Chromosome-level genome assembly of Ctenoplusia agnata and its potential application in Plusiinae pest management

Ctenoplusia agnata is a polyphagous pest affecting bean crops and cruciferous vegetables across East Asian countries, including Korea. Its periodic outbreaks cause significant damage to crops. The lack of a genome assembly has limited research on integrated pest management strategies and understanding its phylogenetic relationships with related species.

We sequenced the genome of a Korean C. agnata using PacBio Revio long-read combined with Pore-C scaffolding. The final assembly (GCA_041146325.1, 406.7 Mb) comprises 70 scaffolds, with the largest 31 scaffolds representing 95.1% of the assembly, corresponding to the expected 31 chromosomes. BUSCO analysis confirmed high completeness with 98.8% gene coverage and 36% GC content. The assembly achieved a scaffold N50 of 13.2 Mb, scaffold L50 of 14, and 28.57% repeat sequence content. A total of 12 726 protein-coding genes were predicted, of which 12 635 (99.28%) were functionally annotated. Comparative analysis with Chrysodeixis includens and Trichoplusia ni, two Plusiinae species, revealed that while C. agnata shares the chromosome number and broad synteny with C. includens; phylogenetic analyses place it closer to T. ni, suggesting distinct evolutionary trajectories despite structural conservation. Analysis of five major detoxification enzyme gene families (CYP, CCE, GST, UGT, and ABC) revealed that C. agnata contains fewer or similar detoxification genes compared to both T. ni and C. includens.

The genome of C. agnata provides a valuable genetic resource for enhancing our understanding of the Plusiinae evolution and developing effective integrated pest management strategies. © 2025 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.