A Comparison of 14 Erythrobacter Genomes Provides Insights into the Genomic Divergence and Scattered Distribution of Phototrophs

Abstract

Aerobic anoxygenic phototrophic bacteria (AAPB) are bacteriochlorophyll a (Bchl a)-containing microbial functional population. Erythrobacter is the first genus that was identified to contain AAPB species. Here, we compared 14 Erythrobacter genomes: seven phototrophic strains and seven non- phototrophic strains. Interestingly, AAPB strains are scattered in this genus based on their phylogenetic relationships. All 14 strains could be clustered into three groups based on phylo-genomic analysis, average genomic nucleotide identity and the phylogeny of signature genes (16S rRNA and virB4 genes). The AAPB strains were distributed in three groups, and gain and loss of phototrophic genes co-occurred in the evolutionary history of the genus Erythrobacter. The organization and structure of photosynthesis gene clusters (PGCs) in seven AAPB genomes displayed high synteny of major regions except for few insertions. The 14 Erythrobacter genomes had a large range of genome sizes, from 2.72 to 3.60 M, and the sizes of the core and pan- genomes were 1231 and 8170 orthologous clusters, respectively. Integrative and conjugative elements (ICEs) were frequently identified in genomes we studied, which might play significant roles in shaping or contributing to the pan-genome of Erythrobacter. Our findings suggest the ongoing evolutionary divergence of Erythrobacter genomes and the scattered distribution characteristic of PGC.

Characteristics and Evolutionary analysis of Photosynthetic Gene Clusters on Extrachromosomal Replicons: from streamlined plasmids to chromids

“…Intriguingly, the PGC of Erythrobacter sp. AP23 is closely related to that of Citromicrobium (Zheng et al , 2016). Moreover, the Gemmatimonadetes strain AP64 is a novel organism that contains bacteriochlorophyll a (BChl a), and has been suggested to have acquired its PGC from photoheterotrophic bacteria of the Proteobacteria via an ancient horizontal gene transfer (HGT) event (Zeng et al , 2014).…”

“…The large PGC superoperon is approximately 35–50 kb in length and contains approximately 40 genes required for the biosynthesis of bacteriochlorophyll, carotenoids, photosynthetic reaction complexes, and light harvesting complexes, in addition to other regulatory functions (Beatty, 1995; Liotenberg et al , 2008; Swingley et al , 2009; Zheng et al , 2011). PGC gene sequences are highly conserved and some essential genes within PGCs (e.g., pufL, pufM, and bchY) in whole PGCs are typically used as molecular markers in phylogenetic analyses to classify phototrophic Proteobacteria and study their ecological diversity and evolutionary relationships (Beja et al , 1992; Yutin et al , 2007; Zeng et al , 2014; Zheng et al , 2016).…”

“…AP23 shares 99.5% 16S rRNA gene sequence identity with Erythrobacter sp. LAMA915, only the former strain contains a PGC within its genome (Zheng et al , 2016). Intriguingly, the PGC of Erythrobacter sp.…”

Succession and Colonization Dynamics of Endolithic Phototrophs within Intertidal Carbonates

“…Erythrobacter are aerobic anoxygenic phototrophs that conduct photoheterotrophy, have a low BChl a content, and require a source of organic carbon [24,56]. Our endolithic sequences were most similar to those in Group I Erythrobacter genomes [57]. Under our hypothesis, these organisms could still be euendoliths, even though their populations remained low throughout the experiment.…”

Evolutionary Genomics of an Ancient Prophage of the Order Sphingomonadales

“…Comparative genomic studies have revealed that the coding potential of different species are highly variable, indicating their divergent evolution (Aylward et al. 2013; Zheng et al. 2016).…”