Table 1.
Genomic features of the Paracoccus strains presented in this study.
Fig 1.
Genome assembly quality assessment and evaluation of the six Paracoccus type strains.
The chart was generated with BUSCO v.5.4.5 showing the relative completeness of each strain’s genome.
Fig 2.
Phylogenetic analysis of the genus Paracoccus.
Type strains and the 8 largest Paracoccus clusters are highlighted in red and black. Detailed output of all available Paracoccus genomes including ANI values is summarized in S4 Table. Modifications were performed with Inkscape v 1.2. [19] (1. Inkscape Project. Inkscape [Internet]. 2020. Available from: https://inkscape.org).
Table 2.
Reclassification of Paracoccus sp. and wrongly assigned Paracoccus.
Fig 3.
Pan-core analysis of six Paracoccus type strain genomes.
A) Pan- and core size accumulation, and B) Cloud and new genes accumulation in the analyzed Paracoccus genomes. C) Distribution of core (center) and cloud (ellipses) gene clusters in pan-genome. The distribution of cloud gene clusters located on the chromosome or extrachromosomal elements is listed under each type strain (chromosome/extrachromosomal element). D) Bar charts of the pan-genome functional classification annotated in COG databases. The function was plotted either according to core (light red, left), shell (light green) and cloud (light blue, green) and according to their genomic localization, chromosomal or extrachromosomal.
Table 3.
Number of detected MGEs and SMs in the analyzed Paracoccus genomes.
Table 4.
Detailed summary of detected fitness and virulence associated genes located in , P–prophage, and extrachromosomal.
Fig 4.
Distribution of IS-families identified in the analyzed Paracoccus type strains.
The elements are members of 20 IS families represented by a different color. Free-living associated strains strains are displayed in grey. Family IS481, IS4, IS1380, IS200/IS605, and ISKRA4 are unique to P. aestuarii DSM19484T, P. alcaliphilus DSM 8512T, P. fistulariae KCTC 22803T, P. saliphilus DSM 18447T, and P. seriniphilus DSM14827T, respectively.
Fig 5.
Comparison of six Paracoccus type strain chromosomes.
Concentric colored rings represent Blast matches according to a percentage identity of (100, 90 and 70%). As reference the largest chromosome was chosen (P. saliphilus DSM 25392T) colored in yellow most inner ring. Putative prophage regions of all investigated strains are depicted in black (3 outer ring, P-), putative Genomic Islands in purple (2nd outer ring, GI-), and secondary metabolite clusters in grey (outer ring, A-). The GC content is shown in black as most inner ring, followed by the GC Skew. The visualization was modified with Inkscape v 1.2. [19].