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

WheatPanRef provides an 18.87-Gb linear pan-reference and coordinate framework for wheat, integrating CS-NP and 37 accessions to improve alignment and enable coordinate translation.

• Why it matters: Assembly-specific coordinate systems hinder reuse of wheat genomics data across studies, especially in the large, repetitive, polyploid genome. A stable coordinate foundation is needed for consistent mapping and multi-omics integration.
• What they did: The team reconciled independent Chinese Spring assemblies into a 14.50-Gb CS-NP consensus, then added 4.37 Gb of non-redundant non-CS sequence from 37 diverse accessions to build WheatPanRef. They also implemented bidirectional coordinate translation between WheatPanRef and individual assemblies.
• The result: WheatPanRef improves read-alignment performance and captures putative wild-relative introgressions plus sequences missing or unanchored in conventional references. The translation system supports accurate projection without remapping, facilitating population-scale integration and reuse.

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