The taxonomic classification of metabolically versatile Paracoccus spp. has been so far performed using polyphasic approach. The topology of single gene phylogenies, however, has highlighted ambiguous species assignments. In the present study, genome based multi-gene phylogenies and overall genome related index were used for species threshold assessment. Comprehensive phylogenomic analysis of Paracoccus genomes (n = 103) showed concordant clustering of strains across multi-gene marker set phylogenies (nMC = 0.08–0.14); as compared to 16S rDNA phylogeny (nMC = 0.37–0.42) suggesting robustness of multi gene phylogenies in drawing phylogenetic inferences. Functional gene content distribution across the genus showed that only 1.7% gene content constitutes the core genome highlighting the significance of extensive genomic variability in the evolution of Paracoccus spp. Further, genome metrics were used to validate characterized strains, identifying classification anomalies (n = 13), and based on this, genome derived taxonomic amendments were notified in present study. Conclusively, validated metric tools can be employed on whole genome sequences, including draft assemblies, for the assessment and assignment of uncharacterized strains and species level ascription of newly isolated Paracoccus strains in future.

代谢多功能副球菌属的分类学分类。到目前为止，已使用多相方法进行。然而，单基因系统发育的拓扑结构突出了模棱两可的物种分配。在本研究中，基于基因组的多基因系统发育和整体基因组相关指数用于物种阈值评估。副球菌基因组的综合系统发育分析（ n = 103）显示跨多基因标记集系统发育的菌株的一致聚类（nMC = 0.08-0.14）；与 16S rDNA 系统发育 (nMC = 0.37–0.42) 相比，表明多基因系统发育在绘制系统发育推断方面的稳健性。整个属的功能基因含量分布表明，只有 1.7% 的基因含量构成核心基因组，突出了广泛的基因组变异在副球菌属进化中的重要性。此外，基因组指标用于验证特征菌株，识别分类异常（n = 13），并基于此，在本研究中通知了基因组衍生的分类修正。最终，经过验证的度量工具可用于全基因组序列，包括组装草图，用于评估和分配未表征的菌株以及未来新分离的副球菌菌株的物种水平归属。