A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families
Abstract Background The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A virus (IAV), harbors almost all subtypes of IAVs and resists to many IAVs which cause extreme virulence in chicken and human. However, the response of duck’s adaptive immune system to IAV infection...
| Main Authors: | , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2024-02-01
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| Series: | BMC Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12915-024-01817-0 |
| _version_ | 1827326202101104640 |
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| author | Jiaxiang Hu Linfei Song Mengfei Ning Xinyu Niu Mengying Han Chuze Gao Xingwei Feng Han Cai Te Li Fangtao Li Huifang Li Daoqing Gong Weitao Song Long Liu Juan Pu Jinhua Liu Jacqueline Smith Honglei Sun Yinhua Huang |
| author_facet | Jiaxiang Hu Linfei Song Mengfei Ning Xinyu Niu Mengying Han Chuze Gao Xingwei Feng Han Cai Te Li Fangtao Li Huifang Li Daoqing Gong Weitao Song Long Liu Juan Pu Jinhua Liu Jacqueline Smith Honglei Sun Yinhua Huang |
| author_sort | Jiaxiang Hu |
| collection | DOAJ |
| description | Abstract Background The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A virus (IAV), harbors almost all subtypes of IAVs and resists to many IAVs which cause extreme virulence in chicken and human. However, the response of duck’s adaptive immune system to IAV infection is poorly characterized due to lack of a detailed gene map of the major histocompatibility complex (MHC). Results We herein reported a chromosome-scale Beijing duck assembly by integrating Nanopore, Bionano, and Hi-C data. This new reference genome SKLA1.0 covers 40 chromosomes, improves the contig N50 of the previous duck assembly with highest contiguity (ZJU1.0) of more than a 5.79-fold, surpasses the chicken and zebra finch references in sequence contiguity and contains a complete genomic map of the MHC. Our 3D MHC genomic map demonstrated that gene family arrangement in this region was primordial; however, families such as AnplMHCI, AnplMHCIIβ, AnplDMB, NKRL (NK cell receptor-like genes) and BTN underwent gene expansion events making this area complex. These gene families are distributed in two TADs and genes sharing the same TAD may work in a co-regulated model. Conclusions These observations supported the hypothesis that duck’s adaptive immunity had been optimized with expanded and diversified key immune genes which might help duck to combat influenza virus. This work provided a high-quality Beijing duck genome for biological research and shed light on new strategies for AIV control. |
| first_indexed | 2024-03-07T14:41:10Z |
| format | Article |
| id | doaj.art-c8e8aa6d2c5b4be6bd94320ee2d2bd22 |
| institution | Directory Open Access Journal |
| issn | 1741-7007 |
| language | English |
| last_indexed | 2024-03-07T14:41:10Z |
| publishDate | 2024-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Biology |
| spelling | doaj.art-c8e8aa6d2c5b4be6bd94320ee2d2bd222024-03-05T20:22:02ZengBMCBMC Biology1741-70072024-02-0122112010.1186/s12915-024-01817-0A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene familiesJiaxiang Hu0Linfei Song1Mengfei Ning2Xinyu Niu3Mengying Han4Chuze Gao5Xingwei Feng6Han Cai7Te Li8Fangtao Li9Huifang Li10Daoqing Gong11Weitao Song12Long Liu13Juan Pu14Jinhua Liu15Jacqueline Smith16Honglei Sun17Yinhua Huang18State Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural UniversityState Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural UniversityState Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural UniversityState Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural UniversityState Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural UniversityState Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural UniversityState Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural UniversityState Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural UniversityState Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural UniversityKey Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural UniversityJiangsu Institute of Poultry ScienceCollege of Animal Science and Technology, Yangzhou UniversityJiangsu Institute of Poultry ScienceCollege of Animal Science and Technology, Yangzhou UniversityKey Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural UniversityKey Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural UniversityThe Roslin Institute and Royal (Dick) School of Veterinary Studies, University of EdinburghKey Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural UniversityState Key Laboratory of Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural UniversityAbstract Background The duck (Anas platyrhynchos) is one of the principal natural hosts of influenza A virus (IAV), harbors almost all subtypes of IAVs and resists to many IAVs which cause extreme virulence in chicken and human. However, the response of duck’s adaptive immune system to IAV infection is poorly characterized due to lack of a detailed gene map of the major histocompatibility complex (MHC). Results We herein reported a chromosome-scale Beijing duck assembly by integrating Nanopore, Bionano, and Hi-C data. This new reference genome SKLA1.0 covers 40 chromosomes, improves the contig N50 of the previous duck assembly with highest contiguity (ZJU1.0) of more than a 5.79-fold, surpasses the chicken and zebra finch references in sequence contiguity and contains a complete genomic map of the MHC. Our 3D MHC genomic map demonstrated that gene family arrangement in this region was primordial; however, families such as AnplMHCI, AnplMHCIIβ, AnplDMB, NKRL (NK cell receptor-like genes) and BTN underwent gene expansion events making this area complex. These gene families are distributed in two TADs and genes sharing the same TAD may work in a co-regulated model. Conclusions These observations supported the hypothesis that duck’s adaptive immunity had been optimized with expanded and diversified key immune genes which might help duck to combat influenza virus. This work provided a high-quality Beijing duck genome for biological research and shed light on new strategies for AIV control.https://doi.org/10.1186/s12915-024-01817-0DuckInfluenza resistanceChromosome-scale genomeAdaptive immunityMHC gene map |
| spellingShingle | Jiaxiang Hu Linfei Song Mengfei Ning Xinyu Niu Mengying Han Chuze Gao Xingwei Feng Han Cai Te Li Fangtao Li Huifang Li Daoqing Gong Weitao Song Long Liu Juan Pu Jinhua Liu Jacqueline Smith Honglei Sun Yinhua Huang A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families BMC Biology Duck Influenza resistance Chromosome-scale genome Adaptive immunity MHC gene map |
| title | A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families |
| title_full | A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families |
| title_fullStr | A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families |
| title_full_unstemmed | A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families |
| title_short | A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families |
| title_sort | new chromosome scale duck genome shows a major histocompatibility complex with several expanded multigene families |
| topic | Duck Influenza resistance Chromosome-scale genome Adaptive immunity MHC gene map |
| url | https://doi.org/10.1186/s12915-024-01817-0 |
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