Lineage-specific contraction of detoxification genes drives host specilization and chemical stress adaptation in Panonychus citri

In this study, we present the first chromosome-level genome assembly of P. citri through PacBio HiFi sequencing integrated with Hi-C chromatin interaction mapping. The 72.37 Mb genome (contig N50 = 24.66 Mb) resolves into three pseudo-chromosomes and encodes 9,767 protein-coding genes, with 95.8% functional annotation coverage. Comparative phylogenomic analysis across four tetranychid species (P. citri, Tetranychus truncates, Tetranychus urticae, Tetranychus piercei) revealed an ancient divergence of P. citri lineage ~370.9 Mya, accompanied by lineage-specific chromosomal fragmentation events. While 6,961 core orthologous gene clusters shared across all four species demonstrated remarkable gene family conservation, branch-specific expansions and positive selection signatures highlighted ongoing adaptive evolution in xenobiotic metabolism and host interaction pathways. But relative to other tetranychids, P. citri exhibits significant contraction in detoxification gene families (P450s, GSTs, CCEs, UGTs) and chemosensory receptors (GRs, ENaCs). Further transcriptomic profiling revealed that upregulation of detoxification-related genes (P450s, GSTs, CCEs, and UGTs) upon exposure to acaricides or plant secondary metabolites. This chromosome-level genomic resource not only elucidates macroevolutionary patterns underlying tetranychid diversification but also establishes a framework for targeted resistance management strategies in crop systems