DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany.
Arch Microbiol. 2011 May;193(5):313-21. doi: 10.1007/s00203-011-0686-9. Epub 2011 Mar 5.
Whole genome sequences are present-day bonanzas for taxonomists. Comparative genomics provides a promising perspective to reveal the evolutionary relationship between organisms, but this strategy is not applicable for extrachromosomal elements due to their high recombination frequencies. Classification of plasmids is based on their compatibility, i.e., the ability to coexist within the same cell. Compatibility testing is a laborious experimental discipline of pairwise comparisons developed for a small set of replicons. Thus, novel approaches are urgently required to deal with the exponentially increasing amount of sequence data. In this minireview, a short overview about the functional role and distribution of plasmids as well as a summary of recent strategies to classify the replicons via phylogenetic analyses is given. Our own work essentially bases on genes of the replication module, i.e., the replicase and two conserved partitioning genes and we exemplified this approach for the four different plasmid types from Alphaproteobacteria. It is suitable for a reliable classification of these replicons and allows in silico predictions about their compatibility. The development of a general classification scheme for plasmids from all microbial lineages will ensure a systematic assessment of the upcoming data flood and help to understand the distribution of extrachromosomal elements.
全基因组序列是当今分类学家的宝贵资源。比较基因组学为揭示生物之间的进化关系提供了一个有前途的视角，但由于外染色体元件的高重组频率，该策略不适用于它们。质粒的分类基于其兼容性，即能够在同一细胞中共存的能力。兼容性测试是一种费力的实验学科，用于对一小部分复制子进行成对比较。因此，迫切需要新的方法来处理指数级增长的序列数据。在这篇综述中，简要概述了质粒的功能和分布，以及通过系统发育分析对复制子进行分类的最新策略。我们自己的工作主要基于复制模块的基因，即复制酶和两个保守的分配基因，我们以四个不同的α变形菌质粒类型为例说明了这种方法。它适用于这些复制子的可靠分类，并允许对其兼容性进行计算机预测。开发适用于所有微生物谱系的质粒通用分类方案将确保对即将到来的数据洪流进行系统评估，并有助于理解外染色体元件的分布。
