A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species
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A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species. / Dai, Xuelei; Bian, Peipei; Hu, Dexiang; Luo, Funong; Huang, Yongzhen; Jiao, Shaohua; Wang, Xihong; Gong, Mian; Li, Ran; Cai, Yudong; Wen, Jiayue; Yang, Qimeng; Deng, Weidong; Nanaei, Hojjat Asadollahpour; Wang, Yu; Wang, Fei; Zhang, Zijing; Rosen, Benjamin D.; Heller, Rasmus; Jiang, Yu.
I: Genome Research, Bind 33, Nr. 8, 08.2023, s. 1284-1298.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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T1 - A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species
AU - Dai, Xuelei
AU - Bian, Peipei
AU - Hu, Dexiang
AU - Luo, Funong
AU - Huang, Yongzhen
AU - Jiao, Shaohua
AU - Wang, Xihong
AU - Gong, Mian
AU - Li, Ran
AU - Cai, Yudong
AU - Wen, Jiayue
AU - Yang, Qimeng
AU - Deng, Weidong
AU - Nanaei, Hojjat Asadollahpour
AU - Wang, Yu
AU - Wang, Fei
AU - Zhang, Zijing
AU - Rosen, Benjamin D.
AU - Heller, Rasmus
AU - Jiang, Yu
N1 - Publisher Copyright: © 2023 Dai et al.
PY - 2023/8
Y1 - 2023/8
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.
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.
U2 - 10.1101/gr.277481.122
DO - 10.1101/gr.277481.122
M3 - Journal article
C2 - 37714713
AN - SCOPUS:85173559002
VL - 33
SP - 1284
EP - 1298
JO - Genome Research
JF - Genome Research
SN - 1088-9051
IS - 8
ER -
ID: 370586270