School of Biotechnology and Bimolecular Sciences, University of New South Wales, 2052 Sydney, NSW, Australia.
BMC Genomics. 2014 Jan 29;15:83. doi: 10.1186/1471-2164-15-83.
Cylindrospermopsis 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.
In 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+).
Our 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.
Cylindrospermopsis raciborskii 是一种入侵性的淡水丝状蓝藻，其某些菌株会产生毒素。零星的毒性可能是由于基因缺失事件、毒素生物合成基因簇的水平转移或其他基因组变量所致，但蓝藻毒素产生的进化驱动因素仍是一个谜。通过检查有毒和无毒 C. raciborskii 菌株的基因组，我们希望更好地了解这些来自同一地理来源的菌株之间的相似程度，以及这些菌株之间的主要差异可能是什么。此外，我们还希望确定为什么有些蓝藻拥有圆柱鱼腥藻毒素生物合成（cyr）基因簇并产生毒素，而其他蓝藻则没有。有人假设，在某些环境条件下，毒性或缺乏毒性可能会给蓝藻带来选择性优势。
为了研究有毒和无毒 C. raciborskii 菌株之间的基本差异，我们对来自澳大利亚热带昆士兰州两个不同湖泊的两个密切相关的分离株 CS-506（CYN+）和 CS-509（CYN-）进行了基因组测序。然后，将这些基因组与第三个（参考）基因组 C. raciborskii CS-505（CYN+）进行了比较。三个菌株的基因组大小相似，G+C 含量几乎相同。至少有 2767 个基因在三个菌株中共享，包括分类学上重要的 rpoc1、ssuRNA、lsuRNA、cpcA、cpcB、nifB 和 nifH，它们的核苷酸同一性为 99.8-100%。菌株 CS-506 和 CS-509 分别含有至少 176 个和 101 个菌株特异性（或非同源）基因，其中大多数与 DNA 修复和修饰、营养吸收和运输或渗透压调节等适应措施有关。然而，在这两个菌株之间观察到的唯一显著遗传差异是圆柱鱼腥藻毒素生物合成基因簇的存在与否。有趣的是，我们还在 CS-509（CYN-）菌株中鉴定出一个隐匿的次级代谢物基因簇，以及在 CS-509 和参考菌株 CS-505（CYN+）中共同存在的第二个隐匿基因簇。
我们的结果证实，导致 C. raciborskii 毒性的最重要因素是 cyr 基因簇的存在与否。我们没有发现任何其他与 CYN 产生相关的远程编码基因或基因簇。有毒和无毒菌株之间的其他基因组差异主要与应激和适应基因有关，这表明 CYN 的产生可能与这些生理过程有关。
