Long-read sequencing and de novo assembly of the cynomolgus macaque genome

Bing Bai; Yi Wang; Ran Zhu; Yaolei Zhang; Hong Wang; Guangyi Fan; Xin Liu; Hong Shi; Yuyu Niu; Weizhi Ji

doi:10.1016/j.jgg.2021.12.013

Volume 49 Issue 10

Oct. 2022

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Article Navigation > Journal of Genetics and Genomics > 2022 > 49(10): 975-978

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Long-read sequencing and de novo assembly of the cynomolgus macaque genome

doi: 10.1016/j.jgg.2021.12.013

Bing Bai^1,2,
Yi Wang^1,2,
Ran Zhu^1,2,
Yaolei Zhang^3,4,
Hong Wang^5,6,
Guangyi Fan^7,8,9,
Xin Liu^7,8,9,
Hong Shi^10,11,
Yuyu Niu^12,13,14,
Weizhi Ji^15,16

1. State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China;
2. Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China;
3. BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China;
4. Translational Immunology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark;
5. State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnnan 650500, China;
6. Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China;
7. BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China;
8. BGI-Shenzhen, Shenzhen, Guangdong 518083, China;
9. China National GeneBank, BGI-Shenzhen, Shenzhen, Guangdong 518120, China;
10. State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China;
11. Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China;
12. State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China;
13. Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China;
14. Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China;
15. State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China;
16. Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China

Funds:

This research was supported by the Natural Science Foundation of Yunnan Province (202001BC070001, 202102AA100053), the National Natural Science Foundation of China General Program (No. 32070580). We also thank Newton O. Otecko for proof reading.

Received Date: 2021-11-24
Accepted Date: 2021-12-29
Rev Recd Date: 2021-12-24
Publish Date: 2022-01-17

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References

Benson, G., 1999. Tandem repeats finder:a program to analyze DNA sequences. Nucleic Acids Res. 27, 573-580

Chen, Y., Yu, J., Niu, Y., Qin, D., Liu, H., Li, G., Hu, Y., Wang, J., Lu, Y., Kang, Y., et al., 2017. Modeling rett syndrome using TALEN-Edited MECP2 mutant cynomolgus monkeys. Cell 169, 945-955

Chin, C.S., Peluso, P., Sedlazeck, F.J., Nattestad, M., Concepcion, G.T., Clum, A., Dunn, C., O'Malley, R., Figueroa-Balderas, R., Morales-Cruz, A., et al. 2016. Phased diploid genome assembly with single-molecule real-time sequencing. Nat Methods 13, 1050-1054

Gschwind, A.R., Singh, A., Certa, U., Reymond, A., Heckel, T., 2017. Diversity and regulatory impact of copy number variation in the primate Macaca fascicularis. BMC Genomics 18, 144

Guo, X., Li, X.J., 2015. Targeted genome editing in primate embryos. Cell Res. 25, 767-768

He, Y., Luo, X., Zhou, B., Hu, T., Meng, X., Audano, P.A., Kronenberg, Z.N., Eichler, E.E., Jin, J., Guo, Y., et al., 2019. Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants. Nat. Commun. 10, 4233

Hsu, P.D., Scott, D.A., Weinstein, J.A., Ran, F.A., Konermann, S., Agarwala, V., Li, Y., Fine, E.J., Wu, X., Shalem, O., et al., 2013. DNA targeting specificity of RNA-guided Cas9 nucleases. Nat. Biotechnol. 31, 827-832

Iwasaki, K., Uno, Y., Utoh, M., Yamazaki, H., 2019. Importance of cynomolgus monkeys in development of monoclonal antibody drugs. Drug Metab. Pharmacokinet. 34, 55-63

Kumar, S., Hedges, S.B., 1998. A molecular timescale for vertebrate evolution. Nature 392, 917-920

Li, L., Stoeckert, C.J., Jr., Roos, D.S., 2003. OrthoMCL:identification of ortholog groups for eukaryotic genomes. Genome Res. 13, 2178-2189

Luo, X., He, Y., Zhang, C., He, X., Yan, L., Li, M., Hu, T., Hu, Y., Jiang, J., Meng, X., et al., 2019. Trio deep-sequencing does not reveal unexpected off-target and on-target mutations in Cas9-edited rhesus monkeys. Nat. Commun. 10, 5525

Ma, Y., Li, J., Wang, G., Ke, Q., Qiu, S., Gao, L., Wan, H., Zhou, Y., Xiang, A.P., Huang, Q., et al., 2016. Efficient production of cynomolgus monkeys with a toolbox of enhanced assisted reproductive technologies. Sci. Rep. 6, 25888

Sharp, A.J., Cheng, Z., Eichler, E.E., 2006. Structural variation of the human genome. Annu. Rev. Genomics Hum. Genet. 7, 407-442

Shiina, T., Blancher, A., 2019. The cynomolgus macaque MHC polymorphism in experimental medicine. Cells 8

Tan, T., Wu, J., Si, C., Dai, S., Zhang, Y., Sun, N., Zhang, E., Shao, H., Si, W., Yang, P., et al., 2021. Chimeric contribution of human extended pluripotent stem cells to monkey embryos ex vivo. Cell 184, 2020-2032 e2014

Tarailo-Graovac, M., Chen, N., 2009. Using RepeatMasker to identify repetitive elements in genomic sequences. Curr. Protoc. Bioinformatics Chapter 4, Unit 4 10

Verdier, J.M., Acquatella, I., Lautier, C., Devau, G., Trouche, S., Lasbleiz, C., Mestre-Frances, N., 2015. Lessons from the analysis of nonhuman primates for understanding human aging and neurodegenerative diseases. Front Neurosci. 9, 64

Walker, B.J., Abeel, T., Shea, T., Priest, M., Abouelliel, A., Sakthikumar, S., Cuomo, C.A., Zeng, Q., Wortman, J., Young, S.K., Earl, A.M., 2014. Pilon:an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 9, e112963

Wang, F., Zhang, W., Yang, Q., Kang, Y., Fan, Y., Wei, J., Liu, Z., Dai, S., Li, H., Li, Z., et al. 2020. Generation of a Hutchinson-Gilford progeria syndrome monkey model by base editing. Protein Cell 11, 809-824

Yan, G., Zhang, G., Fang, X., Zhang, Y., Li, C., Ling, F., Cooper, D.N., Li, Q., Li, Y., van Gool, A.J., et al., 2011. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat. Biotechnol. 29, 1019-1023

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