Comparative phylogenomics of symbiotic associations

Summary Understanding the genetic bases of complex traits has been a main challenge in biology for decades. Comparative phylogenomics offers an opportunity to identify candidate genes associated with these complex traits. This approach initially developed in prokaryotes consists in looking at shared coevolution between genes and traits. It thus requires a precise reconstruction of the trait evolution, a large genomic sampling in the clades of interest and an accurate definition of orthogroups. Recently, with the growing body of sequenced plant genomes, comparative genomics has been successfully applied to plants to study the widespread arbuscular mycorrhizal symbiosis. Here I will use these findings to illustrate the main principles of comparative phylogenomic approaches and propose directions to improve our understanding of symbiotic associations. Contents Summary 89 I. Introduction 89 II. AM symbiosis in plants: one gain and multiple losses 90 III. Evolution of AM symbiosis‐related genes 90 IV. Discovery of new symbiotic genes 91 V. Future perspectives 92 VI. Conclusion 93 References 93