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A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species

文献类型： 外文期刊

作者： Dai, Xuelei 1 ; Bian, Peipei 1 ; Hu, Dexiang 1 ; Luo, Funong 1 ; Huang, Yongzhen 1 ; Jiao, Shaohua 1 ; Wang, Xihong 1 ; Gong, Mian 1 ; Li, Ran 1 ; Cai, Yudong 1 ; Wen, Jiayue 1 ; Yang, Qimeng 1 ; Deng, Weidong 2 ; Nanaei, Hojjat Asadollahpour 1 ; Wang, Yu 1 ; Wang, Fei 1 ; Zhang, Zijing 4 ; Rosen, Benjamin D. 5 ; Heller, Rasmus 6 ; Jiang, Yu 1 ;

作者机构： 1.Northwest A&F Univ, Coll Anim Sci & Technol, Key Lab Anim Genet Breeding & Reprod Shaanxi Prov, Yangling 712100, Shaanxi, Peoples R China

2.Yunnan Agr Univ, Fac Anim Sci & Technol, Kunming 650201, Peoples R China

3.ACECR, Avicenna Res Inst, Reprod Biotechnol Res Ctr, Tehran 1983969412, Iran

4.Henan Acad Agr Sci, Inst Anim Husb & Vet Sci, Zhengzhou 450002, Peoples R China

5.USDA ARS, Anim Genom & Improvement Lab, Beltsville, MD 20705 USA

6.Univ Copenhagen, Dept Biol, DK-2200 Copenhagen, Denmark

7.Northwest A&F Univ, Key Lab Livestock Biol, Yangling 712100, Shaanxi, Peoples R China

期刊名称：GENOME RESEARCH （ 影响因子：7.0； 五年影响因子：11.8 ）

ISSN： 1088-9051

年卷期： 2023 年 33 卷 8 期

页码：

收录情况： SCI

摘要： 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 similar to 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.

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