A tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa

Abstract

Microcystis aeruginosa is one of the most common bloom-forming cyanobacteria in freshwater ecosystems worldwide. This species produces numerous secondary metabolites, including microcystins, which are harmful to human health. We sequenced the genomes of ten strains of M. aeruginosa in order to explore the genomic basis of their ability to occupy varied environments and proliferate. Our findings show that M. aeruginosa genomes are characterized by having a large open pangenome, and that each genome contains similar proportions of core and flexible genes. By comparing the GC content of each gene to the mean value of the whole genome, we estimated that in each genome, around 11% of the genes seem to result from recent horizontal gene transfer events. Moreover, several large gene clusters resulting from HGT (up to 19 kb) have been found, illustrating the ability of this species to integrate such large DNA molecules. It appeared also that all M. aeruginosa displays a large genomic plasticity, which is characterized by a high proportion of repeat sequences and by low synteny values between the strains. Finally, we identified 13 secondary metabolite gene clusters, including three new putative clusters. When comparing the genomes of Microcystis and Prochlorococcus, one of the dominant picocyanobacteria living in marine ecosystems, our findings show that they are characterized by having almost opposite evolutionary strategies, both of which have led to ecological success in their respective environments.

Figure 1. Estimation of the sizes of the pangenome (A) and core genome (B) of Microcystis aeruginosa from the twelve Microcystis aeruginosa genomes (including the two previously-available genomes of PCC 7806 and NIES-843). The upper and lower edges of the boxes indicate the first quartile and third quartile, respectively, of all different input orders (1000) of the genomes. The central horizontal line indicates the sample median (50th percentile). The central vertical lines extend above and below each box as far as the data extend, to a distance of at most 1.5 times the interquartile range.

Figure 2. Distribution of the core and flexible genes from all the Microcystis genomes in the Clusters of Orthologous Groups (COGs).

Only the COG categories containing >1% of the genes in at least one of the two core genomes, are shown in the figure. The functional classifications of the COGs are: Cellular process and signaling: (D) Cell cycle control, cell division, chromosome partitioning; (M) Cell wall/membrane/envelope biogenesis; (N) Cell motility (O) Post-translational modification, protein turnover, and chaperones; (T) Signal transduction mechanisms; (U) Intracellular trafficking, secretion, and vesicular transport; (V) Defense mechanisms; (W) Extracellular structures; (Y) Nuclear structure; (Z) Cytoskeleton. Information storage and processing: (J) Translation, ribosomal structure and biogenesis; (K) Transcription; (L) Replication, recombination and repair. Metabolism: (C) Energy production and conversion; (E) Amino acid transport and metabolism; (F) Nucleotide transport and metabolism; (G) Carbohydrate transport and metabolism; (H) Coenzyme transport and metabolism; (I) Lipid transport and metabolism; (P) Inorganic ion transport and metabolism; (Q) Secondary metabolites biosynthesis, transport, and catabolism. Poorly characterized: (R) General function prediction only; (S) Function unknown.

Figure 3. Phylogenetic relationships (Maximum likelihood method) between the twelve Microcystis aeruginosa genomes (including the two previously-available genomes of PCC 7806 and NIES-843).

A. Phylogeny based on the alignment of seven housekeeping genes (ftsZ, glnA, gltX, gyrB, pgi, recA and tpi; 217 informative sites). B. Phylogeny based on the alignment of 1989 genes belonging to the core genome (SC = Subclade ; 144276 informative sites).

Figure 4. Proportions of repeated sequences according to the size of the genomes in the ten new Microcystis aeruginosa genomes (black diamonds), the two previously-available genomes (PCC 7806 and NIES-843) (gray diamonds) and other cyanobacterial genomes (Prochlorococcus AS9601 (number 1 in the figure) & MIT 9301 (2); Oscillatoria PCC 6506 (16); Nostoc ATCC 29133/PCC 73102 (18) & PCC 7120 (15); Synechococcus PCC 6301 (4), JA-2-3B (7); JA-3-3ab (5); PCC 7002 (5) & CC 9311 (3); Synechocystis PCC 6803 (8), Trichodesmium IMS 101 (17); Anabaena ATCC 29413 (14); Cyanothece PCC 7424 (13), PCC 7425 (12), PCC 8801 (9) & PCC 8802 (11); Gloeobacter PCC 7421 (10); white diamonds).

Figure 5. Proportions of genes displaying a ±20% difference in their GC content, compared to the mean GC content of their whole genome in the twelve Microcystis aeruginosa genomes (including the two previously-available genomes of PCC 7806 and NIES-843) and in other cyanobacterial genomes.

Figure 6. Schematic representation of all the secondary metabolite gene clusters found in the twelve Microcystis aeruginosa genomes (including the two previously-available genomes of PCC 7806 and NIES-843).

For each biosynthesis cluster, the sketch corresponds to the gene cluster present in the reference strain genome, its size in kb and the amino acid sequence identity estimated for the orthologous region in the other Microcystis genomes. The reference strain genome corresponds to the one indicated in Table 2.