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 <i>P. citri</i> 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 (<i>P. citri</i>, <i>Tetranychus truncates</i>, <i>Tetranychus urticae</i>, <i>Tetranychus piercei</i>) revealed an ancient divergence of <i>P. citri</i> 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, <i>P. citri</i> 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