Gapless Complete Genome and Multi-Omics Illuminate Immune Adaptation and Host-Virus Interactions in a Coronavirus Reservoir.
5 affiliations
- 1Jiangxi Provincial Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang, China.
- 2State Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- 3University of Chinese Academy of Sciences, Beijing, China.
- 4School of Karst Science, Guizhou Normal University, Guiyang, China.
- 5State Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
Abstract
Bats are major reservoirs of emerging viruses, including severe acute respiratory syndrome-related coronaviruses, yet they exhibit remarkable tolerance to viral infections with limited clinical manifestations-a longstanding immunological paradox. Here, we generate a telomere-to-telomere (T2T) de novo genome assembly for Rhinolophus sinicus (R. sinicus), designated T2T-RSC1.0 (2.14 Gb), comprising 17 fully anchored autosomes and both sex chromosomes. This gapless assembly resolves 129.19 Mb of previously unresolved regions (PURs) and enables annotation of 848 previously unannotated genes, including 131 protein-coding genes and five pseudogenes on the 33.75 Mb Y chromosome. Using 2.12 × 10⁵ newly identified single-nucleotide polymorphisms within PURs, population genomic analyses resolve three major genetic groups and provide improved resolution of genome-wide population structure. Comparative analyses further reveal population-level associations between major histocompatibility complex polymorphism and viral diversity. Multi-omics and functional analyses reveal a coordinated evolutionary remodeling of antiviral defense, antigen presentation, cytokine signaling, and inflammatory regulation in horseshoe bats. This study provides an unparalleled genomic resource for R. sinicus and establishes an integrated framework for investigating immune evolution, long-term host-virus coexistence, and mammalian adaptive evolution.
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BibTeX
@article{wang2026gapless,
title = {{Gapless Complete Genome and Multi-Omics Illuminate Immune Adaptation and Host-Virus Interactions in a Coronavirus Reservoir.}},
author = {Yuting Wang and Sheng Zhang and Linxia Ouyang and Xin Du and Xin Huang and Zhilin Wang and Huixian Xie and Jiale Tang and Liyi Lou and Wenqing Ling and Weihao Wang and Jiang Zhou and Zhen Liu and Yibo Hu and Fuwen Wei and Guangping Huang},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
year = {2026},
month = oct,
doi = {10.1002/advs.78422},
url = {https://europepmc.org/article/MED/42949635},
note = {CC BY},
}
RIS
TY - JOUR
TI - Gapless Complete Genome and Multi-Omics Illuminate Immune Adaptation and Host-Virus Interactions in a Coronavirus Reservoir.
AU - Yuting Wang
AU - Sheng Zhang
AU - Linxia Ouyang
AU - Xin Du
AU - Xin Huang
AU - Zhilin Wang
AU - Huixian Xie
AU - Jiale Tang
AU - Liyi Lou
AU - Wenqing Ling
AU - Weihao Wang
AU - Jiang Zhou
AU - Zhen Liu
AU - Yibo Hu
AU - Fuwen Wei
AU - Guangping Huang
PY - 2026
DA - 2026/10/28
JO - Advanced science (Weinheim, Baden-Wurttemberg, Germany)
DO - 10.1002/advs.78422
UR - https://europepmc.org/article/MED/42949635
AB - Bats are major reservoirs of emerging viruses, including severe acute respiratory syndrome-related coronaviruses, yet they exhibit remarkable tolerance to viral infections with limited clinical manifestations-a longstanding immunological paradox. Here, we generate a telomere-to-telomere (T2T) de novo genome assembly for Rhinolophus sinicus (R. sinicus), designated T2T-RSC1.0 (2.14 Gb), comprising 17 fully anchored autosomes and both sex chromosomes. This gapless assembly resolves 129.19 Mb of previously unresolved regions (PURs) and enables annotation of 848 previously unannotated genes, including 131 protein-coding genes and five pseudogenes on the 33.75 Mb Y chromosome. Using 2.12 × 10⁵ newly identified single-nucleotide polymorphisms within PURs, population genomic analyses resolve three major genetic groups and provide improved resolution of genome-wide population structure. Comparative analyses further reveal population-level associations between major histocompatibility complex polymorphism and viral diversity. Multi-omics and functional analyses reveal a coordinated evolutionary remodeling of antiviral defense, antigen presentation, cytokine signaling, and inflammatory regulation in horseshoe bats. This study provides an unparalleled genomic resource for R. sinicus and establishes an integrated framework for investigating immune evolution, long-term host-virus coexistence, and mammalian adaptive evolution.
SN - 2198-3844
ER -