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

## TL;DR

Researchers assembled the genome of Ctenoplusia agnata, a damaging pest, to better understand its evolution and improve pest control strategies.

## Contribution

The first chromosome-level genome assembly of Ctenoplusia agnata is presented for pest management and evolutionary studies.

## Key findings

- The genome assembly has high completeness with 98.8% gene coverage and 12,726 predicted protein-coding genes.
- Comparative analysis shows C. agnata shares chromosome structure with C. includens but is phylogenetically closer to T. ni.
- Fewer detoxification genes were found in C. agnata compared to related species, which may impact pesticide resistance.

## Abstract

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.

Assembly of Ctenoplusia agnata genome at the chromosomal level and the use of pest management through comparative genomes with Plusiinae pests.