The Smallest Known Genomes of Multicellular and Toxic Cyanobacteria: Comparison, Minimal Gene Sets for Linked Traits and the Evolutionary Implications

Abstract

Cyanobacterial morphology is diverse, ranging from unicellular spheres or rods to multicellular structures such as colonies and filaments. Multicellular species represent an evolutionary strategy to differentiate and compartmentalize certain metabolic functions for reproduction and nitrogen (N2) fixation into specialized cell types (e.g. akinetes, heterocysts and diazocytes). Only a few filamentous, differentiated cyanobacterial species, with genome sizes over 5 Mb, have been sequenced. We sequenced the genomes of two strains of closely related filamentous cyanobacterial species to yield further insights into the molecular basis of the traits of N2 fixation, filament formation and cell differentiation. Cylindrospermopsis raciborskii CS-505 is a cylindrospermopsin-producing strain from Australia, whereas Raphidiopsis brookii D9 from Brazil synthesizes neurotoxins associated with paralytic shellfish poisoning (PSP). Despite their different morphology, toxin composition and disjunct geographical distribution, these strains form a monophyletic group. With genome sizes of approximately 3.9 (CS-505) and 3.2 (D9) Mb, these are the smallest genomes described for free-living filamentous cyanobacteria. We observed remarkable gene order conservation (synteny) between these genomes despite the difference in repetitive element content, which accounts for most of the genome size difference between them. We show here that the strains share a specific set of 2539 genes with >90% average nucleotide identity. The fact that the CS-505 and D9 genomes are small and streamlined compared to those of other filamentous cyanobacterial species and the lack of the ability for heterocyst formation in strain D9 allowed us to define a core set of genes responsible for each trait in filamentous species. We presume that in strain D9 the ability to form proper heterocysts was secondarily lost together with N2 fixation capacity. Further comparisons to all available cyanobacterial genomes covering almost the entire evolutionary branch revealed a common minimal gene set for each of these cyanobacterial traits.

Molecular separation of two long taxonomically debated cyanobacterial genera Cylindrospermopsis and Raphidiopsis (Nostocales) based on the ITS-L phylogeny

“…This phenomenon may be explained by strain Raphidiopsis brookii D9, which has only 39 of the 55 heterocyte-related genes found in strain Cylindrospermopsis raciborskii CS 505 after genomic comparison by Stucken et al (2010). The amplification of the nifH gene that codes for nitrogenase reductase has not been successfully implemented in any of Raphidiopsis strains (Gugger et al, 2005;Stucken et al, 2010;Wu et al, 2011). The same results were also obtained in the present study, that the 16 Chinese Raphidiopsis strains failed to amplify the nifH gene (Fig.…”

“…The taxonomical validity of the genus Raphidiopsis had been questioned in recent studies (Komà rkova et al, 1999). According to Wu et al (2011), Stucken et al (2010, and Moustaka-Gouni et al (2009), these two genera, Cylindrospermopsis and Raphidiopsis, are congeneric. They based this claim mainly on the following aspects.…”

“…They are phylogenetically intermixed, and both of them can be grouped into two or more clusters, indicating that the two genera are polyphyletic in evolutionary origin (Wu et al, 2011). Second, a genomic comparison showed that strain Cylindrospermopsis raciborskii CS-505 and strain Raphidiopsis brookii D9 share a set of 2539 genes, with an average sequence identity greater than 90% (Stucken et al, 2010).…”

“…Additionally, Gugger et al (2005) and Li et al (2008) found that Raphidiopsis strains turn from green to yellow within a week and are unable to survive in nitrogen-free media, indicating that they cannot form heterocysts to fix nitrogen. This phenomenon may be explained by strain Raphidiopsis brookii D9, which has only 39 of the 55 heterocyte-related genes found in strain Cylindrospermopsis raciborskii CS 505 after genomic comparison by Stucken et al (2010). The amplification of the nifH gene that codes for nitrogenase reductase has not been successfully implemented in any of Raphidiopsis strains (Gugger et al, 2005;Stucken et al, 2010;Wu et al, 2011).…”

“…Moreover, inferring from the phylogenetic analysis of seven concatenated gene loci sequences, namely, psbA, 16S rDNA, rbcL, rbcS, rpoC1, cpcB, and ITS1 that contain no tRNAs (i.e., internal transcribed spacer between 16S and 23S rDNA), Wu et al (2011) found that Cylindrospermopsis and Raphidiopsis strains are intermixed and grouped into a large cluster. Through a genomic comparison between Cylindrospermopsis raciborskii strain CS-505 and Raphidiopsis brookii strain D9, Stucken et al (2010) found that these two share a set of 2539 genes, with an average sequence identity greater than 90%. The authors suggested that these two genera, Cylindrospermopsis and Raphidiopsis, are congeneric.…”