WheatPanRef: a unified linear pan-reference genome for wheat genomics

Niu, J.; Zhao, P.; Du, W.; Zhang, X.; He, H.; Appels, R.; Zhao, J.; Ma, S.; Chen, T.; Haberer, G.; Spannagl, M.; Cao, Z.; Zhang, Y.; Miao, L.; Chen, S.; Zhang, B.; Wu, W.; Wang, L.; Li, G.; Wu, J.; Wang, Z.; Chen, Y.; Jiao, C.; Pozniak, C. J.; Krattinger, S. G.; Choulet, F.; Ling, H.; Jia, J.; Wang, D.; Yan, W.; Hu, Z.; Xin, M.; Peng, H.; Ni, Z.; Grewal, S.; Alaux, M.; Varshney, R. K.; Guo, W.; Deng, X. W.; Sun, Q.

doi:10.64898/2026.11.04.764148

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bioRxiv · 10.64898/2026.11.04.764148

WheatPanRef: a unified linear pan-reference genome for wheat genomics

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Abstract

Linear reference genomes provide coordinates for read mapping, variant discovery and multi-omics data integration, yet assembly-specific coordinate systems limit data reuse, particularly in the large, repetitive and polyploid wheat genome. Here, we present WheatPanRef, a scalable linear pan-reference and coordinate framework that integrates wheat sequence diversity within a stable coordinate system. We reconciled independent Chinese Spring assemblies by resolving structural and sequences discrepancies to constructed a 14.50-Gb consensus sequences CS-NP. Using CS-NP as backbone, we incorporated 4.37 Gb of non-redundant non-CS sequences from 37 diverse wheat accessions, generating WheatPanRef (18.87 Gb). WheatPanRef improves read-alignment performance and captures putative wild-relative introgressions and sequences absent or unanchored in conventional references. Bidirectional coordinate-translation system enables accurate projection between WheatPanRef and individual assemblies without remapping, facilitating genomic resource integration and reuse. WheatPanRef provides a common sequence and coordinate foundation for population-scale wheat genomics, with potential utility for genomic resource integration in other complex crops.

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Niu, J., Zhao, P., Du, W., Zhang, X., He, H., Appels, R., Zhao, J., Ma, S., Chen, T., Haberer, G., Spannagl, M., Cao, Z., Zhang, Y., Miao, L., Chen, S., Zhang, B., Wu, W., Wang, L., Li, G., Wu, J., Wang, Z., Chen, Y., Jiao, C., Pozniak, C. J., Krattinger, S. G., Choulet, F., Ling, H., Jia, J., Wang, D., Yan, W., Hu, Z., Xin, M., Peng, H., Ni, Z., Grewal, S., Alaux, M., Varshney, R. K., Guo, W., Deng, X. W., Sun, Q.. 2026-11-05. WheatPanRef: a unified linear pan-reference genome for wheat genomics. https://doi.org/10.64898/2026.11.04.764148

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