The case for bovine pangenome

Keywords

bovine / genome assembly / genomics / pangenome

References

[1] Miga, K. H., & Wang, T. (2021). The need for a human pangenome reference sequence. Annual Review of Genomics and Human Genetics, 22(1), 81–102.

[2] Smith, T. P., Bickhart, D. M., Boichard, D., Chamberlain, A. J., Djikeng, A., Jiang, Y., Low, W. Y., Pausch, H., Demyda-Peyrás, S., Prendergast, J., Schnabel, R. D., & Rosen, B. D. (2023). The bovine pangenome Consortium: Democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species. Genome Biology, 24(1), 139.

[3] Dai, X., Bian, P., Hu, D., Luo, F., Huang, Y., Jiao, S., Wang, X., Gong, M., Li, R., Cai, Y., Wen, J., Yang, Q., Deng, W., Nanaei, H. A., Wang, Y., Wang, F., Zhang, Z., Rosen, B. D., Heller, R., & Jiang, Y. (2023). A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species. Genome Research, 33(8), 1284–1298.

[4] Aganezov, S., Yan, S. M., Soto, D. C., Kirsche, M., Zarate, S., Avdeyev, P., Taylor, D. J., Shafin, K., Shumate, A., Xiao, C., Wagner, J., McDaniel, J., Olson, N. D., Sauria, M. E. G., Vollger, M. R., Rhie, A., Meredith, M., Martin, S., Lee, J., … Schatz, M. C. (2022). A complete reference genome improves analysis of human genetic variation. Science, 376(6588), eabl3533.

[5] Low, W. Y., Tearle, R., Liu, R., Koren, S., Rhie, A., Bickhart, D. M., Rosen, B. D., Kronenberg, Z. N., Kingan, S. B., Tseng, E., Thibaud-Nissen, F., Martin, F. J., Billis, K., Ghurye, J., Hastie, A. R., Lee, J., Pang, A. W. C., Heaton, M. P., Phillippy, A. M., … Williams, J. L. (2020). Haplotype-resolved genomes provide insights into structural variation and gene content in Angus and Brahman cattle. Nature Communications, 11(1), 2071.

[6] Wulfridge, P., Langmead, B., Feinberg, A. P., & Hansen, K. D. (2019). Analyzing whole genome bisulfite sequencing data from highly divergent genotypes. Nucleic Acids Research, 47(19), e117.

[7] Low, W. Y., Tearle, R., Bickhart, D. M., Rosen, B. D., Kingan, S. B., Swale, T., Thibaud-Nissen, F., Murphy, T. D., Young, R., Lefevre, L., Hume, D. A., Collins, A., Ajmone-Marsan, P., Smith, T. P. L., & Williams, J. L. (2019). Chromosome-level assembly of the water buffalo genome surpasses human and goat genomes in sequence contiguity. Nature Communications, 10(1), 260.

[8] Garrison, E., Sirén, J., Novak, A. M., Hickey, G., Eizenga, J. M., Dawson, E. T., Jones, W., Garg, S., Markello, C., Lin, M. F., Paten, B., & Durbin, R. (2018). Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nature Biotechnology, 36(9), 875–879.

[9] Zhou, Y., Yang, L., Han, X., Han, J., Hu, Y., Li, F., Xia, H., Peng, L., Boschiero, C., Rosen, B. D., Bickhart, D. M., Zhang, S., Guo, A., Van Tassell, C. P., Smith, T. P., & Liu, G. E. (2022). Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history. Genome Research, 32(8), 1585–1601.

[10] Armstrong, J., Hickey, G., Diekhans, M., Fiddes, I. T., Novak, A. M., Deran, A., Fang, Q., Xie, D., Feng, S., Stiller, J., Genereux, D., Johnson, J., Marinescu, V. D., Alföldi, J., Harris, R. S., Lindblad-Toh, K., Haussler, D., Karlsson, E., Jarvis, E. D., … Paten, B. (2020). Progressive Cactus is a multiple-genome aligner for the thousand-genome era. Nature, 587(7833), 246–251.

[11] Li, H., Feng, X., & Chu, C. (2020). The design and construction of reference pangenome graphs with minigraph. Genome Biology, 21(1), 265.

[12] Leonard, A. S., Crysnanto, D., Fang, Z.-H., Heaton, M. P., Vander Ley, B. L., Herrera, C., Bollwein, H., Bickhart, D. M., Kuhn, K. L., Smith, T. P., Rosen, B. D., & Pausch, H. (2022). Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies. Nature Communications, 13(1), 3012.

[13] Liao, W.-W., Asri, M., Ebler, J., Doerr, D., Haukness, M., Hickey, G., Lu, S., Lucas, J. K., Monlong, J., Abel, H. J., Buonaiuto, S., Chang, X. H., Cheng, H., Chu, J., Colonna, V., Eizenga, J. M., Feng, X., Fischer, C., Fulton, R. S., … Paten, B. (2023). A draft human pangenome reference. Nature, 617(7960), 312–324.

[14] Pineda, P. S., Flores, E. B., Herrera, J. R. V., & Low, W. Y. (2021). Opportunities and challenges for improving the productivity of swamp buffaloes in Southeastern Asia. Frontiers in Genetics, 12, 629861.

[15] Low, W. Y., Rosen, B. D., Ren, Y., Bickhart, D. M., To, T.-H., Martin, F. J., Billis, K., Sonstegard, T. S., Sullivan, S. T., Hiendleder, S., Williams, J. L., Heaton, M. P., & Smith, T. P. L. (2022). Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle. BMC Genomics, 23(1), 344.

[16] Dutta, P., Talenti, A., Young, R., Jayaraman, S., Callaby, R., Jadhav, S. K., Dhanikachalam, V., Manikandan, M., Biswa, B. B., Low, W. Y., Williams, J. L., Cook, E., Toye, P., Wall, E., Djikeng, A., Marshall, K., Archibald, A. L., Gokhale, S., Kumar, S., … Prendergast, J. G. D. (2020). Whole genome analysis of water buffalo and global cattle breeds highlights convergent signatures of domestication. Nature Communications, 11(1), 4739.

[17] Pineda, P. S., Flores, E. B., Villamor, L. P., Parac, C. J. M., Khatkar, M. S., Thu, H. T., Smith, T. P. L., Rosen, B. D., Ajmone-Marsan, P., Colli, L., Williams, J. L., Low, W. Y., Low, L., Khatkar, M., Chen, T., Nguyen, H. T. H., Tonhati, H., de Camargo, G. M. F., … Thinh, N. H. (2024). Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project. GigaScience, 13.

RIGHTS & PERMISSIONS

2024 The Author(s). Animal Research and One Health published by John Wiley & Sons Australia, Ltd on behalf of Institute of Animal Science, Chinese Academy of Agricultural Sciences.