A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights
A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights
复制标题
基于基因组见解的原核生物属边界建议
DOI：
10.1128/jb.01688-14
复制
发表时间：
2014-06-01
影响因子：
3.2
通讯作者：
Zhang, Yu-Zhong
中科院分区：
文献类型：
--
作者：
Qin, Qi-Long;Xie, Bin-Bin;Zhang, Yu-Zhong
基因组信息已经被应用于原核生物物种的定义和分类。然而，基因组序列对原核生物属划分的贡献研究较少。为了深入了解原核生物的属定义，我们试图揭示当前原核生物分类系统中属水平的基因组差异，并根据基因组信息划定属的边界。两个基因组之间的平均核苷酸序列同一性可以用于原核生物种的划分，但不适合用于属的划分。我们使用两个菌株之间的保守蛋白百分比（POCP）来估计它们的进化和表型距离。一个全面的基因组调查表明，POCP可以作为一个强大的基因组指标，建立属的原核生物群的边界。基本上，属于同一属的两个物种将共享至少一半的蛋白质。在一个特定的谱系，属和科/目排名显示轻微或没有重叠的POCP值。原核生物属可以被定义为所有成对POCP值高于50%的一组物种。将全基因组数据整合到现有的分类系统中，可以为原核生物属的定义和划界提供全面的信息。
ABSTRACT Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation.