton components can be changed by artificial selection. This morphological change is known to be caused by a nonsense mutation in one of the recently duplicated chordin genes, which are key players in dorsal–ventral (DV) patterning. Since all of the multiple twin‐tail ornamental goldfish strains share the same mutation, it is reasonable to presume that this mutation occurred only once in domesticated goldfish. However, zebrafish with mutated szl gene (another DV patterning‐related gene) also exhibit twin‐tail morphology and higher viability than dino/chordin‐mutant zebrafish. This observation raises the question of whether the szl gene mutation could also reproduce the twin‐tail morphology in goldfish. Here we show that goldfish have at least two subfunctionalized szl genes, designated szlA and szlB, and depletion of these genes in single‐fin goldfish was able to reproduce the bifurcated caudal fin found in twin‐tail ornamental goldfish. Interestingly, several phenotypes were observed in szlA‐depleted fish, while low expressivity of the twin‐tail phenotype was observed in szlB‐depleted goldfish. Thus, even though szl gene mutations may produce twin‐tail goldfish, these szl gene mutations might not be favorable for selection in domestic breeding. These results highlight the uniqueness and rarity of mutations that are able to cause large‐scale morphological changes, such as a bifurcated axial skeleton, with high viability and expressivity in natural and domesticated populations.
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Affiliation(s)
- Gembu Abe
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan.,Laboratory of Organ Morphogenesis, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Shu-Hua Lee
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Ing-Jia Li
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Kinya G Ota
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
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Li IJ, Lee SH, Abe G, Ota KG. Embryonic and postembryonic development of the ornamental twin-tail goldfish. Dev Dyn 2019; 248:251-283. [PMID: 30687996 PMCID: PMC6593469 DOI: 10.1002/dvdy.15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/23/2019] [Accepted: 01/23/2019] [Indexed: 12/22/2022] Open
Abstract
Background Twin‐tail ornamental goldfish have “bifurcated median fins,” a peculiar morphology known to be caused by a mutation in the chdA gene. However, several ambiguities regarding the development of the phenotype remain due to a paucity of detailed observations covering the entire developmental timeframe. Results Here, we report a detailed comparative description of embryonic and postembryonic development for two representative twin‐tail ornamental goldfish strains and single‐tail common goldfish. Our observations reveal a polymorphic developmental process for bifurcated median fins; disrupted axial skeletal development at early larval stages; and modified bilateral location of the pelvic fin. Conclusions Variations in development of bifurcated median fins and disrupted axial skeletal patterns reflect how artificial selection for adult morphological features influenced molecular developmental mechanisms during the domestication of twin‐tail ornamental goldfish. The polymorphic appearance of bifurcated median fins also implies that, unlike previously proposed hypotheses, the development of these structures is controlled by molecular mechanisms independent of those acting on the pelvic fin. Our present findings will facilitate further study of how modifications of preexisting developmental systems may contribute to novel morphological features. Developmental Dynamics 248:251–283, 2019. © 2019 The Authors. Developmental Dynamics published by Wiley Periodicals, Inc. on behalf of American Association of Anatomists. This is the first complete study to describe the developmental progression of twin‐tail goldfish. Disrupted axial skeletal morphology in adults develops from a modified osteogenesis process in vertebral elements. The developmental processes for not only the caudal and anal fins, but also pelvic fin, were changed by artificial selection in twin‐tail goldfish. Polymorphic anal and caudal fin development suggested that in addition to the mutation in the chdA gene, other relevant mutations have accumulated in the twin‐tail goldfish. Our developmental observations pave the way to study how the pre‐existing developmental systems were modified by selective pressure for the formation of a novel morphology.
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Affiliation(s)
- Ing-Jia Li
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
| | - Shu-Hua Lee
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
| | - Gembu Abe
- Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Kinya G Ota
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
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Abe G, Li IJ, Lee SH, Ota KG. A novel allele of the goldfish chdB gene: Functional evaluation and evolutionary considerations. J Exp Zool B Mol Dev Evol 2018; 330:372-383. [PMID: 30387925 PMCID: PMC6587777 DOI: 10.1002/jez.b.22831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 08/07/2018] [Accepted: 09/24/2018] [Indexed: 12/23/2022]
Abstract
The twin tail of ornamental goldfish is known to be caused by a nonsense mutation in one chordin paralogue gene. Our previous molecular studies in goldfish revealed that the ancestral
chordin gene was duplicated, creating the
chdA and
chdB genes, and the subsequent introduction of a stop codon allele in the
chdA gene (
chdAE127X) caused the twin‐tail morphology. The
chdAE127X allele was positively selected by breeders, and the allele was genetically fixed in the ornamental twin‐tail goldfish population. However, little is known about the evolutionary history of the
chdB paralogue, begging the question: are there the functionally distinct alleles at the
chdB locus, and if so, how did they evolve? To address these questions, we conducted molecular sequencing of the
chdB gene from five different goldfish strains and discovered two alleles at the
chdB gene locus; the two alleles are designated
chdB1 and
chdB2. The
chdB1 allele is the major allele and was found in all investigated goldfish strains, whereas the
chdB2 allele is minor, having only been found in one twin‐tail strain. Genetic analyses further suggested that these two alleles are functionally different with regard to survivability (
chdB1 >
chdB2). These results led us to presume that in contrast to the
chdA locus, the
chdB locus has tended to be eliminated from the population. We also discuss how the
chdB2 allele was retained in the goldfish population, despite its disadvantageous function. This study provides empirical evidence of the long‐term retention of a disadvantageous allele under domesticated conditions.
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Affiliation(s)
- Gembu Abe
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan.,Laboratory of Organ Morphogenesis, Department of Ecological Developmental Adaptability Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Ing-Jia Li
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Shu-Hua Lee
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Kinya G Ota
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
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Abe G, Lee SH, Li IJ, Chang CJ, Tamura K, Ota KG. Open and closed evolutionary paths for drastic morphological changes, involving serial gene duplication, sub-functionalization, and selection. Sci Rep 2016; 6:26838. [PMID: 27220684 PMCID: PMC4879570 DOI: 10.1038/srep26838] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 05/09/2016] [Indexed: 12/22/2022] Open
Abstract
Twin-tail goldfish strains are examples of drastic morphological alterations that emerged through domestication. Although this mutation is known to be caused by deficiency of one of two duplicated chordin genes, it is unknown why equivalent mutations have not been observed in other domesticated fish species. Here, we compared the chordin gene morphant phenotypes of single-tail goldfish and common carp (close relatives, both of which underwent chordin gene duplication and domestication). Morpholino-induced knockdown depleted chordin gene expression in both species; however, while knockdown reproduced twin-tail morphology in single-tail goldfish, it had no effect on common carp morphology. This difference can be explained by the observation that expression patterns of the duplicated chordin genes overlap completely in common carp, but are sub-functionalized in goldfish. Our finding implies that goldfish drastic morphological changes might be enhanced by the subsequent occurrence of three different types of evolutionary event (duplication, sub-functionalization, and selection) in a certain order.
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Affiliation(s)
- Gembu Abe
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
- Laboratory of Organ Morphogenesis, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai 980-8578, Japan
| | - Shu-Hua Lee
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
| | - Ing-Jia Li
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
| | - Chun-Ju Chang
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
| | - Koji Tamura
- Laboratory of Organ Morphogenesis, Department of Developmental Biology and Neurosciences, Graduate School of Life Sciences, Tohoku University, Aobayama Aoba-ku, Sendai 980-8578, Japan
| | - Kinya G. Ota
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, 26242, Taiwan
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Li IJ, Chang CJ, Liu SC, Abe G, Ota KG. Postembryonic staging of wild-type goldfish, with brief reference to skeletal systems. Dev Dyn 2015; 244:1485-518. [PMID: 26316229 PMCID: PMC5054871 DOI: 10.1002/dvdy.24340] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 07/10/2015] [Accepted: 08/23/2015] [Indexed: 01/06/2023] Open
Abstract
Background: Artificial selection of postembryonic features is known to have established morphological variation in goldfish (Carassius auratus). Although previous studies have suggested that goldfish and zebrafish are almost directly comparable at the embryonic level, little is known at the postembryonic level. Results: Here, we categorized the postembryonic developmental process in the wild‐type goldfish into 11 different stages. We also report certain differences between the postembryonic developmental processes of goldfish and zebrafish, especially in the skeletal systems (scales and median fin skeletons), suggesting that postembryonic development underwent evolutionary divergence in these two teleost species. Conclusions: Our postembryonic staging system of wild‐type goldfish paves the way for careful and appropriate comparison with other teleost species. The staging system will also facilitate comparative ontogenic analyses between wild‐type and mutant goldfish strains, allowing us to closely study the relationship between artificial selection and molecular developmental mechanisms in vertebrates. Developmental Dynamics 244:1485–1518, 2015. © 2015 Wiley Periodicals, Inc. This study provides the first reliable descriptions of normal post‐embryonic stages of wild type goldfish. Several post‐embryonic features of goldfish and zebrafish are diverged in these two teleost lineages. Goldfish larvae and juvenile provide a novel model for the investigation of the evolutionary relationship between domestication and ontogeny.
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Affiliation(s)
- Ing-Jia Li
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Chun-Ju Chang
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Shi-Chieh Liu
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Gembu Abe
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
| | - Kinya G Ota
- Laboratory of Aquatic Zoology, Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Yilan, Taiwan
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