Chloroplasts arose from cyanobacteria, mitochondria arose from proteobacteria. Both organelles have conserved their prokaryotic biochemistry, but their genomes are reduced, and most organelle proteins are encoded in the nucleus. Endosymbiotic theory posits that bacterial genes in eukaryotic genomes entered the eukaryotic lineage via organelle ancestors. It predicts episodic influx of prokaryotic genes into the eukaryotic lineage, with acquisition corresponding to endosymbiotic events. Eukaryotic genome sequences, however, increasingly implicate lateral gene transfer, both from prokaryotes to eukaryotes and among eukaryotes, as a source of gene content variation in eukaryotic genomes, which predicts continuous, lineage-specific acquisition of prokaryotic genes in divergent eukaryotic groups. Here we discriminate between these two alternatives by clustering and phylogenetic analysis of eukaryotic gene families having prokaryotic homologues. Our results indicate (1) that gene transfer from bacteria to eukaryotes is episodic, as revealed by gene distributions, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria; (2) that gene inheritance in eukaryotes is vertical, as revealed by extensive topological comparison, sparse gene distributions stemming from differential loss; and (3) that continuous, lineage-specific lateral gene transfer, although it sometimes occurs, does not contribute to long-term gene content evolution in eukaryotic genomes.
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We thank the following funding agencies: the European Research Council grants 232975, 666053 (W.F.M.) and 281357 (G.L.; to T. Dagan); the Templeton Foundation grant 48177 (J.O.M.); the Open University of Israel Research Fund (E.H.-C.); the German-Israeli Foundation grant I-1321-203.13/2015 (E.H.-C., W.F.M.), the New Zealand BioProtection CoRE (P.J.L.); the German Academic Exchange Service PhD stipend 57076385 (C.K.); an Alexander von Humboldt Foundation fellowship (D.B.). Computational support of the Zentrum für Informations- und Medientechnologie at the Heinrich-Heine University is acknowledged.
The authors declare no competing financial interests.
Extended data figures and tables
a, Distribution of ESCs. Each black tick indicates the presence of a cluster in a taxon. The 26,117 ESCs (x axis) from 55 eukaryotic genomes (Supplementary Table 1) are sorted according to their distribution across the six eukaryotic supergroups. b, Distribution of taxa in EPCs and monophyly of eukaryotes. Each black tick indicates the presence of a cluster in a taxon. The 2,585 EPCs (x axis) are separated into three sets according to the monophyly of eukaryotes and the results of the AUT and, within each set, are ordered according to their distribution across the six eukaryotic supergroups. Clusters where eukaryotes were resolved as non-monophyletic in the maximum likelihood tree tend to occur more frequently in bacterial taxa. Archaep., Archaeplastida; Opisth., Opisthokonta; Chl., Chloroplastida; Rho., Rhodophyta; Gla., Glaucophyta; Str., Stramenopila; De., Deinococcus-Thermus; oP., other Proteobacteria; Ch., Chlamydiae; Pl., Planctomycetes; Ve., Verrucomicrobia; Spi., Spirochaetae; The., Thermotogae; oB., other Bacteria. For abbreviations of eukaryotes, see Supplementary Table 1.
a, b, Monophyly of eukaryotes in maximum likelihood trees, cluster size, and alignment quality. Cumulative frequency of clusters with different cluster size (a) or different HoT72 column scores (b) is plotted for three sets of EPCs that differ in terms of the monophyly of eukaryotes in the maximum likelihood trees (monophyletic: resolved as monophyletic in the original tree; passed AUT: resolved as non-monophyletic in the original tree, but at least one alternative tree with eukaryote monophyly (see Methods) was as likely at P = 0.05 in an AUT; failed AUT: alternative trees were not as likely as the original tree where eukaryotes were resolved as non-monophyletic). One-sided Kolmogorov–Smirnov two-sample goodness-of-fit test (cluster size/HoT column scores): monophyletic versus passed AUT, 1.04 × 10−13/7.9 × 10−3; monophyletic versus failed AUT, 1.45 × 10−61/2.04 × 10−10; passed AUT versus failed AUT, 3.40 × 10−13/4.00 × 10−3. c, d, Prokaryotic monophyly and gene sharing. c, Proportion of trees showing monophyly for taxonomic group. Prokaryotic phyla and classes (Supplementary Tables 3 and 4) that are monophyletic in the reference trees and that have at least five taxa (genomes in archaea or species in bacteria) are plotted according to the number of taxa and the proportion of EPC trees with at least two sequences from a prokaryotic group where it forms a monophyletic group. The proportion of eukaryote monophyly trees is higher than that of any prokaryotic group, including those with many fewer taxa. d, Gene sharing between a prokaryotic group and other prokaryotes. Using the same procedure for the generation of EPCs, 55 genomes were randomly sampled from a group of bacteria and the number of clusters (EPCs) they shared with prokaryotes not from this group was counted. The average number of shared clusters was mapped for each taxonomic group with 55–150 genomes (error bar, s.d.; number of genomes in parentheses). For E. coli and the eukaryotes (shown for comparison), there was only one sample. Colour coding for taxonomic levels: red, phylum; blue, class; green, order; magenta, family; cyan, genus; orange, species.
After ten sequences (bold) were added to the original data set (EPC E1689_B206_A295), the relationships among Archaeplastida taxa (highlighted in green) changed from non-monophyly (a) to monophyly (b). Abbreviations are shown for eukaryotic sequences (Supplementary Table 2) and NCBI GI numbers for cyanobacterial sequences (Supplementary Table 3; RefSeq accessions are shown for the added sequences).
Extended Data Figure 4 Distribution of prokaryotic taxa in the sister group to eukaryotes, with EPCs sorted by eukaryotic supergroups.
Top: each black tick indicates the presence of a eukaryote taxon in one of the 2,585 EPCs. Bottom: each red tick indicates the presence of a prokaryote taxon in the sister group to eukaryotes in one of the 1,933 EPC maximum likelihood trees where eukaryotes were resolved to be monophyletic. The 2,585 EPCs, proteome size, and cluster size are as in Fig. 1. The number of EPCs present and the frequency of occurrence in the sister group to eukaryotes (‘clusters’) are shown for eukaryotes and prokaryotes, respectively. Archaep., Archaeplastida; Opisth., Opisthokonta; Chl., Chloroplastida; Rho., Rhodophyta; Gla., Glaucophyta; Str., Stramenopila; De., Deinococcus-Thermus; oP., other Proteobacteria; Ch., Chlamydiae; Pl., Planctomycetes; Ve., Verrucomicrobia; Spi., Spirochaetae; The., Thermotogae; oB., other Bacteria. For abbreviations of eukaryotes, see Supplementary Table 1.
Extended Data Figure 5 Distribution of prokaryotic taxa in the sister group to eukaryotes, with EPCs sorted by prokaryotic groups.
Top: each black tick indicates the presence of a eukaryote taxon in one of the 1,933 EPC maximum likelihood trees where eukaryotes were resolved to be monophyletic. Bottom: each red tick indicates the presence of a prokaryote taxon in the sister group to eukaryotes in one of those 1,933 EPC trees. The EPCs (x axis) are ordered according to the taxonomic groups to which the prokaryotes in the sister group to eukaryotes belong (separated into three blocks where only bacteria (1,586 EPCs), only archaea (314 EPCs), or both bacteria and archaea (33 EPCs) are found in the sister group). There are 16 bacterial groups (including ‘other Bacteria’; Firmicutes, Proteobacteria, and the PVC superphylum (Planctomycetes, Verrucomicrobia, and Chlamydiae) are regarded as single groups) and five archaeal groups (the five phyla). The number of EPCs present and the frequency of occurrence in the sister group to eukaryotes are shown for eukaryotes and prokaryotes, respectively. Archaep., Archaeplastida; Opisth., Opisthokonta; Chl., Chloroplastida; Rho., Rhodophyta; Gla., Glaucophyta; Str., Stramenopila; De., Deinococcus-Thermus; oP., other Proteobacteria; Ch., Chlamydiae; Pl., Planctomycetes; Ve., Verrucomicrobia; Spi., Spirochaetae; The., Thermotogae; oB., other Bacteria. For abbreviations of eukaryotes, see Supplementary Table 1.
Extended Data Figure 6 Distribution of taxa in the sister groups consisting purely of cyanobacteria, alphaproteobacteria, or archaea.
Each black tick indicates the presence of a prokaryotic taxon in the sister group to eukaryotes in an EPC tree. a–c, Distributions of taxa in all pure-cyanobacterial (a), pure-alphaproteobacterial (b), and pure-archaeal (c) sister groups. The clusters are ordered alphanumerically according to the eukaryotic cluster numbers (Supplementary Table 5), whereas for archaea (c) the taxa are further sorted by the five archaeal phyla.
Extended Data Figure 7 Comparison of sets of trees for single-copy genes in eukaryotic groups, with more inclusive criteria.
a–f,Cumulative distribution functions (y axis) for scores of minimal tree compatibility with the vertical reference data set (x axis). Values are number of species, sample sizes, and P values of the two-tailed Kolmogorov–Smirnov two-sample goodness-of-fit test in the comparison of the ESC (blue) data sets against the EPC (green) data set and a synthetic data set simulating one LGT (red). Dashed lines delineate the range of distributions in 100 replicates of random down-sampling. The criteria for tree inclusion were less stringent than those for Fig. 3 (see Methods).
a, Eukaryotic evolution by gene loss. Genome sizes (number of EPCs present) were mapped onto the eukaryotic reference tree. Ancestral genome size in each eukaryotic ancestral node was calculated using a loss-only model, with all EPCs in blocks A–C and those in blocks D and E (Fig. 1) entering the eukaryotic lineage via the plastid ancestor (green) or the eukaryote ancestor (wheat colour). Plastid-derived genes are not shown for the ancestral nodes within SAR and Hacrobia, because of current debates about the number and nature of secondary symbioses, but are indicated by the greenish shading. b, Endosymbiotic gene transfer network. The network connecting apparent gene donors to the common ancestor of eukaryotes and Archaeplastida is mapped onto the reference phylogeny (vertical edges) of bacteria (left), eukaryotes (middle), and archaea (right). Grey shading (white to black) in the prokaryote reference trees (70 for archaea and 32 for bacteria) indicates how often a branch associated with a particular node was recovered within the trees of individual genes that were concatenated for inferring the reference topology. Lateral edges indicate gene influx at the origin of eukaryotes and at the origin of plastids. Edge colour corresponds to the frequencies with which a prokaryotic group appears in the sister group to eukaryotes. The archaeal reference tree was rooted between euryarchaeotes and other taxa, and the bacterial tree with Thermotogae. Secondary endosymbiotic transfers are indicated in light green and red. That members of both the Crenarchaeota and the Euryarcheaota are implicated as host relatives is probably because of the small archaeon sample34,35,36.
a, Patterns suggestive of LGT from prokaryotes inferred from EPC trees. All EPC trees were searched for phylogenetic patterns suggestive of gene acquisitions by the common ancestor of each eukaryote lineage within the six supergroups (see Methods). The size of each circle is proportional to the number of such putative acquisitions, with the total number of putative acquisitions shown for each supergroup. The colour shows the age of nodes according to a eukaryotic time tree (blue, younger than 800 million years; red, older than 800 million years). For the four lineages with an asterisk, phylogenetic patterns where SAR/Hacrobia are nested within a clade formed by Archaeplastida were also counted as putative acquisitions to take into account secondary plastid endosymbioses. The numbers of acquisitions without such patterns are indicated in parentheses (and shown as inner circles). b, Eukaryote–prokaryote sequence identities for genes apparently acquired more recently and more anciently in eukaryotes (a). The mean of the average pairwise identities is shown in parentheses. At P = 0.05, a two-sided Wilcoxon rank-sum test either did not reject the null hypotheses that the two sets of genes are not different or suggested the tip-specific eukaryotic genes are less similar to their prokaryotic homologues.
Different thresholds were applied to find eukaryote clusters with prokaryote homologues, including BLAST local identity for each eukaryote–prokaryote hit (30% or 20%) and levels of best-hit correspondence (10–50%) for identifying reciprocal pairs of eukaryote and prokaryote clusters. Distributions of ESCs and EPCs are drawn as in Extended Data Fig. 1a and Fig. 1, respectively.
List of 55 eukaryote genomes organized by six eukaryotic supergroups, sources of genome sequences, 28,702 eukaryotic protein clusters with at least two sequences and maximum-likelihood trees of eukaryote-specific clusters (ESCs) with at least four sequences. (XLSX 4107 kb)
List of 956,053 eukaryotic protein sequences in the sequence abbreviations used in this study and the original headers in the downloaded files. (XLSX 28596 kb)
List of 1,847 bacterial genomes, their taxonomical groupings and 102,089 clusters with at least five sequences, as well as a maximum likelihood reference tree based on 32 nearly universal single-copy genes. (XLSX 22467 kb)
List of 134 archaeal genomes, their taxonomical groupings and 11,992 clusters with at least five sequences. (XLSX 1303 kb)
List of 2,585 eukaryote-prokaryote clusters (EPCs). (XLSX 5328 kb)
Annotations of the functions of the 28,702 eukaryotic clusters and eukaryote monophyly in EPC trees. (XLSX 1659 kb)
Maximum-likelihood trees with at least four sequences reconstructed from eukaryote-prokaryote clusters (EPCs). (TXT 28189 kb)
Frequency of occurrence of prokaryotic taxa in the sister group to eukaryotes and a two-sided Wilcoxon signed rank test comparing the original frequencies and those after randomizations. (XLSX 68 kb)
BLAST analysis of bacterial, mitochondrial and plastid genomes against the nuclear genomes. (PDF 100 kb)
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Ku, C., Nelson-Sathi, S., Roettger, M. et al. Endosymbiotic origin and differential loss of eukaryotic genes. Nature 524, 427–432 (2015). https://doi.org/10.1038/nature14963
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