This composite replicon may have either originated from a plasmid fusion or from a horizontal recombination. The latter explanation is supported by two site-specific XerC recombinase genes (Daep_04383, opposite Daep_04398) that are located head-to-head adjacent to the two replicases repC9-a and repC9-b. This plasmid contains many transposases and putative phage-derived components including a DNA-primase (Daep_04238) and an RNA-directed DNA polymerase (Daep_04390). The general operon structure of this plasmid seems to be scrambled by transposition or recombination events, as illustrated by the type-IV secretion system. pDaep_B174 contains two copies of the characteristic virD-operon comprising the relaxase VirD2 and the coupling protein VirD4 (Table 6).
Moreover, the operon contains a complete, as well as a partial, virB gene cluster for the transmembrane channel . The first four genes in the partial cluster are missing, and the truncated virB4 pseudogene (Daep_04339) is flanked by a transposase. But plasmid stability is probably ensured by a PSK system (Table 6). Finally, the most conspicuous finding on this plasmid is the presence of a complete or nearly complete phenylacetate catabolon (Daep_04356 to Daep_04367), containing paa genes for the following proteins: PaaJ, PaaA, PaaB, PaaC, PaaD, PaaE, PaaZ, PaaY, PaaK, PaaF. The extrachromosomal localization of this catabolon has previously been shown for Silicibacter sp. TM1040, Jannaschia sp. CCS1 and Dinoroseobacter shibae DSM 16493T [60,61], which also belong to the Roseobacter clade.
The 117 kb RepA-I type replicon pDaep_C117 contains a LuxR-type two-component transcriptional regulator (Daep_03918) and a complete rhamnose operon  and is dominated by genes that are required for polysaccharide biosynthesis. P. daeponensis was described as a facultatively anaerobic bacterium that uses nitrate as electron acceptor . We found genes involved in nitrogen metabolism scattered over the chromosome, involved in the pathways of the assimilatory and the dissimilatory nitrate reduction to ammonia (Daep_03263, _03264 and _03265; Daep_03099, _03100, _03263 and _03264) [63-65]. Furthermore, we detected all genes necessary for the dissimilatory nitrate reduction to nitrogen, including a cluster for the nitrate reductase (Daep_03099, _03100), the nitrite reductase (Daep_02798), the nitric oxide reductase (Daep_00020, _00021) and the nitrous oxide reductase (Daep_03697) .
P. daeponensis encodes a gene transfer agent (GTA), a virus-like particle that mediates the transfer of genomic DNA between prokaryotes . The GTA cluster has a length of ~17 kb (Daep_01107 – Daep_01126) and has a high homology to GTAs of other Phaeobacter species, e.g. the P. inhibens strains DSM 17395, 2.10 and T5T Drug_discovery [28,67].