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

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.