Trends in Genetics
UpdateGenome AnalysisAcquisition of prokaryotic genes by fungal genomes
Section snippets
HGT in eukaryotes
HGT, the exchange of genetic material between two species [1], was discovered 50 years ago [2], but it is the current wealth of genomic sequences that is revealing its real impact. Currently, it is widely accepted that HGT is one of the main evolutionary driving forces in prokaryotes, but its relevance for eukaryotes remains controversial 3, 4, 5. The traditional view that HGT in eukaryotes is virtually absent has been recently challenged by genome-wide analyses reporting the transfer of
Detection of inter-domain HGT events in fungi
Using 60 complete fungal genomes and >600 other genomes from prokaryotes and other eukaryotes, we designed a phylogenomic pipeline to detect cases of genes likely to have been acquired through HGT from prokaryotic donors (see the online supplementary material). In brief, we adopted a conservative strategy that searched for genes present in few (<10) fungi and absent in other eukaryotes, but which could be found in a relatively high number of prokaryotic genomes (>30). This procedure detected
Differential impact of HGT across the fungal tree of life
We mapped the 235 HGT events on the fungal tree of life [10], assuming the transfers affected the last common ancestor of all species in a monophyletic group. Our results (Figure 1) show that HGT affected most fungal lineages to various extents. Unexpectedly, nearly two-thirds (65%) of the events are mapped within Pezizomycotina, of which one-third appear at the base of this clade. More recent HGT events affect most Pezizomycotina lineages, suggesting this is an ongoing process. By contrast,
Restoration of the arsenate detoxification pathway
We identified two independent acquisitions of a bacterial arsenate reductase in Yarrowia lipolytica and Rizopus oryzae. The reduction of arsenate to arsenite is an important step in arsenic detoxification [17], a pathway that is carried out in the yeast Saccharomyces cerevisiae by a different arsenate reductase (ARR2) in combination with membrane pumps that expel arsenite from the cytoplasm. Orthology assessment 10, 18 shows that Y. lipolytica, R. oryzae and their close relatives have no
Acquisition of multiple racemase genes
Racemases catalyze the inter-conversion of optical isomers (e.g. D- and L-amino acids). Recent studies describe putative cases of HGT involving various bacterial racemases in eukaryotic genomes. These include alanine racemase in Schizosaccharomyces pombe[11] and Adineta vaga[7], and a proline racemase in C. parapsilosis[15]. Interestingly, our survey detected seven additional HGT instances involving three different racemases: aspartate, hydantoin and mandelate racemases. Most such cases involve
Bacterial catalases in fungal pathogenic species
Through their action in decomposing reactive oxygen species, catalases can help pathogens overcome host defense mechanisms. The potential advantages conferred by the acquisition of foreign catalases have been extensively studied in pathogenic bacteria 21, 22. In fungi, a recent transfer of a bacterial catalase has been described in the microsporidian pathogen Nosema locustae[23]. In our study, we detected similar transfers to three important plant pathogens: the Dothideomycetes Stagonospora
Transfer of a Mur operon
Multiple transfers of functionally-related enzymes are remarkable because they can provide the recipient species with a novel metabolic pathway. Our analyses found, in similar sets of Aspergillus species, the first three enzymes of the bacterial peptidoglycan biosynthesis pathway: MurA, MurB and MurC. Recipient species included Aspergillus terreus, Aspergillus oryzae, Aspergillus flavus, Aspergillus fumigatus and Neosartorya fischeri, although MurC was apparently lost in the latter two species.
Concluding remarks
Our results reveal that inter-domain HGT is widespread in fungi and has played a role in the evolution of this eukaryotic group. We detected 713 transferred genes that, given the high stringency of our phylogenomic criteria, should be considered a minimal estimate. Additional studies will probably reveal further examples of transfers that have escaped our strict criteria (e.g. prokaryotic genes transferred to other eukaryotic groups). The ability of fungi to acquire alien prokaryotic genes
Acknowledgements
MMH and TG are supported by the FUNPATH grant from the ERA-NET pathogenomics network funded by the Spanish Ministry of Science (GEN06-27784).
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