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Pig pangenome graph reveals functional features of non‑reference sequences

Journal of Animal Science and Biotechnology 2024年第3期15卷 956-970页

作者： Jian Miao Xingyu Wei Caiyun Cao Jiabao Sun Yuejin Xu Zhe Zhang Qishan Wang Yuchun Pan Zhen Wang College of Animal Sciences Zhejiang UniversityHangzhou 310058ZhejiangChina Yazhou Bay Science and Technology City Hainan Institute of Zhejiang UniversityYazhou DistrictBuilding 11Yongyou Industrial ParkSanya 572025HainanChina

Background The reliance on a solitary linear reference genome has imposed a significant constraint on our compre-hensive understanding of genetic variation in *** constraint is particularly pronounced for non-reference sequences(NRSs),which have not been extensively *** In this study,we constructed a pig pangenome graph using 21 pig assemblies and identified 23,831 NRSs with a total length of 105 *** findings revealed that NRSs were more prevalent in breeds exhibiting greater genetic divergence from the reference ***,we observed that NRSs were rarely found within coding sequences,while NRS insertions were enriched in immune-related Gene Ontology ***,our investigation also unveiled a close association between novel genes and the immune capacity of *** observed substantial differences in terms of frequencies of NRSs between Eastern and Western pigs,and the heat-resistant pigs exhibited a substantial number of NRS insertions in an 11.6 Mb interval on chromosome ***,we discovered a 665 bp insertion in the fourth intron of the TNFRSF19 gene that may be associated with the ability of heat tolerance in South-ern Chinese *** Our findings demonstrate the potential of a graph genome approach to reveal important functional features of NRSs in pig populations.

关键词： Heat tolerance Immune ability non-reference sequences Pig pangenome

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