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Molecular biology and evolution
Dec 05, 2022;39 (12):

African Suid Genomes Provide Insights into the Local Adaptation to Diverse African Environments.

Hai-Bing Xie, Chen Yan, Adeniyi C Adeola, Kun Wang, Cui-Ping Huang, Ming-Min Xu, Qiang Qiu, Xue Yin, Chen-Yu Fan, Yun-Fei Ma, Ting-Ting Yin, Yun Gao, Jia-Kun Deng, Agboola O Okeyoyin, Olufunke O Oluwole, Oladipo Omotosho, Victor M O Okoro, Ofelia G Omitogun, Philip M Dawuda, Sunday C Olaogun, Lotanna M Nneji, Adeola O Ayoola, Oscar J Sanke, Pam D Luka, Edward Okoth, Isaac Lekolool, Dominic Mijele, Richard P Bishop, Jianlin Han, Wen Wang, Min-Sheng Peng, Ya-Ping Zhang
Author Information
  1. Hai-Bing Xie: State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China.
  2. Chen Yan: State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China.
  3. Adeniyi C Adeola: State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China.
  4. Kun Wang: School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China. ORCID
  5. Cui-Ping Huang: State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China.
  6. Ming-Min Xu: State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China.
  7. Qiang Qiu: School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China.
  8. Xue Yin: State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China.
  9. Chen-Yu Fan: State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming 650091, China.
  10. Yun-Fei Ma: State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China.
  11. Ting-Ting Yin: State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China.
  12. Yun Gao: State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China.
  13. Jia-Kun Deng: State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China.
  14. Agboola O Okeyoyin: National Park Service Headquarter, Federal Capital Territory, Abuja 900108, Nigeria.
  15. Olufunke O Oluwole: Institute of Agricultural Research and Training, Obafemi Awolowo University, Ibadan, Nigeria.
  16. Oladipo Omotosho: Department of Veterinary Medicine, University of Ibadan, Ibadan 200005, Nigeria.
  17. Victor M O Okoro: Department of Animal Science and Technology, School of Agriculture and Agricultural Technology, Federal University of Technology, Owerri 460114, Nigeria. ORCID
  18. Ofelia G Omitogun: Department of Animal Sciences, Obafemi Awolowo University, Ile-Ife 220282, Nigeria.
  19. Philip M Dawuda: Department of Veterinary Surgery and Theriogenology, College of Veterinary Medicine, University of Agriculture Makurdi, Makurdi 970001, Nigeria.
  20. Sunday C Olaogun: Department of Veterinary Medicine, University of Ibadan, Ibadan 200005, Nigeria.
  21. Lotanna M Nneji: State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China.
  22. Adeola O Ayoola: State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China.
  23. Oscar J Sanke: Taraba State Ministry of Agriculture and Natural Resources, Jalingo 660213, Nigeria.
  24. Pam D Luka: National Veterinary Research Institute, Vom 930103, Nigeria.
  25. Edward Okoth: International Livestock Research Institute (ILRI), Nairobi 00100, Kenya.
  26. Isaac Lekolool: Kenya Wildlife Services, Nairobi 00100, Kenya.
  27. Dominic Mijele: Kenya Wildlife Services, Nairobi 00100, Kenya.
  28. Richard P Bishop: International Livestock Research Institute (ILRI), Nairobi 00100, Kenya.
  29. Jianlin Han: International Livestock Research Institute (ILRI), Nairobi 00100, Kenya.
  30. Wen Wang: State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China.
  31. Min-Sheng Peng: State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China.
  32. Ya-Ping Zhang: State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China. ORCID
PMID: 36413509 DOI: 10.1093/molbev/msac256

Abstract

African wild suids consist of several endemic species that represent ancient members of the family Suidae and have colonized diverse habitats on the African continent. However, limited genomic resources for African wild suids hinder our understanding of their evolution and genetic diversity. In this study, we assembled high-quality genomes of a common warthog (Phacochoerus africanus), a red river hog (Potamochoerus porcus), as well as an East Asian Diannan small-ear pig (Sus scrofa). Phylogenetic analysis showed that common warthog and red river hog diverged from their common ancestor around the Miocene/Pliocene boundary, putatively predating their entry into Africa. We detected species-specific selective signals associated with sensory perception and interferon signaling pathways in common warthog and red river hog, respectively, which contributed to their local adaptation to savannah and tropical rainforest environments, respectively. The structural variation and evolving signals in genes involved in T-cell immunity, viral infection, and lymphoid development were identified in their ancestral lineage. Our results provide new insights into the evolutionary histories and divergent genetic adaptations of African suids.

Keywords

African suids common warthog genome local adaptation pig red river hog

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MeSH Term

Animals
Swine
Phylogeny
Species Specificity
Adaptation, Physiological
Africa
Journal Article

Links to CNCB-NGDC Resources

BioProject: PRJCA002378 (The African Suidae genome architectures shed light on the evolution of natural reservoirs of African swine fever virus)
GSA: CRA002456 (The African Suidae genome architectures shed light on the evolution of natural reservoirs of African swine fever virus)
GSA: CRA005799 (The African Suidae genomes)
GSA: CRA011461 (Resequenced genome of Diannan small-ear pig)
GWH: GWHACDT00000000 (Sus scrofa domesticus)
GWH: GWHACEZ00000000 (Phacochoerus africanus)
GWH: GWHACFA00000000 (Potamochoerus porcus)

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