Gene retroposition and functional diversification of retrocopies in the Rhus gall aphid Schlechtendalia chinensis

Gene duplication via retroposition is a crucial mechanism for gene family expansion, and the gene copies produced are referred to as retrocopies. In this study, we assessed gene retroposition in the Rhus gall aphid, Schlechtendalia chinensis, which induces galls on its primary host plant, Rhus chinensis. We identified a total of 491 retrocopies that are further classified into four categories based on their structures, i.e., classified as 62 putative retrogenes (12.6%), 163 chimeric genes (33.2%), 170 pseudogenes (34.6%), and 96 intact retrocopies (19.6%), respectively. The 37 identified putative retrogenes were categorized into 23 gene families; among these, four putative retrogenes belong to the heat shock protein superfamily. Putative retrogenes occupy 15.4% of the total heat shock protein present in the S. chinensis genome. The 90 chimeric genes were classified into 42 distinct protein families and acquired conserved domains from the parent genes, enabling the emergence of new gene functions and physiological adaptations. Most of the chimeric genes in S. chinensis are under purifying selection and a few under positive selection, while the large number of putative retrogenes are under purifying selection. Ks values indicate that 33.74% chimeric genes in this species are ancient. However, 27.42% putative retrogenes that show ancient evolutionary divergence, and only 19.35% might be considered relatively young and have undergone recent evolutionary divergence. These genetic variations contribute to the evolution of retrocopies in the Schlechtendalia chinensis genome.