A new chromosome-scale duck genome shows a major histocompatibility complex with several expanded multigene families

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

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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.

Original languageEnglish
Article number31
Pages (from-to)1-20
Number of pages20
JournalBMC Biology
Issue number1
Early online date5 Feb 2024
Publication statusPublished - 5 Feb 2024

Keywords / Materials (for Non-textual outputs)

  • Animals
  • Humans
  • Ducks/genetics
  • Genome
  • Major Histocompatibility Complex/genetics
  • Chromosomes/genetics
  • Multigene Family


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