TY  - JOUR
A1  - Dai, Xuelei
A1  - Bian, Peipei
A1  - Hu, Dexiang
A1  - Luo, Funong
A1  - Huang, Yongzhen
A1  - Jiao, Shaohua
A1  - Wang, Xihong
A1  - Gong, Mian
A1  - Li, Ran
A1  - Cai, Yudong
A1  - Wen, Jiayue
A1  - Yang, Qimeng
A1  - Deng, Weidong
A1  - Nanaei, Hojjat Asadollahpour
A1  - Wang, Yu
A1  - Wang, Fei
A1  - Zhang, Zijing
A1  - Rosen, Benjamin D.
A1  - Heller, Rasmus
A1  - Jiang, Yu
T1  - A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species
Y1  - 2023/08/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1284 
EP  - 1298 
DO  - 10.1101/gr.277481.122 
VL  - 33 
IS  - 8 
UR  - http://genome.cshlp.org/content/33/8/1284.abstract 
N2  - 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. 
ER  -