Horizontal gene transfer of acetyltransferases, invertases and chorismate mutases from different bacteria to diverse recipients

Abstract

Background: Hoplolaimina plant-parasitic nematodes (PPN) are a lineage of animals with many documented cases of horizontal gene transfer (HGT). In a recent study, we reported on three likely HGT candidate genes in the soybean cyst nematode Heterodera glycines, all of which encode secreted candidate effectors with putative functions in the host plant. Hg-GLAND1 is a putative GCN5-related N-acetyltransferase (GNAT), Hg-GLAND13 is a putative invertase (INV), and Hg-GLAND16 is a putative chorismate mutase (CM), and blastp searches of the non-redundant database resulted in highest similarity to bacterial sequences. Here, we searched nematode and non-nematode sequence databases to identify all the nematodes possible that contain these three genes, and to formulate hypotheses about when they most likely appeared in the phylum Nematoda. We then performed phylogenetic analyses combined with model selection tests of alternative models of sequence evolution to determine whether these genes were horizontally acquired from bacteria.

Results: Mining of nematode sequence databases determined that GNATs appeared in Hoplolaimina PPN late in evolution, while both INVs and CMs appeared before the radiation of the Hoplolaimina suborder. Also, Hoplolaimina GNATs, INVs and CMs formed well-supported clusters with different rhizosphere bacteria in the phylogenetic trees, and the model selection tests greatly supported models of HGT over descent via common ancestry. Surprisingly, the phylogenetic trees also revealed additional, well-supported clusters of bacterial GNATs, INVs and CMs with diverse eukaryotes and archaea. There were at least eleven and eight well-supported clusters of GNATs and INVs, respectively, from different bacteria with diverse eukaryotes and archaea. Though less frequent, CMs from different bacteria formed supported clusters with multiple different eukaryotes. Moreover, almost all individual clusters containing bacteria and eukaryotes or archaea contained species that inhabit very similar niches.

Conclusions: GNATs were horizontally acquired late in Hoplolaimina PPN evolution from bacteria most similar to the saprophytic and plant-pathogenic actinomycetes. INVs and CMs were horizontally acquired from bacteria most similar to rhizobacteria and Burkholderia soil bacteria, respectively, before the radiation of Hoplolaimina. Also, these three gene groups appear to have been frequent subjects of HGT from different bacteria to numerous, diverse lineages of eukaryotes and archaea, which suggests that these genes may confer important evolutionary advantages to many taxa. In the case of Hoplolaimina PPN, this advantage likely was an improved ability to parasitize plants.

Keywords: Evolution; Hoplolaimina; Horizontal gene transfer; Model selection analysis; Phylogenetics; Plant-parasitic nematodes.

Fig. 1

Cladograms of the phylum Nematoda and clade 12 order Tylenchida. Tree topologies of the phylum Nematoda (a) and the clade 12 order Tylenchida (b) are consistent with that described in [3] and are adapted from [55]. (a,b) Nematode species whose genomic (_g), transcriptomic (_t), or both genomic and transcriptomic (_g/t) sequences were included in our searches are listed in parentheses at each leaf. Branches that contain PPN species are illustrated in green. These searches included, but were not limited to, information available in nematode sequence databases (see Methods)

Fig. 2

Suspected timing of appearance of GNATs, INVs and CMs in Hoplolaimina PPN. (a-c) Cladograms are shown as in Fig. 1B. Lineages, and species within, that were found to contain homologs of the HGT genes in question are colored red. The suspected timing of appearance of GNATs (a), INVs (b) and CMs (c) are illustrated with a red circle placed on the appropriate branch. Note that species within a red Hoplolaimina lineage (family or subfamily) that are not colored red does not mean that they do not contain that particular gene, it means that we could not identify that gene in their sequence data, which may be due to insufficient sequence data rather than gene loss. The same goes for the Radopholinae lineage, as Radopholus similis was the only species included, which has only limited EST sequences

Fig. 3

Phylogenetic tree of the GNAT superfamily and newly identified GNATs similar to the Hoplolaimina homologs. Phylogenetic groups containing each GNAT family are collapsed and color-coded with corresponding bootstrap support values indicated at each node. The number of sequences (n) that were used for each GNAT family is indicated within each collapsed phylogenetic group. Organisms that contain each GNAT family are provided in parentheses within each collapsed phylogenetic group. Note that the newly identified GNAT clade with similarity to the Hoplolaimina homologs forms a highly supported monophyletic group with no significant clustering to any other GNAT family, thus indicating a novel GNAT family, which we called Family 7 (FAM7). The raw phylogenetic tree is shown in Additional file 6: Figure S1, and contains all identifiers and species names for all of the sequences that were included in the analysis

Fig. 4

Phylogenetic tree of FAM7 GNATs including the Hoplolaimina homologs. Phylogenetic groups are color-coded according to their taxonomic classifications. Bootstrap support values are indicated at corresponding nodes, and those that support possible HGT events are oversized in red font. Notice a maximum of 10 possible HGT events where eukaryotes and archaea form monophyletic groups with different bacteria, including cyst nematodes with actinomycetes most similar to streptomycetes. The raw phylogenetic tree is shown in Additional file 6: Figure S2, and contains all identifiers and species names for all of the sequences that were included in the analysis

Fig. 5

Phylogenetic tree of INVs similar to the Hoplolaimina homologs. Phylogenetic groups are color-coded according to their taxonomic classifications. Bootstrap support values are indicated at corresponding nodes, and those that support possible HGT events are oversized in red font. Notice a maximum of 8 possible HGT events where eukaryotes and archaea form monophyletic groups with different bacteria, including Hoplolaimina PPN with rhizobacteria (order Rhizobiales). The raw phylogenetic tree is shown in Additional file 6: Figure S4, and contains all identifiers and species names for all of the sequences that were included in the analysis

Fig. 6

Phylogenetic tree of CMs similar to the Hoplolaimina homologs. Phylogenetic groups are color-coded according to their taxonomic classifications. Bootstrap support values are indicated at corresponding nodes, and those that support possible HGT events are oversized in red font. Notice a supported monophyletic grouping of Hoplolaimina PPN with Burkholderia CMs. The raw phylogenetic tree is shown in Additional file 6: Figure S5, and contains all identifiers and species names for all of the sequences that were included in the analysis

Fig. 7

%GC content comparisons of Hoplolaimina HGT genes with distributions constructed from recipients and donors. Distributions of %GC content were constructed using cds from each respective group of Hoplolaimina and donor bacteria listed in each panel. The height of each distribution corresponds to the number of cds at that particular value of %GC content. The x-axis is labeled at the bottom with %GC content. Dots toward the top of each distribution indicate the %GC content for the respective protein domain (transferred form) for the FAM7 GNATs (a), INVs (b) and CMs (c). Dots are included for the donor bacterial genes as reference. Tails on each distribution correspond to the upper and lower limits of two-tailed 95 % confidence intervals. All raw data are provided in Additional files 8 and 9