Abstract: Accurate genomic information is essential for advancing genetic breeding research in specific rice varieties. This study presents a gapless genome assembly of indica rice cultivar ZhongHui 8015 (ZH8015) using PacBio HiFi, Hi-C, and ONT (Oxford Nanopore Technologies) ultra-long sequencing technologies, annotating 43 037 gene structures. Subsequently, utilizing this genome along with transcriptomic and metabolomic techniques, we explored the response of ZH8015 to brown planthopper (BPH) infestation. Continuous transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH feeding. Enrichment analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall formation. Metabolomic results demonstrated marked increases in levels of several monosaccharides as cell wall components and dramatic changes in flavonoid contents. Omics association analysis identified differentially expressed genes associated with key metabolites, shedding light on ZH8015’s response to BPH infestation. In summary, our study constructed a reliable genome sequence resource for ZH8015, and the preliminary multi-omics results will guide future insect-resistant breeding research.

Key words: rice, genome assembly, gapless genome, multi-omics, brown planthopper