A chromosome-level genome assembly provides insights into the environmental adaptability and outbreaks of Chlorops oryzae

Chlorops oryzae is a pest of rice that has caused severe damage to crops in major rice-growing areas in recent years. We generated a 447.60 Mb high-quality chromosome-level genome with contig and scaffold N50 values of 1.17 Mb and 117.57 Mb, respectively. Hi-C analysis anchored 93.22% scaffolds to 4 chromosomes. The relatively high expression level of Heat Shock Proteins (HSPs) and antioxidant genes in response to thermal stress suggests these genes may play a role in the environmental adaptability of C. oryzae. The identification of multiple pathways that regulate reproductive development (juvenile hormone, 20-hydroxyecdsone, and insulin signaling pathways) provides evidence that these pathways also play an important role in vitellogenesis and thus insect population maintenance. These findings identify possible reasons for the increased frequency of outbreaks of C. oryzae in recent years. Our chromosome-level genome assembly may provide a basis for further genetic studies of C. oryzae, and promote the development of novel, sustainable strategies to control this pest. Overall design: Chlorops oryzae female adults were collected for genome analysis.