A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species
- Xuelei Dai1,8,
- Peipei Bian1,8,
- Dexiang Hu1,8,
- Funong Luo1,8,
- Yongzhen Huang1,8,
- Shaohua Jiao1,
- Xihong Wang1,
- Mian Gong1,
- Ran Li1,
- Yudong Cai1,
- Jiayue Wen1,
- Qimeng Yang1,
- Weidong Deng2,
- Hojjat Asadollahpour Nanaei1,3,
- Yu Wang1,
- Fei Wang1,
- Zijing Zhang4,
- Benjamin D. Rosen5,
- Rasmus Heller6 and
- Yu Jiang1,7
- 1Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- 2Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China;
- 3Reproductive Biotechnology Research Center, Avicenna Research Institute, ACECR, Tehran 1983969412, Iran;
- 4Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China;
- 5Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705, USA;
- 6Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark;
- 7Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
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↵8 These authors contributed equally to this work.
Abstract
Chinese indicine cattle harbor a much higher genetic diversity compared with other domestic cattle, but their genome architecture remains uninvestigated. Using PacBio HiFi sequencing data from 10 Chinese indicine cattle across southern China, we assembled 20 high-quality partially phased genomes and integrated them into a multiassembly graph containing 148.5 Mb (5.6%) of novel sequence. We identified 156,009 high-confidence nonredundant structural variants (SVs) and 206 SV hotspots spanning ∼195 Mb of gene-rich sequence. We detected 34,249 archaic introgressed fragments in Chinese indicine cattle covering 1.93 Gb (73.3%) of the genome. We inferred an average of 3.8%, 3.2%, 1.4%, and 0.5% of introgressed sequence originating, respectively, from banteng-like, kouprey-like, gayal-like, and gaur-like Bos species, as well as 0.6% of unknown origin. Introgression from multiple donors might have contributed to the genetic diversity of Chinese indicine cattle. Altogether, this study highlights the contribution of interspecies introgression to the genomic architecture of an important livestock population and shows how exotic genomic elements can contribute to the genetic variation available for selection.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.277481.122.
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Freely available online through the Genome Research Open Access option.
- Received November 8, 2022.
- Accepted June 30, 2023.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
