**1. Introduction**

Anoxygenic photosynthesis is widely distributed among eubacteria and involves a number of genes for the photosynthetic reaction center and for the biosynthesis of photosynthetic pigments, bacteriochlorophylls, and carotenoids, which are essential elements to enable photosynthesis. While the biosynthesis of bacteriochlorophylls is common to all of them, the different structure of the photosynthetic reaction center clearly separates two groups of anoxygenic phototrophic bacteria, those having a type-I and those having a type-II photosystem [1–3].

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Those bacteria employing a photosystem type-II photosynthetic apparatus include the phototrophic purple bacteria (*Proteobacteria*), as well as *Gemmatimonas* and *Chloroflexus,* with their photosynthetic relatives [1,3–5]. Essential components of the type-II photosynthetic apparatus are represented by two membrane-spanning photosynthetic reaction center proteins that are common to all of these bacteria. These PufLM proteins are binding bacteriochlorophyll molecules and are crucial components of the type-II photosynthetic apparatus. Together with an additional protein (PufH = PuhA), they form the core structure of the type-II photosynthetic reaction center in all phototrophic purple bacteria (*Proteobacteria* and *Gemmatimonas*). The PufH protein is absent from the *Chloroflexi* that have chlorosomes attached to the reaction center. In addition, a cytochrome c (PufC) is associated with the reaction center proteins in the majority of phototrophic purple bacteria but is lacking in a number of species [6]. While *pufLMC* genes form a stable genomic cluster (sometimes lacking the *pufC* gene), *pufH* (*puhA*) is located at a different place within the genome, associated with genes of bacteriochlorophyll biosynthesis [6]. It has been demonstrated that sequences of PufLM are excellent tools to study the phylogeny of anoxygenic phototrophic purple bacteria, as well as their diversity and environmental distribution [2,7–9]. In a comprehensive study based on the phylogeny of PufLM, it was shown that distinct lineages of *Proteobacteria* contained phototrophic representatives in 10 orders, including anaerobic as well as aerobic anoxygenic phototrophic purple bacteria [3].

Bacteriochlorophyll biosynthesis is common to all phototrophic bacteria, including those with a type-I and those with a type-II photosynthetic reaction center. A key enzyme in this pathway is the light-independent chlorophyllide reductase BchXYZ. Consequently, this protein enables a broad view on the phylogeny of anoxygenic photosynthetic bacteria with a capacity to synthesize bacteriochlorophyll [10].

In the present work, the phylogeny of anoxygenic phototrophic bacteria was analyzed on the basis of sequences of key proteins of the type-II photosynthetic reaction center PufHLM and of chlorophyllide reductase BchXYZ and was compared with the phylogeny of the 16S rRNA gene (Figure 1). The phylogenetic tree of BchXYZ (Figure 2) gave an overview of all considered strains, while that of combined sequences of PufHLM-BchXYZ (Figure 3) covered all considered phototrophic purple bacteria. In addition, phylogenies of combined PufHLM-BchXYZ sequences and 16S rRNA gene sequences were compared (Figure 4).

#### **2. Material and Methods**

#### *2.1. Cultivation, Sequencing, and Assembly of DNA Sequences*

Cells were grown in the appropriate media, as described for the purple sulfur bacteria [11,12] and several groups of phototrophic purple bacteria [13]. Extraction and sequencing of DNA and the assembly of sequences were described earlier [14].
