Unveiling P450 Gene Diversity: Structural Variants and Expression Divergence in Three <i>Aphis gossypii</i> Haplotypes

The cotton-melon aphid Aphis gossypii Glover is an important agricultural pest that causes severe damage. Cytochrome P450 monooxygenases (P450s) are involved in the metabolism of insecticides and plant secondary metabolites, making A. gossypii widespread and challenging to control. Hap1, Hap3, and Hap4 are considered to be the domain haplotypes of A. gossypii, and high-quality genome assemblies are now available. In this study, 58 P450 genes were identified in A. gossypii, which were classified into four CYP clans: 9 P450 genes belong to the CYP2 clan, 26 P450 genes belong to the CYP3 clan, 17 P450 genes belong to the CYP4 clan, and 6 P450 genes belong to the mitochondrial clans. P450 genes are often arranged in clusters on chromosomes, with more than half distributed on chromosome A1 in A. gossypii. Most insecticide resistance-related P450 genes in A. gossypii are clustered with conserved gene structures among the Hap1, Hap3, and Hap4. Still, they show different expression levels among the three haplotypes of A. gossypii. Five structural variants of the P450 gene among Hap1, Hap3, and Hap4 were characterized in A. gossypii; not all structural variants exhibit regulatory effects on P450 gene expression. The largest P450 gene cluster includes five A. gossypii P450 4C1 genes, with conserved gene structure among the three haplotypes but varying sizes of the three introns, which have a marked effect on gene expression. These findings provide a valuable resource for further investigations into population differentiation and pesticide resistance evolution in A. gossypii.