Fig 1.
The NADK genes of extant eukaryotes originate from two ancient eukaryotic sister clades of uncertain provenance.
Shown is a phylogenetic tree computed by Bayesian inference of NADK genes from the Bacteria (top clades), Eukarya (middle two clades labeled “mito” and cyto”), and the Archaea (bottom gold clade). Most animals (blue clade), plants (green clade), and a few other protist groups (labeled) have genes from both the mito and cyto subclades. Plants have genes from two cyto-subclades, one of which corresponds to the plant plastid-specific NADK2 gene. The asterisked labels “MITOCHONDRIAL”, “CYTOSOLIC”, “STROMAL (CHLOROPLAST)” and others indicate lineages with specific experimental data on protein subcellular localization (see text). Node supports in this tree and all other trees represent posterior probabilities. Asterisks indicate sequences from species classified as Firmicutes but which we suspect are lateral gene transfers or misclassifications (also see S1 Fig).
Table 1.
Episodic NADK duplications associated with clade-defining evolutionary transitions.
Rows are ordered from highest to lowest clade levels. Gene duplications identified in a single species are not shown here.
Fig 2.
Fungi and Chlorophytes have lost mito-clade NADK genes while independently duplicating a cyto-clade gene.
Plants (embryophytes), charophytes, and chlorophytes are each depicted with green icons, while Holomycota (fungi + Fonticula alba) and amoebozoans are each depicted with purplish pink icons. A pair each of the fungal groups of ascomycetes, basidiomycetes, and chytridiomycetes were chosen to represent the fungi. The extra cyto-clades for Holomycota + Amoebozoa and for chlorophytes are highlighted in yellow and are found at the bottom of the eukaryotic cyto-subclade.
Fig 3.
Many eukaryotic protists do not possess the mito-clade NADK gene of plants and animals.
Unlike fungi, amoebozoans, and chlorophytes, all of which have additional NADK cyto-clade genes while missing a mito-clade NADK gene, many eukaryotic protist lineages that are also missing mito-clade NADK genes possess NADK cyto-clade genes that are only recently duplicated, if at all.
Fig 4.
An ancient duplication of NADK characterizes Nematoda.
All nematodes have missing cyto-clade genes, which was lost in connection with a duplication of the ancestral nematode mito-clade gene. Shown is a phylogenetic tree of NADK genes from 11 different nematode genera (highlighted in yellow) that have the ancient nematode duplication of its mito-clade gene into an “nmito” paralog, which encodes an enzyme localized to the mitochondrion in C. elegans, and an “m2c” paralog, which no longer localizes to the mitochondria in C. elegans.
Fig 5.
A fractal-like evolutionary pattern characterizes NADK evolution in the nematode phylum.
Shown is a phylogenetic tree of the nematode mito clade with additional nematode genera that display more recent duplications such as the clade IVb (purplish lineages) in the m2c-subclade and Diploscapter genes in the nmito-subclade of clade V nematodes. Other lineages, such as clade I nematodes appear to have only one identifiable gene within one of the two nematode subclades.
Fig 6.
Rarely, eukaryotic lineages replaced mito NADK genes with horizontal transfer of α-proteobacterial nadK.
Choanoflagellates, euglenozoans, and the cnidarian Stylophora pistillata eukaryotic mito-clade NADK genes while also possessing nadk genes apparently acquired from different lineages of α-proteobacteria. These apparent cases of HGT thus appear to be “α2m” replacements of mito-type NADK.
Fig 7.
A bacterial duplication of nadK in the Firmicutes class of Bacilli.
Identification of a duplication of nadK into ppnKA and ppnKB in the occurred after the Bacilli class split with its sister class of Clostridia. The Bacilli class of Firmicutes corresponds to aerobic endospore formers while the Clostridia class corresponds to anaerobic endospore formers. See S1 Fig for a more complete tree that includes the independent duplications in Actinobacteria and Eukaryotes.