Dynamic gene duplication/loss history marks the unique evolutionary route to fungal multicellularity

Multicellularity has evolved numerous times during eukaryote evolution, yet the genetic prerequisites for these transitions are hardly known. In contrast to other organisms fungi used their own unique evolutionary route to achieve multicellularity with different physiological bases. This raises the question whether the genetic-mechanistic principles of the evolution of multicellularity are common to both fungi and animals and how fungal multicellularity-related gene families evolved during the history of life. Here we reconstruct the evolution of the genetic background of fungal multicellularity based on both known multicellularity-related genes from the literature and genome-wide identification of gene families that evolve in a correlated fashion with multicellularity. Based on literature surveys, we identified 875 genes involved in the establishment and maintenance of cell polarity, vesicular transport and cytoskeletal rearrangement. The evolutionary origins of these genes were examined using complete genomes of 76 unicellular and multicellular eukaryotes. We implemented phylostratigraphic analyses using a custom pipeline, which uncovered the evolutionary origins of multicellularity-related genes, and reconstructed gene duplication and loss histories by COMPARE analysis. These yielded a high-resolution view of the dynamics of these multicellularity-related gene families. Further we could identify 316 gene families, including certain cytochrome P450 families, monocarboxylate permeases and vacuolar aspartyl proteases that show strong correlated evolution with multicellularity, providing candidates for future functional studies. Our results demonstrate that part of the genetic toolkit behind fungal multicellularity was already present in ancestral unicellulars and that some of the hyphal morphogenesis related gene families diversified before the emergence of the first filamentous fungi. This suggests that beside gene duplications and de novo gene family birth, the rewiring of gene regulatory networks could have had a crucial role in the evolution of multicellular fungi.