Phylogenomic analysis of Dendrothele nivosa, a bark-inhabiting and host-specific crust fungus with an enigmatic ecological role

Fungi in the genus Dendrothele (Basidiomycota, Russulales) are known for their obligate associations with the bark of living trees. However, the genus as it is currently defined is polyphyletic, and the phylogenetic placement and ecological roles of many of its species are poorly understood. We focused on Dendrothele nivosa, a common species in eastern North America associated with the bark of living Juniperus species. The taxonomic placement of D. nivosa has shifted among different orders and families since the 19th century. This species is found exclusively on the bark of living Juniperus, and its ecological niche remains unclear, as it is not associated with the bark of dead trees and thus may function as something other than a primary decomposer. Using Illumina short-read technology, we generated the first highquality genome assembly of D. nivosa (71 Mb length; BUSCO completeness of 97.5%, N50: 9572, L50: 1618). We determined its phylogenetic placement by building a whole genome–based phylogeny using publicly available data for the order Russulales. D. nivosa represents a distinct clade separate from its most closely related families, Bondarzewiaceae and Stereaceae. To better understand its ecological niche, we analyzed gene families of D. nivosa and closely related relatives, with an emphasis on carbohydrateassociated enzymes (CAZymes). The CAZyme profile in our assembly suggests that D. nivosa may function primarily as a bark/wood decay fungus, despite its exclusive association with living trees. In contrast to other close relatives, nearly half of the D. nivosa genome consists of transposable elements (TEs) caused by a massive invasion of long terminal repeat (LTR) retrotransposons, suggesting that TEs have played an important role in shaping D. nivosa’s evolution. The clarified phylogenetic position of D. nivosa and robust genomic data serve as a starting point for future work to determine the evolution and ecology of the diverse species of corticioid fungi associated with the bark of living trees.