Use of single molecule sequencing for comparative genomics of an environmental and a clinical isolate of Clostridium difficile ribotype 078
Use of single molecule sequencing for comparative genomics of an environmental and a clinical isolate of Clostridium difficile ribotype 078
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DOI：
10.1186/s12864-016-3346-2
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发表时间：
2016-12-13
期刊：
影响因子：
4.4
通讯作者：
Clokie, Martha R. J.
中科院分区：
文献类型：
--
作者：
Hargreaves, Katherine R.;Thanki, Anisha M.;Clokie, Martha R. J.
背景资料：病原体艰难梭菌如何在自然环境中生存，进化和在水库之间转移还知之甚少。一些核糖体类型在临床和环境中都有发现。这些菌株是否彼此不同并在特定环境中进化尚未确定。具有高度移动的基因组有助于C.很难对遗传多样性的解释受到短读长测序方法产生的片段化组装和对多样性的表观遗传调控的有限理解的限制。为了解决这个问题，在这项研究中使用单分子真实的时间（SMRT）测序，因为它产生高质量的基因组序列，重复区域的分辨率（包括那些发现在移动的元素），并可以生成数据，以确定整个序列（甲基化组）的甲基化修饰。重排发生在两个移动的遗传元件（MGE），Tn 6164和Tn 6293，只存在于M120和CD 105 HS 27基因组中，分别插入位点。这两个转座子的基因内容差异很大，这可能会影响水平基因转移;差异包括CDS编码甲基化酶和接合原噬菌体仅在Tn 6164中。为了研究可能影响MGE转移的机制，对每种菌株的甲基化组、限制性修饰（RM）和CRISPR/Cas系统进行了表征。与临床分离株M120相比，环境分离株CD 105 HS 27不具有C-m4甲基化的共有基序，但多了一个间隔区。结论：这两个分离株在MGE转移的遗传能力方面存在显著差异。基于两种不同的甲基化模式，水平转移基因的携带似乎具有基因组范围的影响。CRISPR/Cas系统似乎很活跃，尽管发展可能很缓慢。数据表明，这两种机制是功能和影响水平基因转移和基因组进化内C。很难
Background: How the pathogen Clostridium difficile might survive, evolve and be transferred between reservoirs within the natural environment is poorly understood. Some ribotypes are found both in clinical and environmental settings. Whether these strains are distinct from each another and evolve in the specific environments is not established. The possession of a highly mobile genome has contributed to the genetic diversity and ongoing evolution of C. difficile. Interpretations of genetic diversity have been limited by fragmented assemblies resulting from short-read length sequencing approaches and by a limited understanding of epigenetic regulation of diversity. To address this, single molecule real time (SMRT) sequencing was used in this study as it produces high quality genome sequences, with resolution of repeat regions (including those found in mobile elements) and can generate data to determine methylation modifications across the sequence (the methylome).Results: Chromosomal rearrangements and ribosomal operon duplications were observed in both genomes. The rearrangements occurred at insertion sites within two mobile genetic elements (MGEs), Tn6164 and Tn6293, present only in the M120 and CD105HS27 genomes, respectively. The gene content of these two transposons differ considerably which could impact upon horizontal gene transfer; differences include CDSs encoding methylases and a conjugative prophage only in Tn6164. To investigate mechanisms which could affect MGE transfer, the methylome, restriction modification (RM) and the CRISPR/Cas systems were characterised for each strain. Notably, the environmental isolate, CD105HS27, does not share a consensus motif for C-m4 methylation, but has one additional spacer when compared to the clinical isolate M120.Conclusions: These findings show key differences between the two strains in terms of their genetic capacity for MGE transfer. The carriage of horizontally transferred genes appear to have genome wide effects based on two different methylation patterns. The CRISPR/Cas system appears active although perhaps slow to evolve. Data suggests that both mechanisms are functional and impact upon horizontal gene transfer and genome evolution within C. difficile.