Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

Abstract

The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a great breadth of morphologies and ecologies; they play key roles in global carbon and nitrogen cycles. The chloroplasts of all photosynthetic eukaryotes can trace their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest as platforms for "green" biotechnology and biofuels. To explore the molecular basis of their different phenotypes and biochemical capabilities, we sequenced the genomes of 54 phylogenetically and phenotypically diverse cyanobacterial strains. Comparison of cyanobacterial genomes reveals the molecular basis for many aspects of cyanobacterial ecophysiological diversity, as well as the convergence of complex morphologies without the acquisition of novel proteins. This phylum-wide study highlights the benefits of diversity-driven genome sequencing, identifying more than 21,000 cyanobacterial proteins with no detectable similarity to known proteins, and foregrounds the diversity of light-harvesting proteins and gene clusters for secondary metabolite biosynthesis. Additionally, our results provide insight into the distribution of genes of cyanobacterial origin in eukaryotic nuclear genomes. Moreover, this study doubles both the amount and the phylogenetic diversity of cyanobacterial genome sequence data. Given the exponentially growing number of sequenced genomes, this diversity-driven study demonstrates the perspective gained by comparing disparate yet related genomes in a phylum-wide context and the insights that are gained from it.

Fig. 1.

Cyanobacterial species tree and the distribution of secondary metabolite biosynthesis. (A) Maximum-likelihood phylogeny of cyanobacteria included in this study (outgroup shown in SI Appendix, Fig. S1). Branches are color coded according to morphological subsection. Taxa names in red are genomes sequenced in this study. Nodes supported with a bootstrap of ≥70% are indicated by a black dot. Morphological transitions that were investigated are denoted by blue triangles, annotated by events 1–8. Phylogenetic subclades are grouped into seven major subclades (A–G), some of which are made up of smaller subgroups. SI Appendix, Table S1 provides reference information for genomes used in this analysis. (B) Distribution of the nonribosomal peptide and polyketide gene clusters.

Fig. 2.

Implications on plastid evolution. (A) Maximum-likelihood phylogenetic tree of plastids and cyanobacteria, grouped by subclades (Fig. 1). The red dot (bootstrap support = 97%) represents the primary endosymbiosis event that gave rise to the Archaeplastida lineage, made up of Glaucophytes (orange), Rhodophytes (red), Viridiplantae (green), and Chromaleveolates (brown). The independent primary endosymbiosis in the amoeba Paulinella chromatophora is shown in purple. (B) Number of predicted eukaryotic, nuclear genes transferred from a cyanobacterial endosymbiont. Colors correspond to the lineage organisms as above. Light and dark shades of colors represent before and after adding the CyanoGEBA genomes, respectively.

Fig. 3.

Increased sequence coverage reveals distinct and highly supported subclades of putative CBPs. (A) Unrooted maximum-likelihood tree of CBP sequences. Putative CBP clades that have emerged as distinct and phylogenetically well supported are labeled in red, and previously described CBP clades are labeled in black. CP43 protein sequences (encoded by the PsbC gene) are provided as an outgroup. (B) Cartoon representation of unique domain architecture of CBPV from Chroococcidiopsis thermalis PCC 7203 (Chro_2988), based on the two separate homology models of (i) the N-terminal CBP domain (red) and (ii) the C-terminal PsaL-like domain (yellow). Potentially chlorophyll-binding histidine residues are shown in green sticks. (C) Gene cluster containing multiple CBP genes from Anabaena cylindrica PCC 7122 (locus tags labeled above, annotations labeled below).