**Comparative Genome Analysis of the Photosynthetic Betaproteobacteria of the Genus** *Rhodocyclus***: Heterogeneity within Strains Assigned to** *Rhodocyclus tenuis* **and Description of** *Rhodocyclus gracilis* **sp. nov. as a New Species**

**John A. Kyndt 1,\* , Fabiola A. Aviles <sup>1</sup> , Johannes F. Imhoff <sup>2</sup> , Sven Künzel <sup>3</sup> , Sven C. Neulinger <sup>4</sup> and Terrance E. Meyer 5,†**


**Abstract:** The genome sequences for *Rhodocyclus purpureus* DSM 168<sup>T</sup> and four strains assigned to *Rhodocyclus tenuis* (DSM 110, DSM 111, DSM 112, and IM 230) have been determined. One of the strains studied (IM 230) has an average nucleotide identity (ANI) of 97% to the recently reported genome of the type strain DSM 109 of *Rcy. tenuis* and is regarded as virtually identical at the species level. The ANI of 80% for three other strains (DSM 110, DSM 111, DSM 112) to the type strain of *Rcy. tenuis* points to a differentiation of these at the species level. *Rcy. purpureus* is equidistant from *Rcy. tenuis* and the new species, based on both ANI (78–80%) and complete proteome comparisons (70% AAI). Strains DSM 110, DSM 111, and DSM 112 are very closely related to each other based on ANI, whole genome, and proteome comparisons but clearly distinct from the *Rcy. tenuis* type strain DSM 109. In addition to the whole genome differentiation, these three strains also contain unique genetic differences in cytochrome genes and contain genes for an anaerobic cobalamin synthesis pathway that is lacking from both *Rcy. tenuis* and *Rcy. purpureus*. Based on genomic and genetic differences, these three strains should be considered to represent a new species, which is distinctly different from both *Rcy. purpureus* and *Rcy. tenuis*, for which the new name *Rhodocyclus gracilis* sp. nov. is proposed.

**Keywords:** *Rhodocyclus*; *purpureus*; *tenuis*; *gracilis*; HiPIP; cobalamin; whole genome sequencing; taxonomy
