Pangenome analyses reveal divergence and extensive introgression in two global corn pests
11 affiliations
- 1Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- 2Yazhouwan National Laboratory, Sanya, 572025 China
- 3State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, Peking University, Beijing, 100871 China
- 4Guangxi Key Laboratory of Agro-Environment and Agric-Products Safety, College of Agriculture, Guangxi University, Nanning, Guangxi 530004 People’s Republic of China
- 5State Key Laboratory of Genome and Multi-Omics Technologies, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- 6Department of Entomology, Max-Planck Institute for Chemical Ecology, Jena, 07745 Germany
- 7Department of Biology, Tufts University, Medford, MA 02155 USA
- 8Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871 China
- 9Institute of Ecology, Peking University, Beijing, 100871 China
- 10Institute for Tibetan Plateau Research, Peking University, Beijing, 100871 China
- 11Medog Biodiversity Observation and Research Station of Xizang Autonomous Region, Nyingchi, 860711 China
Abstract
Background: Introgression between closely related species can profoundly influence evolutionary trajectories, yet how genomic divergence interacts with introgression, especially in invasive hybridization, remains insufficiently understood. Structural variants (SVs), particularly chromosomal inversions, are key contributors to divergence and may modulate patterns of gene flow. The Asian corn borer (ACB) and European corn borer (ECB), two globally important agricultural pests, provide an excellent system to investigate these processes.
Results: We construct a graph-based pangenome from 23 high-quality genome assemblies to characterize genome-wide SVs and introgression between ACB and ECB. We identify over 216,000 SVs, most of which are associated with transposable elements and contribute to interspecific divergence. Population genomic analyses reveal widespread yet asymmetric introgression, predominantly from ACB into ECB populations in China. Introgressed regions are more prevalent in autosomes than in sex chromosomes and are enriched for genes involved in adaptive pathways. In contrast, large inversion regions on the Z chromosome exhibit strong genetic differentiation and reduced introgression, suggesting a role in maintaining species barriers. Notably, a highly divergent region containing the circadian clock gene period (per) shows signatures of selection. Functional validation using CRISPR/Cas9 demonstrates that per significantly influences diapause regulation, linking genomic divergence to adaptive phenotypic variation.
Conclusions: Our results demonstrate that introgression and structural variation jointly shape genomic divergence in these species. While introgression facilitates the spread of adaptive variation, chromosomal inversions restrict gene flow and maintain species integrity. This study provides new insights into the evolutionary mechanisms underlying divergence, adaptation, and invasion in major agricultural pests.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s13059-026-04216-6.
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BibTeX
@article{peng2026pangenome,
title = {{Pangenome analyses reveal divergence and extensive introgression in two global corn pests}},
author = {Yan Peng and Yubo Zhang and Kaikai Mao and Zhuting Zhang and Lei Zhang and Jingyun Zhu and Xinye Liu and Chongjun Zhao and Wenmin Fan and Alexander Yesaya and Hongru Wang and David G. Heckel and Erik B. Dopman and Wei Zhang and Yutao Xiao},
journal = {Genome Biology},
year = {2026},
month = aug,
doi = {10.1186/s13059-026-04216-6},
url = {https://doi.org/10.1186/s13059-026-04216-6},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Pangenome analyses reveal divergence and extensive introgression in two global corn pests
AU - Yan Peng
AU - Yubo Zhang
AU - Kaikai Mao
AU - Zhuting Zhang
AU - Lei Zhang
AU - Jingyun Zhu
AU - Xinye Liu
AU - Chongjun Zhao
AU - Wenmin Fan
AU - Alexander Yesaya
AU - Hongru Wang
AU - David G. Heckel
AU - Erik B. Dopman
AU - Wei Zhang
AU - Yutao Xiao
PY - 2026
DA - 2026/08/07
JO - Genome Biology
DO - 10.1186/s13059-026-04216-6
UR - https://doi.org/10.1186/s13059-026-04216-6
AB - Background: Introgression between closely related species can profoundly influence evolutionary trajectories, yet how genomic divergence interacts with introgression, especially in invasive hybridization, remains insufficiently understood. Structural variants (SVs), particularly chromosomal inversions, are key contributors to divergence and may modulate patterns of gene flow. The Asian corn borer (ACB) and European corn borer (ECB), two globally important agricultural pests, provide an excellent system to investigate these processes. Results: We construct a graph-based pangenome from 23 high-quality genome assemblies to characterize genome-wide SVs and introgression between ACB and ECB. We identify over 216,000 SVs, most of which are associated with transposable elements and contribute to interspecific divergence. Population genomic analyses reveal widespread yet asymmetric introgression, predominantly from ACB into ECB populations in China. Introgressed regions are more prevalent in autosomes than in sex chromosomes and are enriched for genes involved in adaptive pathways. In contrast, large inversion regions on the Z chromosome exhibit strong genetic differentiation and reduced introgression, suggesting a role in maintaining species barriers. Notably, a highly divergent region containing the circadian clock gene period (per) shows signatures of selection. Functional validation using CRISPR/Cas9 demonstrates that per significantly influences diapause regulation, linking genomic divergence to adaptive phenotypic variation. Conclusions: Our results demonstrate that introgression and structural variation jointly shape genomic divergence in these species. While introgression facilitates the spread of adaptive variation, chromosomal inversions restrict gene flow and maintain species integrity. This study provides new insights into the evolutionary mechanisms underlying divergence, adaptation, and invasion in major agricultural pests. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s13059-026-04216-6.
SN - 1474-7596
SN - 1474-760X
ER -