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

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 XiangYingjia 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^*

^*Corresponding author for this work

Department of Biomedical Sciences

Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

38 Citations (Scopus)

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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.

Original language	English
Article number	101754
Journal	iScience
Volume	23
Issue number	11
Online published	2 Nov 2020
DOIs	https://doi.org/10.1016/j.isci.2020.101754
Publication status	Published - 20 Nov 2020

Bibliographical note

Full text of this publication does not contain sufficient affiliation information. With consent from the author(s) concerned, the Research Unit(s) information for this record is based on the existing academic department affiliation of the author(s).

Research Keywords

Biological Sciences
Evolutionary Biology
Genetics
Genomics
Phylogenetics

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This is an open access article under the CC BY-NC-ND license.

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Zhang, Y., Gao, H., Li, H., Guo, J., Ouyang, B., Wang, M., Xu, Q., Wang, J., Lv, M., Guo, X., Liu, Q., Wei, L., Ren, H., Xi, Y., Guo, Y., Ren, B., Pan, S., Liu, C., Ding, X., ... Liu, X. (2020). The White-Spotted Bamboo Shark Genome Reveals Chromosome Rearrangements and Fast-Evolving Immune Genes of Cartilaginous Fish. iScience, 23(11), Article 101754. https://doi.org/10.1016/j.isci.2020.101754

@article{75964ff8fa684fe3a28b591fee02b737,

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

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",

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

note = "Full text of this publication does not contain sufficient affiliation information. With consent from the author(s) concerned, the Research Unit(s) information for this record is based on the existing academic department affiliation of the author(s).",

year = "2020",

month = nov,

day = "20",

doi = "10.1016/j.isci.2020.101754",

language = "English",

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Zhang, Y, Gao, H, Li, H, Guo, J, Ouyang, B, Wang, M, Xu, Q, Wang, J, Lv, M, Guo, X, Liu, Q, Wei, L, Ren, H, Xi, Y, Guo, Y, Ren, B, Pan, S, Liu, C, Ding, X, Xiang, H, Yu, Y, Song, Y, Meng, L, Liu, S, Wang, J, Jiang, Y, Shi, J, Liu, S, Sabir, JSM, Sabir, MJ, Khan, M, Hajrah, NH, Ming-Yuen Lee, S, Xu, X, Yang, H, Wang, J, Fan, G, Yang, N & Liu, X 2020, 'The White-Spotted Bamboo Shark Genome Reveals Chromosome Rearrangements and Fast-Evolving Immune Genes of Cartilaginous Fish', iScience, vol. 23, no. 11, 101754. https://doi.org/10.1016/j.isci.2020.101754

TY - JOUR

T1 - The White-Spotted Bamboo Shark Genome Reveals Chromosome Rearrangements and Fast-Evolving Immune Genes of Cartilaginous Fish

AU - Zhang, Yaolei

AU - Gao, Haoyang

AU - Li, Hanbo

AU - Guo, Jiao

AU - Ouyang, Bingjie

AU - Wang, Meiniang

AU - Xu, Qiwu

AU - Wang, Jiahao

AU - Lv, Meiqi

AU - Guo, Xinyu

AU - Liu, Qun

AU - Wei, Likun

AU - Ren, Han

AU - Xi, Yang

AU - Guo, Yang

AU - Ren, Bingzhao

AU - Pan, Shanshan

AU - Liu, Chuxin

AU - Ding, Xiaoyan

AU - Xiang, Haitao

AU - Yu, Yingjia

AU - Song, Yue

AU - Meng, Lingfeng

AU - Liu, Shanshan

AU - Wang, Jun

AU - Jiang, Yuan

AU - Shi, Jiahai

AU - Liu, Shiping

AU - Sabir, Jamal S.M.

AU - Sabir, Mumdooh J.

AU - Khan, Muhummadh

AU - Hajrah, Nahid H.

AU - Ming-Yuen Lee, Simon

AU - Xu, Xun

AU - Yang, Huanming

AU - Wang, Jian

AU - Fan, Guangyi

AU - Yang, Naibo

AU - Liu, Xin

N1 - Full text of this publication does not contain sufficient affiliation information. With consent from the author(s) concerned, the Research Unit(s) information for this record is based on the existing academic department affiliation of the author(s).

PY - 2020/11/20

Y1 - 2020/11/20

N2 - 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.

AB - 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.

KW - Biological Sciences

KW - Evolutionary Biology

KW - Genetics

KW - Genomics

KW - Phylogenetics

UR - http://www.scopus.com/inward/record.url?scp=85097428624&partnerID=8YFLogxK

UR - https://www.scopus.com/record/pubmetrics.uri?eid=2-s2.0-85097428624&origin=recordpage

U2 - 10.1016/j.isci.2020.101754

DO - 10.1016/j.isci.2020.101754

M3 - RGC 21 - Publication in refereed journal

C2 - 33251490

SN - 2589-0042

VL - 23

JO - iScience

JF - iScience

IS - 11

M1 - 101754

ER -

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

Abstract

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