The pangenome of the flooded gum, Eucalyptus grandis

Eucalyptus grandis serves as a model for understanding woody plant biology. We produced high-quality, de novo phased assemblies for 24 diverse E. grandis genotypes resulting in 48 haplotype-resolved assemblies (average 553.4 Mbp) and annotations (average 39,581 genes, BUSCO completeness >98.50%). We report a pangenome that catalogues structural variants (SVs) and pangene families in these individuals. The pangene catalogue has 123,938 pangene families (19,961 core, 1,730 softcore, 65,165 shell and 37,082 private gene families). Comparison to the phased reference (V4.2, TAG0014_HAP1) revealed 37,561 non-redundant SVs and 128,487 non-redundant non-aligned regions across the haplotype-resolved assemblies. Focusing on lignin biosynthesis, we show that while the pathway is highly conserved at the pangenome level, key enzymatic modules such as 4CL, CCR, CAD, and COMT exhibit substantial CNV and orthogroup diversification, revealing hidden functional plasticity within an otherwise core metabolic pathway. This resource provides a critical foundation for exploring functional biology and deciphering genome evolution.