Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210(T) (= DSM 26640(T) = BS107(T))

Abstract

Phaeobacter gallaeciensis CIP 105210(T) (= DSM 26640(T) = BS107(T)) is the type strain of the species Phaeobacter gallaeciensis. The genus Phaeobacter belongs to the marine Roseobacter group (Rhodobacteraceae, Alphaproteobacteria). Phaeobacter species are effective colonizers of marine surfaces, including frequent associations with eukaryotes. Strain BS107(T) was isolated from a rearing of the scallop Pecten maximus. Here we describe the features of this organism, together with the complete genome sequence, comprising eight circular replicons with a total of 4,448 genes. In addition to a high number of extrachromosomal replicons, the genome contains six genomic island and three putative prophage regions, as well as a hybrid between a plasmid and a circular phage. Phylogenomic analyses confirm previous results, which indicated that the originally reported P. gallaeciensis type-strain deposit DSM 17395 belongs to P. inhibens and that CIP 105210(T) (= DSM 26640(T)) is the sole genome-sequenced representative of P. gallaeciensis.

Keywords: Alphaproteobacteria; Phaeobacter inhibens; Plasmid wealth; Replication systems; Roseobacter group; Sister species.

Figure 1

Phylogenetic tree highlighting the position of P. gallaeciensis relative to the type strains of the other species within the genus Phaeobacter and the neighboring genus Leisingera. The tree was inferred from 1,381 aligned characters of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion as previously described [9]. Ruegeria spp. were included in the dataset for use as outgroup taxa. The branches are scaled in terms of the expected number of substitutions per site. Numbers adjacent to the branches are support values from 1,000 ML bootstrap replicates (left) and from 1,000 maximum-parsimony bootstrap replicates (right) if larger than 60% [9]. Lineages with type strain genome sequencing projects registered in GOLD [10] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks. Genome sequences are available for P. arcticus (DQ514304) [11], P. inhibens (AY177712) [12], P. caeruleus (AM943630) [13], P. daeponensis (DQ981416) [14], P. gallaeciensis (IMG2545691711, this publication), L. aquimarina (AM900415) [15], L. methylohalidivorans (AY005463) [16] and R. pomeroyi (AF098491) [17].

Figure 2

Scanning electron micrograph of P. gallaeciensis CIP 105210T.

Figure 3a

Circular graphical map of the chromosome. From margin to center: Genes on forward strand (colored by COG categories), genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 3b

Circular graphical map of the extrachromosomal replicon pGal_A255. From margin to center: Genes on forward strand (colored by COG categories), genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 3c

Circular graphical map of the extrachromosomal replicon pGal_B134. From margin to center: Genes on forward strand (colored by COG categories), genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 3d

Circular graphical map of the extrachromosomal replicon pGal_C110. From margin to center: Genes on forward strand (colored by COG categories), genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 3e

Circular graphical map of the extrachromosomal replicon pGal_D78. From margin to center: Genes on forward strand (colored by COG categories), genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 3f

Circular graphical map of the extrachromosomal replicon pGal_E78. From margin to center: Genes on forward strand (colored by COG categories), genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 3g

Circular graphical map of the extrachromosomal replicon pGal_F69. From margin to center: Genes on forward strand (colored by COG categories), genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 3h

Circular graphical map of the extrachromosomal replicon pGal_G40. From margin to center: Genes on forward strand (colored by COG categories), genes on reverse strand (colored by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.

Figure 4

Summary and representation of the assortment of replicons in CIP 105210^T as previously described in [47]. Bars show the relative frequency of functional classes according to the database of clusters of orthologous groups of proteins (COGs). The cluster dendrogram arranges the replicons according to their overall codon usage. Codon-usage matrices were generated using yet unpublished scripts for the statistical analysis software R (version 2.15.0.) [54]. The hierarchical clustering analysis was conducted using the pvclust function [55] with “complete” as agglomeration method. Pvclust also returns the AU (Approximately Unbiased) values as statistical support for clusters in percent. Support values >95% are given in bold. Asterisks indicate the presence of genes for conjugation (T4SS) as listed in Table 7.

Figure 5

Phylogenetic tree inferred from the MARE-filtered supermatrix under the maximum likelihood (ML) criterion [77] and rooted using the midpoint rooting approach [84]. The branches are scaled in terms of the expected number of substitutions per site. Numbers above the branches (from left to right) are bootstrap support values [85] (if greater than 60%) from ML/MP MARE-filtered supermatrix; ML/MP unfiltered (full) supermatrix; ML/MP core-genes supermatrix; ML/MP gene-content matrix; ML/MP ortholog-content matrix. Values larger than 95% are shown in bold; dots indicate branches with maximum support under all settings. Genomes marked with stars have been renamed according to this study and [3].