Deep Insight into the genome of a major rice pest, Scripophaga incertulas

The yellow stem borer, Scripophaga incertulas (Crambidae, Lepidoptera), is a highly destructive pest damaging rice crops. Here, we combined Illumina, PacBio sequencing and Hi-C scaffolding to generate a high-quality chromosome-level genome assembly of S. incertulas. We initially obtained an 839.78 Mb assembly with scoffold N50 of 1.13 Mb. Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis demonstrated that this genome assembly has a high-level completeness of 97.5% gene coverage. The assembly contained 45.67% repetitive sequences (383.50 Mb), and has been annotated with 19,874 protein-coding genes. Next, 3,369 scaffolds were anchored to 26 chromosomes, resulting in an increase of the N50 to 32.16 Mb. Our research provides insights into the evolution and ecology of S. incertulas, offering valuable resources for future pest management.