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.

Keywords: Erythrobacter; aerobic anoxygenic phototrophic bacteria; comparative genomics; integrative and conjunctive element; photosynthesis gene cluster.

Figure 1

Neighbor-joining phylogenetic trees based on the 16S rRNA gene (A) and concatenated amino acids sequences of 1167 universally conserved genes (B). Bootstrap percentages from both neighbor-joining (above nodes) and maximum likelihood (below nodes) are shown. (C) Cluster analysis based on the ANI from pairwise genome comparison. ^⋆Represents the strain containing PGC.

Figure 2

COG function classification of core (A) and flexible (B) genes from 14 Erythrobacter genomes.

Figure 3

Structure and arrangement of PGCs in Erythrobacter. Green, bch genes; red, puf and regulator genes; pink, puh genes; orange, crt genes; blue, hem and cyc gene; yellow, lhaA gene; blank, uncertain or unrelated genes; and gray, hypothetical protein. The horizontal arrows represent putative transcripts.

Figure 4

Neighbor joining phylogenetic analysis of concatenated amino acids sequences of 27 universally conserved genes (9415 positions) in PGCs from GenBank database. The core genes are bchBCDFGHILMNOPXYZ-crtCF-pufABLM-lhaA-puhABCE-ascF. Bar, 0.1 substitutions per amino acids position.

Figure 5

Structure and composition of ICE. Seven hotspots (from No. 1 to 7) carrying exogenous genes were detected in the ICEs.

Figure 6

Neighbor-joining phylogenetic trees based on Integrase (A, 430 amino acid positions) and TraC (B, 846 amino acid positions). Bootstrap percentages from both neighbor-joining (above nodes) and maximum likelihood (below nodes) are shown.