Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.
Animal Biodiversity and Evolution, Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain.
Mol Biol Evol. 2020 Sep 1;37(9):2601-2615. doi: 10.1093/molbev/msaa110.
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 are 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 Acyrthosiphon pisum 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 us to tackle the history of duplicated genes to pave the road toward understanding the role of gene duplication in ecological adaptation.
昆虫生态学的范围非常广泛，这反映了它们在我们星球的大多数环境中具有很强的适应能力。蚜虫有超过 4000 种，它们已经发展出一系列适应能力，包括高度表型可塑性和能够以植物韧皮部汁液为食的能力，韧皮部汁液富含光合作用产生的糖分。最近对蚜虫基因组的分析表明，高度共享的祖先基因重复可能是遗传创新和广泛适应的基础。此外，还有大量的最近出现的、物种特异性的基因重复，它们在适应中的作用仍不清楚。在这里，我们通过结合比较基因组学、转录组学和染色质可及性分析，测试了特定于豌豆蚜 Acyrthosiphon pisum 的基因重复是否与基因组创新有关。与大量的新功能化一致，我们发现最近的大多数基因重复对进化表现出不对称性，表现出正选择和基因表达的分歧模式。受选择的基因涉及大量的生物学功能，这表明新功能化和组织特异性等进化机制协调了豌豆蚜最近的同源基因的进化，并可能促进了宿主共生体的合作。我们全面的系统发生基因组学分析使我们能够解决重复基因的历史，为理解基因重复在生态适应中的作用铺平道路。
