GEPHE SUMMARY
Print
Gephebase Gene
Entry Status
Published
GepheID
GP00002349
Main curator
Courtier
PHENOTYPIC CHANGE
Trait Category
Trait State in Taxon A
eyes of standard size
wild goldfish and many strains of domesticated goldfish
wild goldfish and many strains of domesticated goldfish
Trait State in Taxon B
enlarged eyes
4 four Telescope-eye strains of domesticated goldfish
4 four Telescope-eye strains of domesticated goldfish
Ancestral State
Taxon A
Taxonomic Status
Taxon A
Latin Name
Common Name
goldfish
Synonyms
Carassius carassius auratus; Cyprinus auratus; goldfish; Carassius auratus (Linnaeus, 1758); Cyprinus auratus Linnaeus, 1758; Carassius auratis
Rank
species
Lineage
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Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Otomorpha; Ostariophysi; Otophysi; Cypriniphysae; Cypriniformes; Cyprinoidei; Cyprinidae; Cyprininae; Carassius
Parent
NCBI Taxonomy ID
is Taxon A an Infraspecies?
No
Taxon B
Latin Name
Common Name
goldfish
Synonyms
Carassius carassius auratus; Cyprinus auratus; goldfish; Carassius auratus (Linnaeus, 1758); Cyprinus auratus Linnaeus, 1758; Carassius auratis
Rank
species
Lineage
Show more ...
Actinopterygii; Actinopteri; Neopterygii; Teleostei; Osteoglossocephalai; Clupeocephala; Otomorpha; Ostariophysi; Otophysi; Cypriniphysae; Cypriniformes; Cyprinoidei; Cyprinidae; Cyprininae; Carassius
Parent
NCBI Taxonomy ID
is Taxon B an Infraspecies?
No
GENOTYPIC CHANGE
Generic Gene Name
LRP2
Synonyms
DBS; GP330; LRP-2
String
Sequence Similarities
Belongs to the LDLR family.
GO - Molecular Function
GO:0005509 : calcium ion binding
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GO - Biological Process
GO:0043066 : negative regulation of apoptotic process
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GO - Cellular Component
GO:0016021 : integral component of membrane
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UniProtKB
Homo sapiens
Homo sapiens
Mutation #1
Presumptive Null
Molecular Type
Aberration Type
SNP Coding Change
Nonsense
Molecular Details of the Mutation
-
Experimental Evidence
| Taxon A | Taxon B | Position | |
|---|---|---|---|
| Codon | - | - | - |
| Amino-acid | Tyr | STP | 3425 |
Authors
Kon T; Omori Y; Fukuta K; Wada H; Watanabe M; Chen Z; Iwasaki M; Mishina T; et al.
... show more
Abstract
Although domesticated goldfish strains exhibit highly diversified phenotypes in morphology, the genetic basis underlying these phenotypes is poorly understood. Here, based on analysis of transposable elements in the allotetraploid goldfish genome, we found that its two subgenomes have evolved asymmetrically since a whole-genome duplication event in the ancestor of goldfish and common carp. We conducted whole-genome sequencing of 27 domesticated goldfish strains and wild goldfish. We identified more than 60 million genetic variations and established a population genetic structure of major goldfish strains. Genome-wide association studies and analysis of strain-specific variants revealed genetic loci associated with several goldfish phenotypes, including dorsal fin loss, long-tail, telescope-eye, albinism, and heart-shaped tail. Our results suggest that accumulated mutations in the asymmetrically evolved subgenomes led to generation of diverse phenotypes in the goldfish domestication history. This study is a key resource for understanding the genetic basis of phenotypic diversity among goldfish strains.
Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.
Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.
Additional References
Mutation #2
Presumptive Null
Molecular Type
Aberration Type
SNP Coding Change
Nonsense
Molecular Details of the Mutation
-
Experimental Evidence
| Taxon A | Taxon B | Position | |
|---|---|---|---|
| Codon | - | - | - |
| Amino-acid | Gly | STP | 4480 |
Authors
Kon T; Omori Y; Fukuta K; Wada H; Watanabe M; Chen Z; Iwasaki M; Mishina T; et al.
... show more
Abstract
Although domesticated goldfish strains exhibit highly diversified phenotypes in morphology, the genetic basis underlying these phenotypes is poorly understood. Here, based on analysis of transposable elements in the allotetraploid goldfish genome, we found that its two subgenomes have evolved asymmetrically since a whole-genome duplication event in the ancestor of goldfish and common carp. We conducted whole-genome sequencing of 27 domesticated goldfish strains and wild goldfish. We identified more than 60 million genetic variations and established a population genetic structure of major goldfish strains. Genome-wide association studies and analysis of strain-specific variants revealed genetic loci associated with several goldfish phenotypes, including dorsal fin loss, long-tail, telescope-eye, albinism, and heart-shaped tail. Our results suggest that accumulated mutations in the asymmetrically evolved subgenomes led to generation of diverse phenotypes in the goldfish domestication history. This study is a key resource for understanding the genetic basis of phenotypic diversity among goldfish strains.
Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.
Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.
Additional References
Mutation #3
Presumptive Null
Molecular Type
Aberration Type
Insertion Size
10-100 kb
Molecular Details of the Mutation
13-kbp retrotransposon insertion of a foamy-like endogenous retrovirus in intron 45 in the Black Telescope-eye strain. Almost no normal lrp2aL mRNA was expressed in the Black Telescope-eye strain.
Experimental Evidence
Authors
Kon T; Omori Y; Fukuta K; Wada H; Watanabe M; Chen Z; Iwasaki M; Mishina T; et al.
... show more
Abstract
Although domesticated goldfish strains exhibit highly diversified phenotypes in morphology, the genetic basis underlying these phenotypes is poorly understood. Here, based on analysis of transposable elements in the allotetraploid goldfish genome, we found that its two subgenomes have evolved asymmetrically since a whole-genome duplication event in the ancestor of goldfish and common carp. We conducted whole-genome sequencing of 27 domesticated goldfish strains and wild goldfish. We identified more than 60 million genetic variations and established a population genetic structure of major goldfish strains. Genome-wide association studies and analysis of strain-specific variants revealed genetic loci associated with several goldfish phenotypes, including dorsal fin loss, long-tail, telescope-eye, albinism, and heart-shaped tail. Our results suggest that accumulated mutations in the asymmetrically evolved subgenomes led to generation of diverse phenotypes in the goldfish domestication history. This study is a key resource for understanding the genetic basis of phenotypic diversity among goldfish strains.
Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.
Copyright © 2020 The Authors. Published by Elsevier Inc. All rights reserved.
Additional References
RELATED GEPHE
Related Genes
No matches found.
Related Haplotypes
No matches found.
EXTERNAL LINKS
COMMENTS
@TE In mouse LRP2 plays the role of sonic hedgehog (shh) clearance receptor and regulates shh-induced cell proliferation at the retinal margin, resulting in a large eye phenotype.
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