Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication

Domestic ducks are raised for meat, eggs and feather down, and almost all varieties are descended from the Mallard (Anas platyrhynchos). Here, we report chromosome-level high-quality genome assemblies for meat and laying duck breeds, and the Mallard. Our new genomic databases contain annotations for...

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Published inNature communications Vol. 12; no. 1; pp. 5932 - 11
Main Authors Zhu, Feng, Yin, Zhong-Tao, Wang, Zheng, Smith, Jacqueline, Zhang, Fan, Martin, Fergal, Ogeh, Denye, Hincke, Maxwell, Lin, Fang-Bing, Burt, David W., Zhou, Zheng-Kui, Hou, Shui-Sheng, Zhao, Qiang-Sen, Li, Xiao-Qin, Ding, Si-Ran, Li, Guan-Sheng, Yang, Fang-Xi, Hao, Jing-Pin, Zhang, Ziding, Lu, Li-Zhi, Yang, Ning, Hou, Zhuo-Cheng
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 11.10.2021
Nature Publishing Group
Nature Portfolio
Subjects
38
45
45/23
45/91
631/208/212
631/208/8
Anas platyrhynchos
Annotations
Aquatic birds
Assemblies
Chromosomes
Cytotoxicity
Domestication
Ducks
Egg shells
Genes
Genetic improvement
Genetics
Genomes
Genomics
Humanities and Social Sciences
Lymphocytes T
Meat
Mineralization
multidisciplinary
Mutation
Oviparity
Science
Science (multidisciplinary)
Waterfowl
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Abstract Domestic ducks are raised for meat, eggs and feather down, and almost all varieties are descended from the Mallard (Anas platyrhynchos). Here, we report chromosome-level high-quality genome assemblies for meat and laying duck breeds, and the Mallard. Our new genomic databases contain annotations for thousands of new protein-coding genes and recover a major percentage of the presumed “missing genes” in birds. We obtain the entire genomic sequences for the C-type lectin (CTL) family members that regulate eggshell biomineralization. Our population and comparative genomics analyses provide more than 36 million sequence variants between duck populations. Furthermore, a mutant cell line allows confirmation of the predicted anti-adipogenic function of NR2F2 in the duck, and uncovered mutations specific to Pekin duck that potentially affect adipose deposition. Our study provides insights into avian evolution and the genetics of oviparity, and will be a rich resource for the future genetic improvement of commercial traits in the duck. Domestic ducks are descended from the Mallard and have been bred for several purposes. Here the authors present three high-quality duck genome assemblies which recover previously missing genes and provide a rich resource of variants potentially related to domestication.
AbstractList Domestic ducks are raised for meat, eggs and feather down, and almost all varieties are descended from the Mallard (Anas platyrhynchos). Here, we report chromosome-level high-quality genome assemblies for meat and laying duck breeds, and the Mallard. Our new genomic databases contain annotations for thousands of new protein-coding genes and recover a major percentage of the presumed “missing genes” in birds. We obtain the entire genomic sequences for the C-type lectin (CTL) family members that regulate eggshell biomineralization. Our population and comparative genomics analyses provide more than 36 million sequence variants between duck populations. Furthermore, a mutant cell line allows confirmation of the predicted anti-adipogenic function of NR2F2 in the duck, and uncovered mutations specific to Pekin duck that potentially affect adipose deposition. Our study provides insights into avian evolution and the genetics of oviparity, and will be a rich resource for the future genetic improvement of commercial traits in the duck. Domestic ducks are descended from the Mallard and have been bred for several purposes. Here the authors present three high-quality duck genome assemblies which recover previously missing genes and provide a rich resource of variants potentially related to domestication.
Domestic ducks are raised for meat, eggs and feather down, and almost all varieties are descended from the Mallard (Anas platyrhynchos). Here, we report chromosome-level high-quality genome assemblies for meat and laying duck breeds, and the Mallard. Our new genomic databases contain annotations for thousands of new protein-coding genes and recover a major percentage of the presumed “missing genes” in birds. We obtain the entire genomic sequences for the C-type lectin (CTL) family members that regulate eggshell biomineralization. Our population and comparative genomics analyses provide more than 36 million sequence variants between duck populations. Furthermore, a mutant cell line allows confirmation of the predicted anti-adipogenic function of NR2F2 in the duck, and uncovered mutations specific to Pekin duck that potentially affect adipose deposition. Our study provides insights into avian evolution and the genetics of oviparity, and will be a rich resource for the future genetic improvement of commercial traits in the duck.
Domestic ducks are raised for meat, eggs and feather down, and almost all varieties are descended from the Mallard (Anas platyrhynchos). Here, we report chromosome-level high-quality genome assemblies for meat and laying duck breeds, and the Mallard. Our new genomic databases contain annotations for thousands of new protein-coding genes and recover a major percentage of the presumed "missing genes" in birds. We obtain the entire genomic sequences for the C-type lectin (CTL) family members that regulate eggshell biomineralization. Our population and comparative genomics analyses provide more than 36 million sequence variants between duck populations. Furthermore, a mutant cell line allows confirmation of the predicted anti-adipogenic function of NR2F2 in the duck, and uncovered mutations specific to Pekin duck that potentially affect adipose deposition. Our study provides insights into avian evolution and the genetics of oviparity, and will be a rich resource for the future genetic improvement of commercial traits in the duck.Domestic ducks are raised for meat, eggs and feather down, and almost all varieties are descended from the Mallard (Anas platyrhynchos). Here, we report chromosome-level high-quality genome assemblies for meat and laying duck breeds, and the Mallard. Our new genomic databases contain annotations for thousands of new protein-coding genes and recover a major percentage of the presumed "missing genes" in birds. We obtain the entire genomic sequences for the C-type lectin (CTL) family members that regulate eggshell biomineralization. Our population and comparative genomics analyses provide more than 36 million sequence variants between duck populations. Furthermore, a mutant cell line allows confirmation of the predicted anti-adipogenic function of NR2F2 in the duck, and uncovered mutations specific to Pekin duck that potentially affect adipose deposition. Our study provides insights into avian evolution and the genetics of oviparity, and will be a rich resource for the future genetic improvement of commercial traits in the duck.
Domestic ducks are raised for meat, eggs and feather down, and almost all varieties are descended from the Mallard (Anas platyrhynchos). Here, we report chromosome-level high-quality genome assemblies for meat and laying duck breeds, and the Mallard. Our new genomic databases contain annotations for thousands of new protein-coding genes and recover a major percentage of the presumed “missing genes” in birds. We obtain the entire genomic sequences for the C-type lectin (CTL) family members that regulate eggshell biomineralization. Our population and comparative genomics analyses provide more than 36 million sequence variants between duck populations. Furthermore, a mutant cell line allows confirmation of the predicted anti-adipogenic function of NR2F2 in the duck, and uncovered mutations specific to Pekin duck that potentially affect adipose deposition. Our study provides insights into avian evolution and the genetics of oviparity, and will be a rich resource for the future genetic improvement of commercial traits in the duck.Domestic ducks are descended from the Mallard and have been bred for several purposes. Here the authors present three high-quality duck genome assemblies which recover previously missing genes and provide a rich resource of variants potentially related to domestication.
Domestic ducks are descended from the Mallard and have been bred for several purposes. Here the authors present three high-quality duck genome assemblies which recover previously missing genes and provide a rich resource of variants potentially related to domestication.
ArticleNumber 5932
Author Yin, Zhong-Tao
Hou, Shui-Sheng
Wang, Zheng
Zhu, Feng
Smith, Jacqueline
Li, Guan-Sheng
Zhang, Ziding
Zhang, Fan
Lin, Fang-Bing
Hincke, Maxwell
Hao, Jing-Pin
Zhou, Zheng-Kui
Ding, Si-Ran
Lu, Li-Zhi
Zhao, Qiang-Sen
Burt, David W.
Yang, Fang-Xi
Li, Xiao-Qin
Ogeh, Denye
Hou, Zhuo-Cheng
Martin, Fergal
Yang, Ning
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Snippet Domestic ducks are raised for meat, eggs and feather down, and almost all varieties are descended from the Mallard (Anas platyrhynchos). Here, we report...
Domestic ducks are descended from the Mallard and have been bred for several purposes. Here the authors present three high-quality duck genome assemblies which...
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SubjectTerms 38
45
45/23
45/91
631/208/212
631/208/8
Anas platyrhynchos
Annotations
Aquatic birds
Assemblies
Chromosomes
Cytotoxicity
Domestication
Ducks
Egg shells
Genes
Genetic improvement
Genetics
Genomes
Genomics
Humanities and Social Sciences
Lymphocytes T
Meat
Mineralization
multidisciplinary
Mutation
Oviparity
Science
Science (multidisciplinary)
Waterfowl
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Title Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication
URI https://link.springer.com/article/10.1038/s41467-021-26272-1
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https://www.proquest.com/docview/2581290128
https://pubmed.ncbi.nlm.nih.gov/PMC8505442
https://doaj.org/article/975b3a2b5b854653a870d7d859a96884
Volume 12
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