Haplotype-resolved telomere-to-telomere genome assembly of the hybrid Eucalyptus urophylla × E. grandis

The hybrid Eucalyptus urophylla × E. grandis integrates strong stress tolerance with rapid growth traits, holding significant value for genetic improvement and industrial application. However, its highly heterozygous and complex genome has hindered the development of high-quality reference assemblies. Here, we report the first haplotype-resolved, gap-free telomere-to-telomere (T2T) genome assembly of E. urophylla × E. grandis, using a combination of Illumina, PacBio HiFi, Oxford Nanopore, and Hi-C sequencing technologies. The two haplotype assemblies span 528.93 Mb and 563.25 Mb, with scaffold N50 values of 50.21 Mb and 55.05 Mb, respectively, and were successfully anchored to 11 pseudochromosomes, including the precise determination of 11 centromeres and 22 telomeres. Quality assessment demonstrated exceptional completeness and accuracy, with both assemblies achieving over 98.3% BUSCO completeness and base-level consensus quality values (QV) exceeding 50. Gene annotation predicted 33,924 and 36,336 protein-coding genes for the respective haplotypes, with functional annotation rates above 97%. This high-quality, haplotype-resolved T2T genome represents a foundational genomic resource for the Eucalyptus genus.