Abstract
The yellow stem borer Scirpophaga incertulas is the dominant pest of rice in tropical Asia. However, the lack of genomic resources makes it difficult to understand their invasiveness and ecological adaptation. A high-quality chromosome-level genome of S. incertulas, a monophagous rice pest, was assembled by combining Illumina short reads, PacBio HiFi long sequencing, and Hi-C scaffolding technology. The final genome size was 695.65 Mb, with a scaffold N50 of 28.02 Mb, and 93.50% of the assembled sequences were anchored to 22 chromosomes. BUSCO analysis demonstrated that this genome assembly had a high level of completeness, with 97.65% gene coverage. A total of 14,850 protein-coding genes and 366.98 Mb of transposable elements were identified. In addition, comparative genomic analyses indicated that chemosensory processes and detoxification capacity may play critical roles in the specialized host preference of S. incertulas. In summary, the chromosome-level genome assembly of S. incertulas provides a valuable genetic resource for understanding the biological characteristics of its invasiveness and developing an efficient management strategy.