Phylotaxogenomics for the Reappraisal of the Genus Roseomonas With the Creation of Six New Genera

Abstract

The genus Roseomonas is a significant group of bacteria which is invariably of great clinical and ecological importance. Previous studies have shown that the genus Roseomonas is polyphyletic in nature. Our present study focused on generating a lucid understanding of the phylogenetic framework for the re-evaluation and reclassification of the genus Roseomonas. Phylogenetic studies based on the 16S rRNA gene and 92 concatenated genes suggested that the genus is heterogeneous, forming seven major groups. Existing Roseomonas species were subjected to an array of genomic, phenotypic, and chemotaxonomic analyses in order to resolve the heterogeneity. Genomic similarity indices (dDDH and ANI) indicated that the members were well-defined at the species level. The Percentage of Conserved Proteins (POCP) and the average Amino Acid Identity (AAI) values between the groups of the genus Roseomonas and other interspersing members of the family Acetobacteraceae were below 65 and 70%, respectively. The pan-genome evaluation depicted that the pan-genome was an open type and the members shared 958 core genes. This claim of reclassification was equally supported by the phenotypic and chemotaxonomic differences between the groups. Thus, in this study, we propose to re-evaluate and reclassify the genus Roseomonas and propose six novel genera as Pararoseomonas gen. nov., Falsiroseomonas gen. nov., Paeniroseomonas gen. nov., Plastoroseomonas gen. nov., Neoroseomonas gen. nov., and Pseudoroseomonas gen. nov.

Keywords: Roseomonas; average amino acid Identity (AAI); percentage of conserved proteins (POCP); phylotaxogenomics; reclassification.

FIGURE 1

NJ phylogenetic tree based on the 16S rRNA gene sequences showing the phylogenetic relationship between the members of the genus Roseomonas and other closely related members of the family Acetobacteraceae. Elioraea tepidiphila DSM 17972^T was used as an outgroup. Numbers at nodes represent bootstrap values (given as percentages of 1,000 replications) of >50% shown at branch points (NJ/ML/ME). The GenBank accession numbers for the 16S rRNA gene sequences are shown in parentheses. Bar, 0.01 accumulated changes per nucleotide substitutions (red color indicates the availability of their genomes).

FIGURE 2

Phylogenomic tree constructed using 92 core genes tool based on the Up-to-date Bacterial Core Gene (UBCG) (Na et al., 2018). The tree was generated using the MEGA7 software (NJ) with Stella humosa DSM 5900^T (RJKX00000000) as an outgroup.

FIGURE 3

Core-pan-genome analysis of Roseomonas type strains. (A) Flower-pot diagram representing core, accessory, and unique genomes of the genomes of all strains. (B) Core-pan-plot for all the genomes. (C) KEGG distribution of core, accessory, and unique genes (1. R. gilardi subsp. rosea ATCC BAA-691^T; 2. R. gilardi subsp. rosea NCTC 13290^T; 3. R. mucosa ATCC BAA-692^T; 4. R. mucosa NCTC 13291^T; 5. R. rosea DSM 14916 ^T; 6. R. aerilata DSM 19363^T; 7. R. pecuniae N75^T; 8. R. sp. vinacea DSM 19362^T; 9. R. harenae CPCC 101081^T; 10. R. stagni DSM 19981^T; 11. R. algicola PeD5 ^T; 12. R. bella CQN31^T; 13. R. frigidaquae JCM 15073^T; 14. R. selenitidurans BU-1^T; 15. R. arctica LMG 28251^T; 16. “R. hellenica” LMG 31523^T; 17. R. oryzicola KCTC 22478^T; 18. R. oryzicola LMG 31230^T; 19. R. alkaliterrae DSM 25895 ^T; 20. R. alkaliterrae LMG 31230^T; 21. R. lacus CGMCC 1.3617^T; 22. R. eburnea LMG 31228^T; 23. R. terrae LMG 31159^T; 24. R. soli LMG 31523^T; 25. R. deserti M3^T; 26. R. aerophila NBRC 108923^T; 27. R. cervicalis ATCC 49957 ^T; 28. R. coralli M0104^T; 29. R. ludipueritiae DSM 14915^T; 30. R. oryzae KCTC 42542 ^T; 31. R. rhizosphaerae YW11^T; 32. R. vastitatis CPCC 101021^T; 33. R. wenyumeiae Z23^T).

FIGURE 4

Diagrammatic representation of the ANI, AAI, and POCP values in between the members of each group of the genus Roseomonas.