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Peer-reviewedCC BY 4.0PeerJ

Pan-genome insights into the evolutionary dynamics and functional diversification of genes in monkeypox virus

  • Yan Liu1
  • Yinggen Tang1
  • Yunhai Xu2
  • Xizi Long1
  • Zhaozhong Zhu1,3
  1. 1School of Public Health, University of South China, Hengyang, China
  2. 2Hunan Provincial Key Laboratory for Geochemical Processes and Resource Environmental Effects, Changsha, China
  3. 3Hunan Provincial Key Laboratory of Medical Virology, Bioinformatics Center, College of Biology, Hunan University, Changsha, China
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Abstract

Monkeypox virus (MPXV) continues to emerge as a global health threat. While genetically diverse, its genomic structure and evolution remain undercharacterized. This study analyzed 157 non-redundant MPXV genomes (subtypes Ia, Ib, IIa, IIb), identifying 183 core and 222 non-core genes via pan-genome analysis—indicative of an open pan-genome. Over half (55.8%) of MPXV genes show gene number variation. Non-core genes exhibit a higher ratio of insertions/deletions compared to core genes. Additionally, selection pressure analysis indicated that non-core genes are more prone to positive selection. Furthermore, interaction analysis revealed that core viral proteins target immune-related human pathways, while non-core proteins engage with viral infection-associated proteins. These results deepen our understanding of MPXV evolution and inform future research directions.

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Cite

BibTeXRIS
BibTeX
@article{liu2026pangenome,
  title = {{Pan-genome insights into the evolutionary dynamics and functional diversification of genes in monkeypox virus}},
  author = {Yan Liu and Yinggen Tang and Yunhai Xu and Xizi Long and Zhaozhong Zhu},
  journal = {PeerJ},
  year = {2026},
  month = oct,
  doi = {10.7717/peerj.21846},
  url = {https://peerj.com/articles/21846},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Pan-genome insights into the evolutionary dynamics and functional diversification of genes in monkeypox virus
AU  - Yan Liu
AU  - Yinggen Tang
AU  - Yunhai Xu
AU  - Xizi Long
AU  - Zhaozhong Zhu
PY  - 2026
DA  - 2026/10/26
JO  - PeerJ
DO  - 10.7717/peerj.21846
UR  - https://peerj.com/articles/21846
AB  - Monkeypox virus (MPXV) continues to emerge as a global health threat. While genetically diverse, its genomic structure and evolution remain undercharacterized. This study analyzed 157 non-redundant MPXV genomes (subtypes Ia, Ib, IIa, IIb), identifying 183 core and 222 non-core genes via pan-genome analysis—indicative of an open pan-genome. Over half (55.8%) of MPXV genes show gene number variation. Non-core genes exhibit a higher ratio of insertions/deletions compared to core genes. Additionally, selection pressure analysis indicated that non-core genes are more prone to positive selection. Furthermore, interaction analysis revealed that core viral proteins target immune-related human pathways, while non-core proteins engage with viral infection-associated proteins. These results deepen our understanding of MPXV evolution and inform future research directions.
SN  - 2167-8359
ER  -