Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison.
Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison.
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DOI：
10.4056/sigs.531120
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发表时间：
2010-01-28
影响因子：
--
通讯作者：
Göker M
中科院分区：
文献类型：
--
作者：
Auch AF;von Jan M;Klenk HP;Göker M
细菌和古细菌的实用物种概念最终是基于DNA-DNA杂交（DDH）。虽然从原则上讲，这种技术使分类学家能够获得两个菌株基因组之间总体相似性的估计，但这种技术冗长且容易出错，不能用于逐步建立比较数据库。基因组测序领域的最新技术进步要求生物信息学方法用计算机基因组与基因组的比较取代湿实验室的DDH。在这里，我们研究了最先进的方法来推断全基因组距离在他们模仿DDH的能力。有效确定高分片段对或最大唯一匹配的算法作为推断基因组间距离的基础表现良好。所研究的距离函数能够处理大量减少的基因组和重复序列区域，在模拟DDH时优于先前描述的与错误率的相关性。对不完全测序基因组的模拟表明，一些距离公式对基因组信息缺失部分具有很强的鲁棒性。与DDH值相比，数字衍生的基因组到基因组距离与16S rRNA基因序列距离的相关性更好。讨论了基于基因组信息的物种分类学的发展前景，并提出了基于基因组信息的物种划分方法。
The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the overall similarity between the genomes of two strains, this technique is tedious and error-prone and cannot be used to incrementally build up a comparative database. Recent technological progress in the area of genome sequencing calls for bioinformatics methods to replace the wet-lab DDH by in-silico genome-to-genome comparison. Here we investigate state-of-the-art methods for inferring whole-genome distances in their ability to mimic DDH. Algorithms to efficiently determine high-scoring segment pairs or maximally unique matches perform well as a basis of inferring intergenomic distances. The examined distance functions, which are able to cope with heavily reduced genomes and repetitive sequence regions, outperform previously described ones regarding the correlation with and error ratios in emulating DDH. Simulation of incompletely sequenced genomes indicates that some distance formulas are very robust against missing fractions of genomic information. Digitally derived genome-to-genome distances show a better correlation with 16S rRNA gene sequence distances than DDH values. The future perspectives of genome-informed taxonomy are discussed, and the investigated methods are made available as a web service for genome-based species delineation.
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DOI：
10.1073/pnas.0409727102
发表时间：
2005-02-15
影响因子：
11.1
作者：
Konstantinidis, KT;Tiedje, JM
通讯作者：
Tiedje, JM
影响因子：
3.4
作者：
Göker M;Grimm GW
通讯作者：
Grimm GW
DOI：
10.1099/00207713-23-4-308
发表时间：
1973-01-01
期刊：
INTERNATIONAL JOURNAL OF SYSTEMATIC BACTERIOLOGY
影响因子：
--
作者：
JOHNSON, JL
通讯作者：
JOHNSON, JL
影响因子：
3.2
作者：
Deloger, Marc;El Karoui, Meriem;Petit, Marie-Agnes
通讯作者：
Petit, Marie-Agnes
影响因子：
5.8
作者：
Henz, SR;Huson, DH;Schuster, SC
通讯作者：
Schuster, SC