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African suid genomes provide insights into the local adaptation to diverse African environments

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Title African suid genomes provide insights into the local adaptation to diverse African environments
 
Creator Hai-Bing Xie
Chen Yan
Adeola, A.C.
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
Okeyoyin, A.O.
Oluwole, O.O.
Omotosho, O.
Okoro, V.M.O.
Omitogun, O.G.
Dawuda, P.M.
Olaogun, S.C.
Nneji, L.M.
Ayoola, A.O.
Sanke, O.J.
Luka, P.D.
Okoth, Edward A.
Lekolool, I.
Mijele, D.
Bishop, Richard P.
Jianlin Han
Wen Wang
Min-Sheng Peng
Ya-Ping Zhang
 
Subject suidae
swine
pig breeds
genomes
african swine fever
genetics
molecular biology
 
Description 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.
 
Date 2022-12-05
2022-11-28T10:40:58Z
2022-11-28T10:40:58Z
 
Type Journal Article
 
Identifier Xie, H.-B., Yan, C., Adeola, A.C., Wang, K., Huang, C.-P., Xu, M.-M., Qiu, Q., Yin, X., Fan, C.-Y., Ma, Y.-F., Yin, T.-T., Gao, Y., Deng, J.-K., Okeyoyin, A.O., Oluwole, O.O., Omotosho, O., Okoro, V.M.O., Omitogun, O.G., Dawuda, P.M., Olaogun, S.C., Nneji, L.M., Ayoola, A.O., Sanke, O.J., Luka, P.D., Okoth, E., Lekolool, I., Mijele, D., Bishop, R.P., Han, J., Wang, W., Peng, M.-S. and Zhang, Y.-P. 2022. African suid genomes provide insights into the local adaptation to diverse African environments. Molecular Biology and Evolution 39(12): msac256.
0737-4038
https://hdl.handle.net/10568/125687
https://doi.org/10.1093/molbev/msac256
 
Language en
 
Rights CC-BY-NC-4.0
Open Access
 
Format msac256
 
Publisher Oxford University Press
 
Source Molecular Biology and Evolution