The White-Spotted Bamboo Shark Genome Reveals Chromosome Rearrangements and Fast-Evolving Immune Genes of Cartilaginous Fish

Yaolei Zhang; Haoyang Gao; Hanbo Li; Jiao Guo; Bingjie Ouyang; Meiniang Wang; Qiwu Xu; Jiahao Wang; Meiqi Lv; Xinyu Guo; Qun Liu; Likun Wei; Han Ren; Yang Xi; Yang Guo; Bingzhao Ren; Shanshan Pan; Chuxin Liu; Xiaoyan Ding; Haitao Xiang; Yingjia Yu; Yue Song; Lingfeng Meng; Shanshan Liu; Jun Wang; Yuan Jiang; Jiahai Shi; Shiping Liu; Jamal S M Sabir; Mumdooh J Sabir; Muhummadh Khan; Nahid H Hajrah; Simon Ming-Yuen Lee; Xun Xu; Huanming Yang; Jian Wang; Guangyi Fan; Naibo Yang; Xin Liu

doi:10.1016/j.isci.2020.101754

The White-Spotted Bamboo Shark Genome Reveals Chromosome Rearrangements and Fast-Evolving Immune Genes of Cartilaginous Fish

iScience. 2020 Nov 2;23(11):101754. doi: 10.1016/j.isci.2020.101754. eCollection 2020 Nov 20.

Authors

Yaolei Zhang^{1

2

3}, Haoyang Gao^{1

2}, Hanbo Li^{1

2}, Jiao Guo^{1

2}, Bingjie Ouyang^{1

2}, Meiniang Wang^{4

2}, Qiwu Xu^{1

2}, Jiahao Wang^{1

2}, Meiqi Lv^{1

2}, Xinyu Guo^{1

2}, Qun Liu^{1

2}, Likun Wei⁵, Han Ren^{4

2}, Yang Xi^{4

2}, Yang Guo^{1

2}, Bingzhao Ren^{1

2}, Shanshan Pan^{1

2}, Chuxin Liu^{4

2}, Xiaoyan Ding^{1

2}, Haitao Xiang^{4

2}, Yingjia Yu^{1

2}, Yue Song^{1

2}, Lingfeng Meng^{1

2}, Shanshan Liu^{1

2}, Jun Wang^{1

2}, Yuan Jiang^{4

6}, Jiahai Shi⁵, Shiping Liu^{4

2}, Jamal S M Sabir⁷, Mumdooh J Sabir⁷, Muhummadh Khan⁷, Nahid H Hajrah⁷, Simon Ming-Yuen Lee⁸, Xun Xu^{4

2}, Huanming Yang^{4

9}, Jian Wang^{4

9}, Guangyi Fan^{1

8

2}, Naibo Yang^{4

6}, Xin Liu^{1

4

2}

Affiliations

¹ BGI-Qingdao, BGI-Shenzhen, Qingdao 266555, China.
² China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China.
³ Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Lyngby, Denmark.
⁴ BGI-Shenzhen, Shenzhen 518083, China.
⁵ City University of Hongkong, Kowloon, Hongkong SAR.
⁶ Complete Genomics, Inc., San Jose, CA 95134, USA.
⁷ Department of Biological Sciences, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia.
⁸ State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China.
⁹ James D. Watson Institute of Genome Sciences, Hangzhou 310058, China.

Abstract

Chondrichthyan (cartilaginous fish) occupies a key phylogenetic position and is important for investigating evolutionary processes of vertebrates. However, limited whole genomes impede our in-depth knowledge of important issues such as chromosome evolution and immunity. Here, we report the chromosome-level genome of white-spotted bamboo shark. Combing it with other shark genomes, we reconstructed 16 ancestral chromosomes of bamboo shark and illustrate a dynamic chromosome rearrangement process. We found that genes on 13 fast-evolving chromosomes can be enriched in immune-related pathways. And two chromosomes contain important genes that can be used to develop single-chain antibodies, which were shown to have high affinity to human disease markers by using enzyme-linked immunosorbent assay. We also found three bone formation-related genes were lost due to chromosome rearrangements. Our study highlights the importance of chromosome rearrangements, providing resources for understanding of cartilaginous fish diversification and potential application of single-chain antibodies.

Keywords: Biological Sciences; Evolutionary Biology; Genetics; Genomics; Phylogenetics.