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The immunogenomic landscape of cattle

By Tingting Li, Tian Xia, Jiaqi Wu, Hao Hong, Zhaolin Sun, Ming Wang, Fangrong Ding, Jing Wang, Shuai Jiang, Jin Li, Jie Pan, Guang Yang, Jiannan Feng, Yunping Dai, Xuemin Zhang, Tao Zhou, Tao Li

Posted 01 Jun 2022
bioRxiv DOI: 10.1101/2022.05.31.493931

Here, we report the de novo assembly of a cattle genome using ultra-long-read nanopore sequencing in conjunction with other advanced technologies. The assembled genome contains only 145 contigs (N50 ~ 74.0 Mb). Compare to the current reference cattle genome ARS-UCD1.2, 154 gaps are closed, and 467 scaffolds are further placed in our assembly. Importantly, except two remained gaps in the T-cell receptor /{delta}(TRA/TRD) region, the gene loci of other TRs and immunoglobulins (IGs) are seamlessly assembled and exquisitely annotated. With the characterization of 258 IG genes and 626 TR genes that distributed in seven genomic loci, we illustrate the highest immune gene diversity in mammals to our knowledge. Moreover, the gene structures of major histocompatibility complex (MHC) are integrally depicted with properly phased haplotypes. Thus, our work not only reports a cattle genome with the most continuity and completeness, but also provide a comprehensive view of the complex immune-genome.

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