Chromosome-scale genome assembly of the rice stink bug (Hemiptera: Oebalus pugnax) illuminates genome structure and gene family evolution in Pentatomidae.

Abstract

The rice stink bug (Oebalus pugnax; RSB) is a major agricultural pest that poses significant threats to rice production throughout the United States. Yet, despite its economic significance, almost nothing is known about genome structure, function, and evolution in this species. Here, we sequenced, assembled, and annotated the first high-quality reference genome for RSB and conducted comparative analyses with related hemipteran genomes to understand its historical evolutionary context. The assembly spans 826.62 Mb across 211 contigs, with an N50 of 17.25 Mb, the largest contig of 67.15 Mb, and a BUSCO representation of 99.30% completeness. Hi-C-based scaffolding supported six putative chromosome-scale scaffolds. Genome-wide repeats comprised 47.55% of the genome, consisting largely of interspersed elements, including DNA transposons, LINEs, and LTRs, with evidence of recent expansions. Our annotation identified 13,175 putative genes, with predicted functions for 97.87% of them. We further uncovered candidate genes and enzyme families involved in detoxification and insecticide resistance, including cytochrome P450s, UDP-glycosyltransferases, and glycoside hydrolases. Comparative analyses revealed rapid expansion and contraction of gene families associated with feeding, host specialization, and insecticide resistance. Together, these resources provide a new framework for future investigations into genome structure, function, and evolution in this ecologically and economically important insect clade.