Summary Mutualistic symbioses, such as lichens formed between fungi and green algae or cyanobacteria, have contributed to major transitions in the evolution of life and are at the center of extant ecosystems. However, our understanding of their evolution and function remains elusive in most cases. Here, we investigated the evolutionary history and the molecular innovations at the origin of lichens in green algae. We de novo sequenced the genomes or transcriptomes of 12 lichen-forming and closely related non-lichen-forming algae and performed comparative phylogenomics with 22 genomes previously generated. We identified 39 functional categories and 11 orthogroups significantly enriched in lichen-forming chlorophyte green algae. Among them, functions such as carbohydrates metabolism and stress tolerance could be related to the pioneer characteristics of lichens. We detected lichen-specific expansions of glycosyde hydrolase gene families known to remodel cell walls, including the glycosyde hydrolase 8 (GH8) which encodes a glucanase and was acquired in lichenizing Trebouxiophyceae by horizontal gene transfer from bacteria, concomitantly with the ability to form lichens. Mining genome-wide orthogroups, we found additional evidence supporting at least two independent origins of lichen-forming ability in chlorophyte green algae. Highlights We sequenced 12 lichen-forming and non-lichen-forming chlorophytes Lichens evolved independently in Ulvophyceae and Trebouxiophyceae Gene family expansion correlate with the ability to form lichens Horizontal Gene Transfer of a glycoside hydrolase is linked with lichenization
