Genome evolution in cyanobacteria: the stable core and the variable shell

Abstract

Cyanobacteria are the only known prokaryotes capable of oxygenic photosynthesis, the evolution of which transformed the biology and geochemistry of Earth. The rapid increase in published genomic sequences of cyanobacteria provides the first opportunity to reconstruct events in the evolution of oxygenic photosynthesis on the scale of entire genomes. Here, we demonstrate the overall phylogenetic incongruence among 682 orthologous protein families from 13 genomes of cyanobacteria. However, using principal coordinates analysis, we discovered a core set of 323 genes with similar evolutionary trajectories. The core set is highly conserved in amino acid sequence and contains genes encoding the major components in the photosynthetic and ribosomal apparatus. Many of the key proteins are encoded by genome-wide conserved small gene clusters, which often are indicative of protein-protein, protein-prosthetic group, and protein-lipid interactions. We propose that the macromolecular interactions in complex protein structures and metabolic pathways retard the tempo of evolution of the core genes and hence exert a selection pressure that restricts piecemeal horizontal gene transfer of components of the core. Identification of the core establishes a foundation for reconstructing robust organismal phylogeny in genome space. Our phylogenetic trees constructed from 16S rRNA gene sequences, concatenated orthologous proteins, and the core gene set all suggest that the ancestral cyanobacterium did not fix nitrogen and probably was a thermophilic organism.

Fig. 1.

Distribution of tree topologies among 682 sets of orthologs. Both NJ (black bars) and ML (red bars) tree topologies give similar distribution patterns. There is no unanimous support for a single topology; rather, most of the orthologs (58% and 67% for NJ and ML trees, respectively) appear as singletons that associate with unique topologies.

Fig. 2.

Representative backbone tree topologies. Phylogenetic trees were constructed by using both 16S rRNA gene and orthologous proteins through phylogenomic approaches (see Materials and Methods for details). Phylogenetic tree construction methods are highlighted with colored horizontal bars and text. Conserved monophyletic subgroups are shaded. Row one shows the proportion of orthologs giving a particular tree topology (NJ, black bar; ML, red bar). Also shown are examples of proteins corresponding to that topology. Row five indicates number of datasets accepting (Left) or rejecting (Right) a particular topology in a Shimodaira–Hasegawa (SH) (55) test (SI Fig. 7). Row six shows the evaluation of the five backbone topologies, using the concatenated 323-core-gene set (Fig. 3) through Kishino–Hasegawa (72) (Left), SH (55) (Center), and expected likelihood weight (73) (Right) tests, which infer a confidence tree set. ANA, Anabaena sp. PCC7120; AVA, Anabaena variabilis ATCC29413; CWA, Crocosphaera watsonii WH8501; GVI, G. violaceus PCC7421; NPU, N. punctiforme ATCC29133; PMM, P. marinus MED4; PMT, P. marinus MIT9313; PMS, P. marinus SS120; SCO, S. elongatus PCC7942; SYW, Synechococcus sp. WH8102; SYN, Synechocystis sp. PCC6803; TEL, T. elongatus BP-1; TER, Trichodesmium erythraeum IMS101.

Fig. 3.

PCoA of trees compared with topological distance. (A) Plot of the two first axes of the PCoA made from 628 ML trees. The other 54 genes are excluded as a result of axis demarcation. The same experiment with NJ trees gave very similar results. The ellipse depicts 323 orthologs in the densest region (the core) of the cloud that share a common phylogenetic signal, whereas trees present in the marginal area (the shell) are much more likely to be perturbed by horizontal transfers. Photosynthetic genes are color coded based on their respective pathways. Also shown are examples of conserved clusters of ribosomal (red text) and photosynthetic (green text) genes that are present in the core. (B) The PCoA plotted against the protein variability. Protein variability was measured by taking the total length of a corresponding tree as measured by total amino acid substitutions per site, divided by the number of sequences in the tree (48). The legend is the same except that photosynthetic genes are collectively designated as green dots.

Fig. 4.

Frequency distribution of genes belonging to designated categories within each 1.0 interval of protein variability. Protein variability was measured according to Rujan and Martin's method (48). Dashed lines denote the threshold that segregates the predominance of distribution of genes in different categories.

Fig. 5.

Phylogenetic tree reconstructed based on the concatenation of the 323 core proteins. The topology shown agrees with the consensus topology of the 682 orthologs (T3 in Fig. 2) and is supported by almost all individual datasets (Fig. 2 and SI Fig. 7). Bootstrap probabilities estimated by NJ-Γ/QP/ProtML with 1,000 replications are shown for each internal branch. The scale bar refers to the number of amino acid substitutions per site. The dashed line designates the split between diazotrophic and nondiazotrophic taxa.