Telomere-to-telomere, gap-free genome assembly of the Chinese holly, Ilex cornuta

The Chinese holly ( Ilex cornuta Lindl. & Paxton), a prominent ornamental species in the Aquifoliaceae family, is valued for its aesthetic appeal, medicinal properties, and robust stress tolerance. Despite its potential for breeding and functional studies, the lack of a high-quality reference genome has constrained genetic dissection of its key traits. We present the first telomere-to-telomere (T2T) gap-free genome assembly for I. cornuta , achieved through the integration of PacBio long reads, ONT ultra-long reads, and Hi-C data. The final assembly, totaling ~ 890.50 Mb with a scaffold N50 of 44.26 Mb, was organized into 20 gap-free chromosomes. We identified 40 telomeres and 20 putative centromere regions. Crucially, both our T2T genome assembly and independent root‑tip karyotype analysis definitively establish the basic chromosome number of I. cornuta as 20 (2n = 2x = 40), settling a long-standing controversy. The genome annotation yielded 35,437 protein-coding genes, demonstrating high completeness (98.33% BUSCO) and accuracy (QV of 48.97). Comparative genomics uncovered two whole-genome duplication events and lineage-specific gene family expansions, particularly those involved in secondary metabolism, which represent candidate gene sets that could potentially contribute to environmental adaptability; further transcriptomic or functional assays will be required to verify their biological roles. This first gap-free T2T reference genome for the genus Ilex not only provides a crucial resource for understanding the genomic architecture and evolutionary history of hollies but also serves as a powerful foundation for molecular breeding and genetic improvement of I. cornuta and its relatives.