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A Graph-based Goat Pangenome Reveals Structural Variations Involved in Domestication and Adaptation
Peipei Bian1, Jiaxin Li1, Shishuo Zhou1
1Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
We created a goat pangenome and structural variation database to understand genome complexity. This resource identified novel genetic variations linked to goat domestication, immunity, and adaptation.
Area of Science:
- Genomics
- Animal Genetics
- Evolutionary Biology
Background:
- Understanding genome complexity is crucial for species evolution.
- Goat pangenomes offer insights into genetic diversity and adaptation.
Purpose of the Study:
- To construct a comprehensive goat pangenome and structural variation database.
- To identify genetic variations associated with goat domestication and adaptation.
Main Methods:
- De novo phased long-read assemblies of eight goat breeds.
- Construction of a graph-based pangenome and a long-read structural variation database.
- Graph-based genotyping and selection signal analysis.
Main Results:
- Discovery of 113-Mb novel autosomal sequences in goats.
- Identification of 59,325 deletions, 84,910 insertions, and 24,954 complex SV alleles.
- Detection of a novel immune-related domestication locus (galectin-9 and LGALS9L) and SVs linked to cashmere production and high-altitude adaptation.
Conclusions:
- The goat pangenome and SV database are valuable resources for studying complex genomic variations.
- Structural variations play a significant role in goat evolution, domestication, and adaptation.
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