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To understand the molecular mechanisms underlying aphid\u2013plant 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\u2013plant interactions.<\/jats:p>","DOI":"10.1093\/jisesa\/ieaf053","type":"journal-article","created":{"date-parts":[[2025,4,17]],"date-time":"2025-04-17T05:43:21Z","timestamp":1744868601000},"source":"Crossref","is-referenced-by-count":1,"title":["Identification of candidate host-manipulating effector genes in\n                    <i>Aphis gossypii<\/i>\n                    (Hemiptera: Aphididae) using a combination of transcriptome, genome, and differential gene expression data"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3378-3163","authenticated-orcid":false,"given":"Chaoyang","family":"Zhao","sequence":"first","affiliation":[{"name":"National Soil Dynamics Laboratory, USDA-ARS , Auburn, AL,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-4816-6997","authenticated-orcid":false,"given":"Nicholas","family":"Mueller","sequence":"additional","affiliation":[{"name":"Department of Entomology and Plant Pathology, Auburn University , Auburn, AL,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Isabella","family":"Owens","sequence":"additional","affiliation":[{"name":"Department of Entomology and Plant Pathology, Auburn University , Auburn, AL,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7133-0785","authenticated-orcid":false,"given":"Raman","family":"Bansal","sequence":"additional","affiliation":[{"name":"San Joaquin Valley Agricultural Sciences Center, USDA-ARS , Parlier, CA,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1296-4654","authenticated-orcid":false,"given":"Alana L","family":"Jacobson","sequence":"additional","affiliation":[{"name":"Department of Entomology and Plant Pathology, Auburn University , Auburn, AL,","place":["USA"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,5,28]]},"reference":[{"key":"2026032004012953100_CIT0001","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/jisesa\/iey094","article-title":"Conserved and unique putative effectors expressed in the salivary glands of three related gall midge species","volume":"18","author":"Al-Jbory","year":"2018","journal-title":"J. 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