Genomic plasticity in prokaryotes: the case of the square haloarchaeon
Genomic plasticity in prokaryotes: the case of the square haloarchaeon
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DOI：
10.1038/ismej.2007.35
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发表时间：
2007-07-01
期刊：
影响因子：
11
通讯作者：
Rodriguez-Valera, Francisco
中科院分区：
文献类型：
--
作者：
Cuadros-Orellana, Sara;Martin-Cuadrado, Ana-Belen;Rodriguez-Valera, Francisco
原核生物近缘菌株间基因组含量的变异性是基因组学最显著的发现之一。接近这种所谓的泛基因组描述的一种方法是将一个参考菌株基因组与来自环境的宏基因组序列进行比较。我们已经将这种方法应用于一个极端的水生生物栖息地，在一个太阳盐场饱和盐水。将Haloquadratum walsbyi菌株DSM 16790的基因组与从其分离的确切位点获得的环境宏基因组进行比较。这种方法揭示了菌株基因组的某些区域在宏基因组中几乎没有代表。在这里，我们分析了DSM 16790基因组中的这些基因组岛（GI），并将它们与环境文库中的一些化石的完整序列进行了比较。其中两个岛GI 2和GI 4与两个大的富含鸟嘌呤和胞嘧啶（GC）的区域重叠，这些区域通过移动的元件显示出高变异性的证据。GI 3似乎是由参考基因组获得的噬菌体或噬菌体残余物，但不存在于大多数环境谱系中。大多数差异基因含量与小分子运输和检测有关，可能反映了对不同有机养分库的适应。GI 1不具有痕量的移动的元素并且具有正常的GC含量。这个岛包含的主要集群的细胞包膜糖蛋白和发现的变异性是不同于其他地理标志。它不是由不同的基因组成，而是由相似性较低的同源物组成。这种变异可能反映了噬菌体逃避策略。
The variability in genome content among closely related strains of prokaryotes has been one of the most remarkable discoveries of genomics. One way to approach the description of this so- called pan- genome is to compare one reference strain genome with metagenomic sequences from the environment. We have applied this approach to one extreme aquatic habitat, saturated brines in a solar saltern. The genome of Haloquadratum walsbyi strain DSM 16790 was compared to an environmental metagenome obtained from the exact site of its isolation. This approach revealed that some regions of the strain genome were scarcely represented in the metagenome. Here we have analyzed these genomic islands ( GI) in the genome of DSM 16790 and compared them with the complete sequence of some fosmids from the environmental library. Two of the islands, GI 2 and GI 4, overlapped with two large guanine and cytosine ( GC)- rich regions that showed evidence of high variability through mobile elements. GI 3 seemed to be a phage or phage- remnant acquired by the reference genome, but not present in most environmental lineages. Most differential gene content was related to small molecule transport and detection, probably reflecting adaptation to different pools of organic nutrients. GI 1 did not possess traces of mobile elements and had normal GC content. This island contained the main cluster of cell envelope glycoproteins and the variability found was different from the other GIs. Rather than containing different genes it consisted of homologs with low similarity. This variation might reflect a phage evasion strategy.