A Graph-based Goat Pangenome Reveals Structural Variations Involved in Domestication and Adaptation
Pangenomes can facilitate a deeper understanding of genome complexity. Using de novo phased long-read assemblies of eight representative goat breeds, we constructed a graph-based pangenome of goats (Capra hircus) and discovered 113-Mb autosomal novel sequences. Combining this multi-assembly pangenome with low-coverage PacBio HiFi sequences, we constructed a long-read structural variations (SVs) database containing 59,325 SV deletions, 84,910 SV insertions, and 24,954 other complex SV alleles. This resource allowed reliable graph-based genotyping from short reads of 79 wild and 1,148 worldwide domestic goats. Selection signal analysis of SV captured a novel immune-related domestication locus containing the galectin-9 gene and extra copies of the ruminant-specific galectin-9-like genes (LGALS9L), which have high tissue specificity. A segmental duplication in domestic goats generates three additional LGALS9L copies. Ancient goat genome sequences show a gradual increase in frequency of this duplication from the Neolithic to the present. Two other newly detected SVs also have higher selection signals than adjacent SNPs, a truncated-LINE1 deletion in EDAR2 associated with cashmere production and a VNTR-related insertion in PAPSS2 linked to high-altitude adaptation. In summary, the multi-assembly goat pangenome and long-read SV database facilitates detecting complex variations that are important in evolution and selection.
Authors
- Johannes Arjen Lenstra (ORCID: https://orcid.org/0000-0003-1745-7739)
- Qimeng Yang (ORCID: https://orcid.org/0000-0002-9830-2466)
- Xihong Wang (ORCID: https://orcid.org/0000-0002-8277-969X)
- Joram M. Mwacharo (ORCID: https://orcid.org/0000-0001-6981-8140)
- Shuhong Huang (ORCID: https://orcid.org/0000-0003-2302-4200)
- Gang Ren (ORCID: https://orcid.org/0000-0001-9690-5995)
- Ali Mujtaba Shah (ORCID: https://orcid.org/0000-0003-3698-6775)
- Mian Gong (ORCID: https://orcid.org/0000-0002-1785-0621)
- Peipei Bian (ORCID: https://orcid.org/0000-0002-3948-4052)
- Cong Li (ORCID: https://orcid.org/0000-0001-5514-9580)
- Jiaxin Li (ORCID: https://orcid.org/0000-0001-7228-2877)
- Rongrong Li (ORCID: https://orcid.org/0000-0001-9717-6931)
- Ran Li (ORCID: https://orcid.org/0000-0002-8584-4100)
- Xi Guo
- Yudong Cai (ORCID: https://orcid.org/0000-0001-5902-0901)
- Xiaolong Wang (ORCID: https://orcid.org/0000-0003-1620-1344)
- Shilong Wang (ORCID: https://orcid.org/0000-0001-6086-0481)
- Wenxin Zheng (ORCID: https://orcid.org/0000-0002-5199-0847)
- Shuai Zhou (ORCID: https://orcid.org/0009-0006-6325-6355)
- Funong Luo
- Jiaqi Fu (ORCID: https://orcid.org/0009-0008-7625-2251)
Institutions
- Roslin Institute (GB)
- International Center for Agricultural Research in the Dry Areas (LB)
- Utrecht University (NL)
- Scotland's Rural College (GB)
- Xinjiang Academy of Animal Science (CN)
- Chinese Academy of Agricultural Sciences (CN)
- Northwest A&F University (CN)
Publication Details
- Journal
- Molecular Biology and Evolution
- Published
- 2024-12-01
- DOI
- https://doi.org/10.1093/molbev/msae251
- Citations
- 17
- Primary Topic
- Galectins and Cancer Biology
- Type
- article
- Field-Weighted Citation Impact
- 4.09
Funders
- National Science Foundation
- National Natural Science Foundation of China
- National Key Research and Development Program of China