Phylotaxonomic assessment based on four core gene sets and proposal of a genus definition among the families Paracoccaceae and Roseobacteraceae - supplementary material

 The families Paracoccaceae and Roseobacteraceae comprised of metabolically, phenotypically, and genotypically diverse members, and circumscribed heavily based on 16S rRNA gene analysis previously. Hundreds of genera have been reported within the two families, and misclassifications have been a reoccurring problem, though the taxonomies have been established based on genome-scale phylogenetic reconstructions. In this study, we conducted a comprehensive phylotaxonomic assessment of the families Paracoccaceae and Roseobacteraceae based on four ubiquitous gene sets, bac120 (120 genes in Bacteria), rhodo268 (268 genes in “Rhodobacteraceae”, defined in this study), rp1 (16 ribosomal protein genes in Prokaryote) and rp2 (23 ribosomal protein genes in Prokaryote), using two tree-inferring applications and two approaches (supermatrix and consensus). The results suggested that the four supermatrix trees based on bac120 and rhodo268 shared high proportion of common nodes (>88.4%) and the topology was reproducible among all the trees within most of genera. The evolutionary distance (ED) analysis showed significant overlapping between intergeneric and intrageneric comparison, implying that the proposal of some genera seems to be needless. In addition, the bac120 gene set and the program FastTree were found to be the most cost-effective way to conduct phylogenomic analysis of the families Paracoccaceae and Roseobacteraceae; and the ED threshold of 0.21-0.23 based on either bac120 or rhodo268 was proposed as one standard for later genus delimitation in these families. As conclusions, a comprehensive phylogenetic framework was presented in this study, and the proposed genus definition will promote to establish a more reasonable taxonomy in the families Paracoccaceae and Roseobacteraceae.