Fig. 2

Phylogenomic trees of the genus Paracoccus constructed using the pipelines EasyCGTree, UBCG, and bcgTree. Note: A EasyCGTree using 90 genes of the UBCG gene set (gene families TIGR03625 and TIGR01044 were excluded because of low prevalence) as the HMM and other default options. B UBCG using default options. C EasyCGTree using the essential gene set as the HMM and IQ-TREE for phylogeny inference with best-fit model Q.yeast + F + I + I + R5. D bcgTree using default options. Clades with identical topology among the four trees are collapsed and marked in the same color. Support confidence (A, 0–1; B, 0–1/≤ 0–92; C and D, 0–100) is indicated in the middle of branches or near the nodes. Support values in A and the former of those in B are calculated by using the Shimodaira-Hasegawa test with FastTree, and later of those in B are the gene support indices (GSI, the gene trees supporting the clade) generated by the UBCG pipeline. Support values in C and D are standard bootstraps generated by IQ-TREE and RaxML, respectively. Support values, > 0.7 for A and B, 64 for B (> 70% out of the 92 gene trees), and 70 for C and D, are considered as significant. All the trees were rooted at the outgroup Roseobacter litoralis Och 149 (GCF_000154785.2), which was omitted. Bar, 0.05 substitutions per amino acid position