Toward a more robust assessment of intraspecies diversity, using fewer genetic markers
Toward a more robust assessment of intraspecies diversity, using fewer genetic markers
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DOI：
10.1128/aem.01398-06
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发表时间：
2006-11-01
影响因子：
4.4
通讯作者：
Tiedje, James M.
中科院分区：
文献类型：
--
作者：
Konstantinidis, Konstantinos T.;Ramette, Alban;Tiedje, James M.
单基因或多基因的系统发育序列分析一直是密切相关细菌遗传多样性研究和普查的主要内容。然而，目前尚不清楚的是，基于基因组中少数基因的结果如何与基于全基因组的亲缘关系相关联，以及哪些基因（如果有的话）最能反映全基因组水平的亲缘关系，因此应该优先使用以节省成本和提高准确性。我们在此表明，基于其共享基因的平均核苷酸同一性（ANI）的密切相关生物体的系统发生与基于其全基因组序列的最新分析的系统发生准确对应。我们使用ANI来评估基因组中每个基因的系统发育稳健性，并表明几乎所有核心基因，无论其在基因组中的功能和位置如何，在显示80 - 95% ANI （16S rRNA同一性，> 98.5%）的菌株中都提供了稳健的系统发育重建。缺乏经过的时间，在较小程度上，水平转移和重组使得基因的选择对于针对种内水平的应用更为关键，即根据当前标准显示> 95% ANI的菌株。根据我们的分析，与通常用于该群体系统发育目的的八个基因的串联比对相比，仅基于三个表现最佳的基因就获得了大肠杆菌群体的更准确的系统发育。我们的结果在沙门氏菌、伯克霍尔德菌和希瓦氏菌群中是可重复的，因此预计对微进化研究具有普遍适用性，包括宏基因组调查。
Phylogenetic sequence analysis of single or multiple genes has dominated the study and census of the genetic diversity among closely related bacteria. It remains unclear, however, how the results based on a few genes in the genome correlate with whole-genome-based relatedness and what genes (if any) best reflect whole-genome-level relatedness and hence should be preferentially used to economize on cost and to improve accuracy. We show here that phylogenies of closely related organisms based on the average nucleotide identity (ANI) of their shared genes correspond accurately to phylogenies based on state-of-the-art analysis of their whole-genome sequences. We use ANI to evaluate the phylogenetic robustness of every gene in the genome and show that almost all core genes, regardless of their functions and positions in the genome, offer robust phylogenetic reconstruction among strains that show 80 to 95% ANI (16S rRNA identity, > 98.5%). Lack of elapsed time and, to a lesser extent, horizontal transfer and recombination make the selection of genes more critical for applications that target the intraspecies level, i.e., strains that show > 95% ANI according to current standards. A much more accurate phylogeny for the Escherichia coli group was obtained based on just three best-performing genes according to our analysis compared to the concatenated alignment of eight genes that are commonly employed for phylogenetic purposes in this group. Our results are reproducible within the Salmonella, Burkholderia, and Shewanella groups and therefore are expected to have general applicability for microevolution studies, including metagenomic surveys.