Comparative genomics of Cylindrospermopsis raciborskii strains with differential toxicities

Abstract

BackgroundCylindrospermopsis raciborskii is an invasive filamentous freshwater cyanobacterium, some strains of which produce toxins. Sporadic toxicity may be the result of gene deletion events, the horizontal transfer of toxin biosynthesis gene clusters, or other genomic variables, yet the evolutionary drivers for cyanotoxin production remain a mystery. Through examining the genomes of toxic and non-toxic strains of C. raciborskii, we hoped to gain a better understanding of the degree of similarity between these strains of common geographical origin, and what the primary differences between these strains might be. Additionally, we hoped to ascertain why some cyanobacteria possess the cylindrospermopsin biosynthesis (cyr) gene cluster and produce toxin, while others do not. It has been hypothesised that toxicity or lack thereof might confer a selective advantage to cyanobacteria under certain environmental conditions.ResultsIn order to examine the fundamental differences between toxic and non-toxic C. raciborskii strains, we sequenced the genomes of two closely related isolates, CS-506 (CYN+) and CS-509 (CYN-) sourced from different lakes in tropical Queensland, Australia. These genomes were then compared to a third (reference) genome from C. raciborskii CS-505 (CYN+). Genome sizes were similar across all three strains and their G + C contents were almost identical. At least 2,767 genes were shared among all three strains, including the taxonomically important rpoc1, ssuRNA, lsuRNA, cpcA, cpcB, nifB and nifH, which exhibited 99.8-100% nucleotide identity. Strains CS-506 and CS-509 contained at least 176 and 101 strain-specific (or non-homologous) genes, respectively, most of which were associated with DNA repair and modification, nutrient uptake and transport, or adaptive measures such as osmoregulation. However, the only significant genetic difference observed between the two strains was the presence or absence of the cylindrospermopsin biosynthesis gene cluster. Interestingly, we also identified a cryptic secondary metabolite gene cluster in strain CS-509 (CYN-) and a second cryptic cluster common to CS-509 and the reference strain, CS-505 (CYN+).ConclusionsOur results confirm that the most important factor contributing to toxicity in C. raciborskii is the presence or absence of the cyr gene cluster. We did not identify any other distally encoded genes or gene clusters that correlate with CYN production. The fact that the additional genomic differences between toxic and non-toxic strains were primarily associated with stress and adaptation genes suggests that CYN production may be linked to these physiological processes.

Trichodesmium genome maintains abundant, widespread noncoding DNA in situ, despite oligotrophic lifestyle

“…do not have the conventionally defined streamlined genomes seen in other marine taxa (40,42,(45)(46)(47). Similar to IMS101, these genomes are enriched in predicted insertion sequences, repeats, and regulatory proteins (41,48,49), yet despite this fact still retain much larger coding percentages (≥80%) than Trichodesmium. Until now, the low gene density and large intergenic spacers have only been observed in the genome of IMS101 that has been maintained in culture for approximately two decades.…”

Microbial communities reflect temporal changes in cyanobacterial composition in a shallow ephemeral freshwater lake

“…There is an evident difficulty in correlating many environmental parameters with cyanobacterial community composition, toxicity or toxigenicity across such studies (Rinta-Kanto et al, 2009;Al-Tebrineh et al, 2011;Otten et al, 2012;Lee et al, 2014;Ngwa et al, 2014). In part, this lack of correlation can be attributed to genomic variability among closely related strains (Humbert et al, 2013;Sinha et al, 2014), giving rise to differing growth optima and potential to produce a myriad of toxic and non-toxic metabolites (Humbert et al, 2013), changes in the genome copy number throughout the growth phase (Griese et al, 2011) and uncertainty regarding the control of regulatory systems that direct the expression of toxic metabolites (Kaebernick et al, 2000;Alexova et al, 2011;Carneiro et al, 2013;Neilan et al, 2013;Rzymski and Poniedziałek, 2014;Makower et al, 2015).…”

Constitutive Cylindrospermopsin Pool Size in Cylindrospermopsis raciborskii under Different Light and CO 2 Partial Pressure Conditions

“…The CYN biosynthesis gene cluster (cyr), which has been elucidated in C. raciborskii strains AWT205 (11), CS505 (12), and CS506 (13), is comprised of 15 open reading frames, spanning a total of 43 kb, and is flanked by hyp (hydrogenase pleitrophy) genes which are thought to be under the control of the global nitrogen regulator gene ntcA (11). These studies, therefore, have provided evidence that CYN pool size may be linked to one or more environmental drivers.…”