Phylogenomics identifies an ancestral burst of gene duplications predating the diversification of aphidomorpha

Aphids (Aphidoidea) are a diverse group of hemipteran insects that feed on plant sap. A common finding in studies of aphid genomes is the presence of a large number of paralogous. However, when these duplications occurred remains unclear, partly due to the high relatedness of sequenced species. To help understanding the origin of aphid duplications we sequenced and assembled the genome of Cinara cedri, which represents an early branching lineage (Lachninae) of the Aphididae family. We performed a phylogenomic comparison of this genome with twenty other sequenced genomes, including the available genomes of five other aphids, and with the transcriptomes of two species from Adelgidae and Coccoidea. We found that gene duplication have been pervasive throughout the evolution of aphids, including many parallel waves of recent, species-specific duplications. Most notably, we identied a consistent set of very ancestral duplications, originating from a large-scale gene duplication predating the diversification of Aphidomorpha (which includes aphids, phylloxerids, and adelgids). Genes duplicated at this ancestral wave are enriched in functions related to traits shared by Aphidomorpha, such as association with endosymbionts, and adaptation to plant defenses and plant-sap based diet. The ancestral nature of this duplication wave (69-178 Mya) and the lack of sufficiently conserved synteny among the analyzed species makes it difficult to conclude whether it originated from a whole genome duplication event or, alternatively, from a burst of large-scale segmental duplications. Genome sequencing of other aphid species belonging to different aphidomorpha and related lineages may clarify these findings.