Identification of candidate host-manipulating effector genes in <i>Aphis gossypii</i> (Hemiptera: Aphididae) using a combination of transcriptome, genome, and differential gene expression data

The cotton aphid, Aphis gossypii Glover, is an important plant disease vector and a highly polyphagous agricultural pest that feeds on a broad range of host plants. During feeding, its salivary glands serve as a route for the transmission of circulative plant viruses and produce a range of secretory proteins, called effectors, to modulate host cellular processes. To understand the molecular mechanisms underlying aphid-plant interactions, we developed a bioinformatics pipeline that incorporated the salivary gland transcriptome, genome, and head vs abdomen differential gene expression data to predict secretory protein-encoding genes enriched in the salivary glands of A. gossypii. Annotation of the 351 predicted genes showed that the most abundant functional categories were associated with cellular signaling and metabolism processes, and revealed that 98 genes were hemipteran-specific. Notably, 51 genes encode secretory proteins matching the putative saliva proteins identified in prior proteomics studies. Quantitative PCR analysis validated differential expression of 4 selected genes between heads and abdomens and indicated that alate adults exhibited the highest gene expression, suggesting these genes may play key roles in host colonization. Additionally, 25 genes showed sequence similarities to functionally characterized hemipteran effectors, with some appearing to form effector groups with distinct evolutionary patterns. Collectively, this study identified numerous putative plant-manipulating genes in A. gossypii and provided valuable insights into the mechanisms of aphid-plant interactions.