Phylogenomic analysis demonstrates a pattern of rare and ancient horizontal gene transfer between plants and fungi

Abstract

Horizontal gene transfer (HGT) describes the transmission of genetic material across species boundaries and is an important evolutionary phenomenon in the ancestry of many microbes. The role of HGT in plant evolutionary history is, however, largely unexplored. Here, we compare the genomes of six plant species with those of 159 prokaryotic and eukaryotic species and identify 1689 genes that show the highest similarity to corresponding genes from fungi. We constructed a phylogeny for all 1689 genes identified and all homolog groups available from the rice (Oryza sativa) genome (3177 gene families) and used these to define 14 candidate plant-fungi HGT events. Comprehensive phylogenetic analyses of these 14 data sets, using methods that account for site rate heterogeneity, demonstrated support for nine HGT events, demonstrating an infrequent pattern of HGT between plants and fungi. Five HGTs were fungi-to-plant transfers and four were plant-to-fungi HGTs. None of the fungal-to-plant HGTs involved angiosperm recipients. These results alter the current view of organismal barriers to HGT, suggesting that phagotrophy, the consumption of a whole cell by another, is not necessarily a prerequisite for HGT between eukaryotes. Putative functional annotation of the HGT candidate genes suggests that two fungi-to-plant transfers have added phenotypes important for life in a soil environment. Our study suggests that genetic exchange between plants and fungi is exceedingly rare, particularly among the angiosperms, but has occurred during their evolutionary history and added important metabolic traits to plant lineages.

Figure 1.

Phylogenetic Evidence for Plant-Fungi HGT. Results of phylogenetic analyses of three candidates for which the tree topology results support a case for HGT between plants and fungi. All phylogenies are reduced versions of the full tree topologies (see corresponding Supplemental Figures 1 to 3 online for full details). Black dots are used when the relevant node is supported with 85% or more bootstrap support by both bootstrap methods. Open circles show cases when both bootstrap results are between 60 and 84%. For key nodes, actual support values are marked in the order Bayesian posterior probability/PhyML bootstrap/RAxML bootstrap/PhyML node-by-node SH test. Fungi groups are marked in yellow and plants in green. The transferred genes are marked by thick and colored ovals. Nonformal and nonequivalent higher taxonomic names are labeled on each phylogeny. (A) Phylogeny of the putative l-fucose permease sugar transporter. (B) Phylogeny of the putative zinc binding alcohol dehydrogenase. (C) Phylogeny of the putative major facilitator superfamily membrane transporter.

Figure 2.

Phylogenetic Evidence for Plant-Fungi HGT with Weak Topology Support Values but Confirmed by Alternative Topology Tests. (A) The phylogeny of the phospholipase/carboxylesterase family protein demonstrates moderate support for a fungi-to-plant HGT by PhyML bootstrap methods but weak support by all three other topology support assessment methods. Alternative topology tests gave strong support for the placement of the Selaginella sequences within the specific ascomycete cluster, suggesting an ascomycete-to-Selaginella HGT. (B) The Selaginella sequences do not form a monophyletic cluster in the phylogeny. To test this, we performed a second analysis focusing the taxon sampling on the branches local to the Selaginella group and increasing character sampling. The phylogenetic trees shown are reduced versions of the full tree topologies (see Supplemental Figure 4 online for full details). The figures are labeled using the same conventions described for Figure 1.

Figure 3.

Evidence for Plant-Fungi HGT Based on a Prokaryote Tagged-Chain Transfer Hypothesis. In the absence of strong phylogenetic tree topological support, it has been argued that a putative eukaryote-to-eukaryote HGT can be inferred when it is rooted by an uncontroversial case of prokaryote-to-eukaryote HGT. We detected two additional examples of HGT supported by this form of evidence. (A) Phylogeny of the putative bifunctional iucA/iucC siderophore biosynthesis protein. (B) Phylogeny of the unknown/conserved hypothetical protein. All phylogenies are reduced versions of the tree figure and the phylogenetic analysis implemented. See Supplemental Figures 5 and 6 online for full details. The figures are labeled using the same conventions described for Figure 1.

Figure 4.

Evidence for Plant-Fungi HGT Based on Gene Family Taxon Distribution. Phylogenetic analyses of taxonomic distribution of HGT candidates among plants, a subsection of fungi, and (in two cases) a very restricted distribution of prokaryotes. These highly punctate taxon distributions suggest that these three genes have been horizontally transferred from plants to fungi. Phylogenies are shown to summarize the taxon distribution of this gene family. (A) Phylogeny of the DUF239 domain protein. (B) Phylogeny of the phosphate-responsive 1 family protein. (C)Phylogeny of the unknown/conserved hypothetical protein with similarity to zinc finger (C2H2 type) protein. All phylogenies are reduced versions of the full tree topologies (see Supplemental Figures 7 to 9 online for full details). The figures are labeled using the same conventions described for Figure 1.

Figure 5.

Results of Analyses of the Genome Contigs of Recipient Taxa Demonstrating the Evolutionary Ancestry of Genes Linked to the Plant-Fungi HGT. This analysis demonstrates the location of the HGTs with respect to transposable elements and vertically inherited genes. In all nine cases, the analyses shows that the HGT is linked to a gene showing vertical phylogenetic inheritance or representing a gene family for which the taxon distribution suggests vertical inheritance. Because all nine HGTs are nested within a portion of native genome, DNA contamination can be ruled out as a possible source of artifact among the plant-fungus HGTs. Furthermore, in both cases that involve HGT from a fungus to the bryophyte moss P. patens, the HGT is positioned next to a putative transposable element. The alphanumeric label given in to the top right of each genome contig corresponds to Figures 1A to 4C. These data are reported in more detail in Supplemental Table 2 online.

Figure 6.

A Model of the Plant-Fungi Transferome. Schematic representation of how the nine candidate HGT events relate to the evolutionary history of plants and fungi. The point of origin and point of receipt of each HGT are marked by best approximation, based on available phylogenetic data. Candidates are labeled 1A to 4C and correspond to the trees shown in Figures 1A to 4C.