Genome sequence-based species delimitation with confidence intervals and improved distance functions.
Genome sequence-based species delimitation with confidence intervals and improved distance functions.
复制标题
DOI：
10.1186/1471-2105-14-60
复制
发表时间：
2013-02-21
影响因子：
3
通讯作者：
Göker M
中科院分区：
文献类型：
--
作者：
Meier-Kolthoff JP;Auch AF;Klenk HP;Göker M
在过去的25年里，原核生物（细菌和细菌）的物种划分在很大程度上是基于DNA-DNA杂交（DDH），这是20世纪70年代初设计的一种繁琐的实验室程序，在没有破译基因组序列的情况下，它的目的非常好。随着基因组测序技术的快速发展，直接利用现有的、易于生成的基因组序列进行物种定界的时代已经到来。GBDP（Genome Blast Distance Phylogeny，基因组爆炸距离系统发生学）推断完全或部分测序的基因组对之间的基因组到基因组的距离，这是一种用于基因组相关性的数字化、高度可靠的估计。它最近被引入作为DDH的硅替代品。实施这种应用的主要挑战是产生数字DDH值，该数字DDH值必须尽可能接近模拟湿实验室DDH值，以确保原生物种概念的一致性。相关和回归分析用于确定最佳性能的方法和最有影响力的参数。GBDP进一步丰富了一组新的功能，如通过恢复或通过DDH预测的统计模型和一个额外的距离函数家族获得的基因组间距离的置信区间。在以前的分析中，GBDP获得了最高的协议与湿实验室DDH所有测试的方法，但改进的模型导致DDH预测的准确性进一步提高。从统计模型中推断出的置信区间产生了稳定的结果，而那些通过重新计算得到的结果显示出潜在的距离函数之间的显着差异。尽管基于GBDP的DDH预测精度很高，但从有限的经验数据得出的推论总是与一定程度的不确定性相关联。因此，通过置信区间估计丰富计算机模拟DDH替代至关重要，使用户能够统计评估结果。这些方法上的进步，很容易通过网站http://ggdc.dsmz.de获得，是实现一致和真正基于基因组序列的微生物分类的关键步骤。
For the last 25 years species delimitation in prokaryotes (Archaea and Bacteria) was to a large extent based on DNA-DNA hybridization (DDH), a tedious lab procedure designed in the early 1970s that served its purpose astonishingly well in the absence of deciphered genome sequences. With the rapid progress in genome sequencing time has come to directly use the now available and easy to generate genome sequences for delimitation of species. GBDP (Genome Blast Distance Phylogeny) infers genome-to-genome distances between pairs of entirely or partially sequenced genomes, a digital, highly reliable estimator for the relatedness of genomes. Its application as an in-silico replacement for DDH was recently introduced. The main challenge in the implementation of such an application is to produce digital DDH values that must mimic the wet-lab DDH values as close as possible to ensure consistency in the Prokaryotic species concept. Correlation and regression analyses were used to determine the best-performing methods and the most influential parameters. GBDP was further enriched with a set of new features such as confidence intervals for intergenomic distances obtained via resampling or via the statistical models for DDH prediction and an additional family of distance functions. As in previous analyses, GBDP obtained the highest agreement with wet-lab DDH among all tested methods, but improved models led to a further increase in the accuracy of DDH prediction. Confidence intervals yielded stable results when inferred from the statistical models, whereas those obtained via resampling showed marked differences between the underlying distance functions. Despite the high accuracy of GBDP-based DDH prediction, inferences from limited empirical data are always associated with a certain degree of uncertainty. It is thus crucial to enrich in-silico DDH replacements with confidence-interval estimation, enabling the user to statistically evaluate the outcomes. Such methodological advancements, easily accessible through the web service at http://ggdc.dsmz.de, are crucial steps towards a consistent and truly genome sequence-based classification of microorganisms.
登录
查看更多内容
影响因子：
--
作者：
Auch AF;von Jan M;Klenk HP;Göker M
通讯作者：
Göker M
DOI：
10.1177/109434200101500211
发表时间：
2001-06-01
影响因子：
3.1
作者：
Bader, DA;Pennington, R
通讯作者：
Pennington, R
影响因子：
6.8
作者：
AKAIKE, H
通讯作者：
AKAIKE, H
影响因子：
5.8
作者：
Henz, SR;Huson, DH;Schuster, SC
通讯作者：
Schuster, SC
影响因子：
3.2
作者：
Clarke, GDP;Beiko, RG;Charlebois, RL
通讯作者：
Charlebois, RL