Phylogenomics, trophic ecology, and systematics of the truffle-forming <i>Morchellaceae</i>

The family <i>Morchellaceae</i> contains four truffle-forming genera: <i>Fischerula</i>, <i>Imaia</i>, <i>Kalapuya</i>, and <i>Leucangium</i>. In North America, some <i>Imaia</i>, <i>Kalapuya</i>, and <i>Leucangium</i> species are highly regarded gourmet edible fungi. In this study, we address longstanding questions about the evolution, systematics, and trophic mode of these fungal genera. We used high-throughput sequencing and a custom genome assembly pipeline to sequence and assemble 41 new genomes of epigeous and hypogeous <i>Morchellaceae</i> genera and outgroup taxa from the sister family <i>Discinaceae</i>. Phylogenomic reconstructions based on high-quality <i>de novo</i> genomes and published reference genomes support a single transition from epigeous to hypogeous habit within the <i>Morchellaceae</i>. These results are corroborated by phylogenetic evidence from LSU, <i>tef1</i>, and <i>rpb</i>2 with a larger dataset of specimens and publicly available sequences. We also provide direct morphological and molecular evidence that one species of <i>Leucangium</i> from North America forms ectomycorrhizas on <i>Pseudotsuga menziesii</i> in a natural habitat. Stable isotope analysis further supports the hypothesis that other species of truffle-forming <i>Morchellaceae</i> also obtain carbon via ectomycorrhizal symbiosis. Phylogenetic and morphological analysis supports the description of two new species and one new combination of <i>Leucangium</i> as well as one new species and one new combination of <i>Imaia</i> from North America. We also discuss additional, undescribed diversity detected in our phylogenetic analyses of these genera derived from fungarium specimens, mycophagous mammal scat samples, and other environmental samples. <b>Citation:</b> Lemmond B, Bonito G, Healy R, Van Wyk J, Dawson HA, Noffsinger CR, Stephens R, Sow A, Trappe JM, Orihara T, Mleczko P, Kaounas V, Smith ME (2025). Phylogenomics, trophic ecology, and systematics of the truffle-forming <i>Morchellaceae</i>. <i>Persoonia</i> <b>55</b>: 59-91. doi: 10.3114/persoonia.2025.55.02.