Gene transfer into the fungi

Abstract

A growing body of data suggests that fungi have gained genes by horizontal gene transfer (HGT). This is an exciting result because fungi at first glance represent the most recalcitrant of all organisms to gene transfer, possessing robust cell walls and having lost phagotrophic capacities because they feed exclusively by osmotrophy. Nonetheless, a number of mechanisms have been implicated in gene transfer including: anastomosis of cellular structures, conjugation-like transfer between bacteria and yeasts, and exchange of supernumerary chromosomes. Despite absence of clearly identified mechanisms driving gene transfer in fungi, genome analysis has provided evidence for a number of fungal genes derived from foreign genomes by HGT. We briefly summarise current approaches to identifying HGT using genome data and make the case that phylogenetic analysis is the best approach to find and test potential examples of HGT. By applying this approach we have collected as many datasets as we could find for which phylogenetic analyses have been used as evidence of HGT and re-tested all 340 examples using updated taxon sampling. This approach enabled us to provide further supporting evidence for 323 examples of HGT, representing a significant pattern of transfer from both prokaryotes (mainly bacteria) and fungi into fungal genomes. Annotation of the HGTs suggests that these transfers have added to the core nutrient-processing metabolic network of many fungi, expanding the sugar, nitrogen, amino acid, nucleobase, and macromolecule metabolism of fungal microbes. Furthermore, these transfers appear to have added a significant number of new genes to the secretome and transporter repertoire of fungi, implying that gene transfer has added to the osmotrophic capacity of many fungal species.