Selection following gene duplication shapes recent genome evolution in the pea aphid Acyrthosiphon pisum

Abstract

<jats:title>Abstract</jats:title><jats:p>Ecology of insects is as wide as their diversity, which reflects their high capacity of adaptation in most of the environments of our planet. Aphids, with over 4,000 species, have developed a series of adaptations including a high phenotypic plasticity and the ability to feed on the phloem-sap of plants, which is enriched in sugars derived from photosynthesis. Recent analyses of aphid genomes have indicated a high level of shared ancestral gene duplications that might represent a basis for genetic innovation and broad adaptations. In addition, there is a large number of recent, species-specific gene duplications whose role in adaptation remains poorly understood. Here, we tested whether duplicates specific to the pea aphid <jats:italic>Acyrthosiphon pisum</jats:italic> are related to genomic innovation by combining comparative genomics, transcriptomics, and chromatin accessibility analyses. Consistent with large levels of neofunctionalization, we found that most of the recent pairs of gene duplicates evolved asymmetrically, showing divergent patterns of positive selection and gene expression. Genes under selection involved a plethora of biological functions, suggesting that neofunctionalization and tissue specificity, among other evolutionary mechanisms, have orchestrated the evolution of recent paralogs in the pea aphid and may have facilitated host-symbiont cooperation. Our comprehensive phylogenomics analysis allowed to tackle the history of duplicated genes to pave the road towards understanding the role of gene duplication in ecological adaptation.</jats:p>

Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

“…Genome sequencing of a small number of aphid species has also revealed dynamic patterns of genome evolution, with extensive gene duplication having occurred throughout aphid diversification (IAGC 2010;Mathers et al 2017;Thorpe et al 2018;Fernández et al 2019;Julca et al 2019;. However, the majority of aphid genomes assembled to date are highly fragmented and chromosome-scale genome assemblies have not yet been used to investigate the evolution of diverse aphid karyotypes.…”