Building a cattle pan-genome using more de novo assemblies

Mian Gong; Peng Yang; Wenwen Fang; Ran Li; Yu Jiang

doi:10.1016/j.jgg.2022.01.003

Volume 49 Issue 9

Sep. 2022

Turn off MathJax

Article Contents

Article Navigation > Journal of Genetics and Genomics > 2022 > 49(9): 906-908

PDF( 695 KB)

Building a cattle pan-genome using more de novo assemblies

doi: 10.1016/j.jgg.2022.01.003

Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China

Funds:

This project was supported by grants from the National Natural Science Foundation of China (31822052) to Y.J. and the National Natural Science Foundation of China (31802027) to R.L. We thank High-Performance Computing (HPC) of Northwest A&F University (NWAFU) for providing computing resources.

Received Date: 2021-10-01
Accepted Date: 2022-01-17
Rev Recd Date: 2022-01-14
Publish Date: 2022-01-31

Abstract

FullText(HTML)

References(14)

References

Chen, N., Cai, Y., Chen, Q., Li, R., Wang, K., Huang, Y., Hu, S., Huang, S., Zhang, H., Zheng, Z., et al., 2018. Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia. Nature communications 9, 2337.

Crysnanto, D., Leonard, A.S., Fang, Z.H.,Pausch, H., 2021. Novel functional sequences uncovered through a bovine multiassembly graph. Proceedings of the National Academy of Sciences of the United States of America 118.

Crysnanto, D.,Pausch, H., 2020. Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discovery. Genome Biol 21, 184.

Crysnanto, D., Wurmser, C.,Pausch, H., 2019. Accurate sequence variant genotyping in cattle using variation-aware genome graphs. Genet Sel Evol 51, 21.

Li, H., Feng, X.,Chu, C., 2020. The design and construction of reference pangenome graphs with minigraph. Genome Biology 21, 265.

Li, Q., Tian, S., Yan, B., Liu, C.M., Lam, T.-W., Li, R.,Luo, R., 2021. Building a Chinese pan-genome of 486 individuals. Communications Biology 4, 1016.

Li, R., Fu, W., Su, R., Tian, X., Du, D., Zhao, Y., Zheng, Z., Chen, Q., Gao, S., Cai, Y., et al., 2019a. Towards the Complete Goat Pan-Genome by Recovering Missing Genomic Segments From the Reference Genome. Frontiers in Genetics 10, 1169.

Li, R., Li, Y., Zheng, H., Luo, R., Zhu, H., Li, Q., Qian, W., Ren, Y., Tian, G., Li, J., et al., 2010. Building the sequence map of the human pan-genome. Nature Biotechnology 28, 57-63.

Li, R., Tian, X., Yang, P., Fan, Y., Li, M., Zheng, H., Wang, X.,Jiang, Y., 2019b. Recovery of non-reference sequences missing from the human reference genome. BMC Genomics 20, 746.

Nicolas, L.-P., Ghislain, D., Narayanan, K., Sukanta, M., Rong, P.M., Pierre, C.,Fortier, M.A., 2011. The Multidrug Resistance-Associated Protein 4(MRP4) Appears as a Functional Carrier of Prostaglandins Regulated by Oxytocin in the Bovine Endometrium. Endocrinology, 4993-5004.

Sherman, R.M., Forman, J., Antonescu, V., Puiu, D., Daya, M., Rafaels, N., Boorgula, M.P., Chavan, S., Vergara, C., Ortega, V.E., et al., 2019. Assembly of a pan-genome from deep sequencing of 910 humans of African descent. Nature genetics 51, 30-35.

Tian, X., Li, R., Fu, W., Li, Y., Wang, X., Li, M., Du, D., Tang, Q., Cai, Y., Long, Y., et al., 2020. Building a sequence map of the pig pan-genome from multiple de novo assemblies and Hi-C data. Science China Life sciences 63, 750-763.

Verdugo, M.P., Mullin, V.E., Scheu, A., Mattiangeli, V., Daly, K.G., Maisano Delser, P., Hare, A.J., Burger, J., Collins, M.J., Kehati, R., et al., 2019. Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent. Science (New York, NY)365, 173-176.

Wu, D.D., Ding, X.D., Wang, S., Wojcik, J.M., Zhang, Y., Tokarska, M., Li, Y., Wang, M.S., Faruque, O., Nielsen, R., et al., 2018. Pervasive introgression facilitated domestication and adaptation in the Bos species complex. Nature Ecology and Evolution 2, 1139-1145

Relative Articles

Supplements(0)

Cited By

Proportional views