Comparative genomics of Cylindrospermopsis raciborskii strains with differential toxicities.
Comparative genomics of Cylindrospermopsis raciborskii strains with differential toxicities.
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DOI：
10.1186/1471-2164-15-83
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发表时间：
2014-01-29
期刊：
影响因子：
4.4
通讯作者：
Neilan BA
中科院分区：
文献类型：
--
作者：
Sinha R;Pearson LA;Davis TW;Muenchhoff J;Pratama R;Jex A;Burford MA;Neilan BA
raciborskii是一种入侵的丝状淡水蓝藻，其中一些菌株产生毒素。散发性毒性可能是基因缺失事件、毒素生物合成基因簇的水平转移或其他基因组变量的结果，但蓝藻毒素产生的进化驱动因素仍然是一个谜。通过对有毒和无毒的C. raciborskii，我们希望更好地了解这些共同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，我们希望弄清楚为什么有些蓝藻拥有柱孢菌素生物合成（cyr）基因簇并产生毒素，而另一些则没有。有人假设，在某些环境条件下，毒性或缺乏毒性可能会赋予蓝细菌选择性优势。为了研究有毒和无毒C。raciborskii菌株，我们测序了两个密切相关的分离物，CS-506（CYN+）和CS-509（CYN-）来源于澳大利亚热带昆士兰州的不同湖泊。然后将这些基因组与来自C. raciborskii CS-505（CYN+）。所有三种菌株的基因组大小相似，G + C含量几乎相同。在所有三个菌株中至少有2，767个基因是共享的，包括分类学上重要的rpoc 1，ssuRNA，lsuRNA，cpcA，cpcB，nifB和nifH，它们表现出99.8-100%的核苷酸同源性。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，其中大部分与DNA修复和修饰、营养吸收和运输或适应性措施（如光合调节）相关。然而，在两种菌株之间观察到的唯一显著遗传差异是存在或不存在柱孢菌蛋白酶生物合成基因簇。有趣的是，我们还在菌株CS-509（CYN-）中鉴定了一个隐藏的次级代谢物基因簇，以及CS-509和参考菌株CS-505（CYN+）共有的第二个隐藏簇。我们的研究结果证实，最重要的因素造成的毒性，在C。raciborskii是cyr基因簇的存在或不存在。我们没有发现任何其他远端编码基因或基因簇与CYN的生产。有毒和无毒菌株之间的额外基因组差异主要与应激和适应基因相关的事实表明，CYN的产生可能与这些生理过程有关。
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.
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影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
14.9
作者：
Ansari, MZ;Yadav, G;Mohanty, D
通讯作者：
Mohanty, D
影响因子：
4.4
作者：
Ishida, Keishi;Welker, Martin;de Marsac, Nicole Tandeau
通讯作者：
de Marsac, Nicole Tandeau
影响因子：
2.9
作者：
Briand, JF;Leboulanger, C;Dufour, P
通讯作者：
Dufour, P
DOI：
10.1093/bioinformatics/btp698
发表时间：
2010-03-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Li H;Durbin R
通讯作者：
Durbin R