RT Journal
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
JF Genome Research 
JO Genome Research 
YR 2023 
FD August 01 
VO 33 
IS 8 
SP 1284 
OP 1298 
DO 10.1101/gr.277481.122 
UL http://genome.cshlp.org/content/33/8/1284.abstract 
AB 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.