Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566(T.)

Abstract

Phaeobacter arcticus Zhang et al. 2008 belongs to the marine Roseobacter clade whose members are phylogenetically and physiologically diverse. In contrast to the type species of this genus, Phaeobacter gallaeciensis, which is well characterized, relatively little is known about the characteristics of P. arcticus. Here, we describe the features of this organism including the annotated high-quality draft genome sequence and highlight some particular traits. The 5,049,232 bp long genome with its 4,828 protein-coding and 81 RNA genes consists of one chromosome and five extrachromosomal elements. Prophage sequences identified via PHAST constitute nearly 5% of the bacterial chromosome and included a potential Mu-like phage as well as a gene-transfer agent (GTA). In addition, the genome of strain DSM 23566(T) encodes all of the genes necessary for assimilatory nitrate reduction. Phylogenetic analysis and intergenomic distances indicate that the classification of the species might need to be reconsidered.

Keywords: Alphaproteobacteria; Roseobacter clade; aerobic; assimilatory nitrate reduction; extrachromosomal elements; high-quality draft; motile; prophage-like structures; psychrophilic.

Figure 1

Phylogenetic tree highlighting the position of P. arcticus relative to the type strains of the other species within the genus Phaeobacter and neighboring genera such as Leisingera. The tree was inferred from 1,385 aligned characters [6,7] of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion [8]. Oceanicola species were included in the dataset 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 [9] (left) and from 1,000 maximum-parsimony bootstrap replicates [10] (right) if larger than 60%. Lineages with type-strain genome sequencing projects registered in GOLD [11] are labeled with one asterisk, those also listed as 'Complete and Published' with two asterisks [12]. Two novel genome sequences were published in this issue [58,59].

Figure 2

Scanning electron micrograph of P. arcticus DSM 23566^T

Figure 3a

Graphical map of the Phaeobacter arcticus DSM 23566^T chromosome cArct_4215. From bottom to the top: Genes on forward strand (color 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 3b

Graphical map of the Phaeobacter arcticus DSM 23566^T extrachromosomal element pArct_A280. From outside to the center: Genes on forward strand (color 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 3c

Graphical map of the Phaeobacter arcticus DSM 23566^T extrachromosomal element pArct_B229. From outside to the center: Genes on forward strand (color 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

Graphical map of the Phaeobacter arcticus DSM 23566^T extrachromosomal element pArct_C203. From bottom to the top: Genes on forward strand (color 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 3e

Graphical map of the Phaeobacter arcticus DSM 23566^T extrachromosomal element pArct_D92. From bottom to the top: Genes on forward strand (color 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

Graphical map of the Phaeobacter arcticus DSM 23566^T extrachromosomal element pArct_E29. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.