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全基因组测序将成为细菌分类必须做的一项指征

已有 8988 次阅读 2014-5-20 11:27 |个人分类:根瘤菌进化、发育与系统学|系统分类:科研笔记| 基因组, 分类

2014年3月份的Antonie Van Leeuwenhoek杂志上,Vandamme和Peeters联合撰文,提议以后的细菌多相分类中,特别是新种的鉴定与发表中,必须增加全基因组信息,以及采用快速高效的表型鉴定系统对细菌必需特征进行测定。而最近我投到SAM(Syst. Appl. Microbiol.)的一篇新种论文,编辑也以没有模式菌株的基因组信息(the genome sequence of at least the type strain),以及稿件太多,又只是一个新种描述,没有其他的创新性而给拒绝了。由于需要增加基因组测序的信息,设了这个槛后,以后新种的投稿及发表速度将会降下来。


http://www.ncbi.nlm.nih.gov/pubmed/?term=Time+to+revisit+polyphasic+taxonomy.+Antonie+Van+Leeuwenhoek

 

Vandamme P1, Peeters C.

2014 Mar 15. [Epub ahead of print]

Time to revisit polyphasic taxonomy.
Abstract

Although the International Code of Nomenclature of Bacteria does not specify a working strategy, editors and reviewers of taxonomic journals commonly request a polyphasic taxonomic approach that includes phenotypic, genotypic and chemotaxonomic information for the description of novel bacterial species. Whole genome sequences provide an insight into the genetic nature of microbial species, yield new and superior tools for delineating bacterial species and for studying their phylogeny, and provide a window on an organism's metabolic potential. These new insights and tools are gradually introduced in the polyphasic taxonomic practice. The genus Burkholderia, a controversial group of bacteria with both benign and devastating characteristics, is used as an example to show that the modern practice of polyphasictaxonomy is counterproductive in light of the tremendous number of bacterial species that awaits formal description and naming. Bacterial taxonomists must urgently reconsider how to describe and name novel bacteria in the genomic era, and should consider using a full genome sequence and a minimal description of phenotypic characteristics as a basic, sufficient, cost-effective and appropriate biological identity card for a species description.


而今天查文献,发现IJSEM上的2014年的新种论文,已使用基因组信息了。

http://www.ncbi.nlm.nih.gov/pubmed/24664579

2014 Mar 24. doi: 10.1099/ijs.0.060426-0. [Epub ahead of print]
Bradyrhizobium paxllaeri sp. nov. and Bradyrhizobium icense sp. nov., nitrogen-fixing rhizobial symbionts of Lima bean (Phaseolus lunatus L.) in Peru.

 




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