De novo genome assembly depicts the immune genomic characteristics of cattle

Ting-Ting Li, Tian Xia, Jia-Qi Wu, Hao Hong, Zhao-Lin Sun, Ming Wang, Fang-Rong Ding, Jing Wang, Shuai Jiang, Jin Li, Jie Pan, Guang Yang, Jian-Nan Feng, Yun-Ping Dai, Xue-Min Zhang, Tao Zhou () and Tao Li ()
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Ting-Ting Li: National Center of Biomedical Analysis
Tian Xia: National Center of Biomedical Analysis
Jia-Qi Wu: National Center of Biomedical Analysis
Hao Hong: National Center of Biomedical Analysis
Zhao-Lin Sun: Beijing Institute of Pharmacology and Toxicology
Ming Wang: China Agricultural University
Fang-Rong Ding: China Agricultural University
Jing Wang: Beijing Institute of Pharmacology and Toxicology
Shuai Jiang: National Center of Biomedical Analysis
Jin Li: National Center of Biomedical Analysis
Jie Pan: National Center of Biomedical Analysis
Guang Yang: Beijing Institute of Pharmacology and Toxicology
Jian-Nan Feng: Beijing Institute of Pharmacology and Toxicology
Yun-Ping Dai: China Agricultural University
Xue-Min Zhang: National Center of Biomedical Analysis
Tao Zhou: National Center of Biomedical Analysis
Tao Li: National Center of Biomedical Analysis

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: Abstract Immunogenomic loci remain poorly understood because of their genetic complexity and size. Here, we report the de novo assembly of a cattle genome and provide a detailed annotation of the immunogenomic loci. The assembled genome contains 143 contigs (N50 ~ 74.0 Mb). In contrast to the current reference genome (ARS-UCD1.2), 156 gaps are closed and 467 scaffolds are located in our assembly. Importantly, the immunogenomic regions, including three immunoglobulin (IG) loci, four T-cell receptor (TR) loci, and the major histocompatibility complex (MHC) locus, are seamlessly assembled and precisely annotated. With the characterization of 258 IG genes and 657 TR genes distributed across seven genomic loci, we present a detailed depiction of immune gene diversity in cattle. Moreover, the MHC gene structures are integrally revealed with properly phased haplotypes. Together, our work describes a more complete cattle genome, and provides a comprehensive view of its complex immune-genome.

Date: 2023
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DOI: 10.1038/s41467-023-42161-1

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