Comparative genomics reveals a dynamic genome evolution in the ectomycorrhizal milk‐cap (<i>Lactarius</i>) mushrooms

<jats:title>Summary</jats:title><jats:p> <jats:list list-type="bullet"> <jats:list-item><jats:p>Ectomycorrhizal fungi play a key role in forests by establishing mutualistic symbioses with woody plants. Genome analyses have identified conserved symbiosis‐related traits among ectomycorrhizal fungal species, but the molecular mechanisms underlying host specificity remain poorly known.</jats:p></jats:list-item> <jats:list-item><jats:p>We sequenced and compared the genomes of seven species of milk‐cap fungi (<jats:italic>Lactarius</jats:italic>, Russulales) with contrasting host specificity. We also compared these genomes with those of symbiotic and saprotrophic Russulales species, aiming to identify genes involved in their ecology and host specificity.</jats:p></jats:list-item> <jats:list-item><jats:p>The size of <jats:italic>Lactarius</jats:italic> genomes is significantly larger than other Russulales species, owing to a massive accumulation of transposable elements and duplication of dispensable genes. As expected, their repertoire of genes coding for plant cell wall‐degrading enzymes is restricted, but they retained a substantial set of genes involved in microbial cell wall degradation. Notably, <jats:italic>Lactarius</jats:italic> species showed a striking expansion of genes encoding proteases, such as secreted ectomycorrhiza‐induced sedolisins. A high copy number of genes coding for small secreted LysM proteins and <jats:italic>Lactarius</jats:italic>‐specific lectins were detected, which may be linked to host specificity.</jats:p></jats:list-item> <jats:list-item><jats:p>This study revealed a large diversity in the genome landscapes and gene repertoires within Russulaceae. The known host specificity of <jats:italic>Lactarius</jats:italic> symbionts may be related to mycorrhiza‐induced species‐specific genes, including secreted sedolisins.</jats:p></jats:list-item> </jats:list> </jats:p>