Date:
David S. Hibbett
Professor of Biology, Clark University
Phylogenetics and phylogenomics of Lentinula and the origin of cultivated shiitake mushrooms
Abstract: Lentinula is a well-known, broadly-distributed group of Agaricomycetes that contains shiitake mushrooms, L. edodes sensu lato. For the last 25 years, our understanding of phylogenetic relationships in Lentinula has been informed mainly by analyses of ribosomal ITS sequences. We analyzed 24 genomes representing eight of eleven accepted species and several unnamed lineages of Lentinula. We also assembled and analyzed 60 genomes of L. edodes from China that were previously published as raw Illumina reads. Lentinula comprises four major lineages that arose in the Oligocene; three are restricted to the Americas and one is in Asia-Australasia. Bayesian species delimitation analyses under the multispecies coalescent model suggest at least 11 species that are largely corroborated by prior taxonomy. Shiitake contains two major lineages. One is represented in our dataset by a single isolate from Nepal, while the other occurs throughout Asia. The latter contains two major populations, one composed of wild isolates and the other mostly containing cultivar strains. Two populations of hybrid origin are also resolved. The pangenome of L. edodes contains 20,308 groups of orthologous genes, but only 6438 orthogroups (32%) are shared among all strains. Wild populations of L. edodes sensu lato contain a high proportion of the accessory genome and should be targeted for conservation. There are at least five lineages (potential species) of Lentinula in Asia, South America, and Africa for which we have no genomes. Several are known from only a single collection. Our study highlights the importance of herbarium collections and the need for fieldwork, even in “well-known” groups of Fungi.
