Abstract
Bacteria of the genus Photobacterium thrive worldwide in oceans and show substantially varied lifestyles, including free-living, commensal, pathogenic, symbiotic, and piezophilic. Here, we present the genome sequence of a luminous, piezophilic Photobacterium phosphoreum strain, ANT-2200, isolated from a water column at 2,200 m depth in the Mediterranean Sea. It is the first genomic sequence of the P. phosphoreum group. An analysis of the sequence provides insight into the adaptation of bacteria to the deep-sea habitat.
GENOME ANNOUNCEMENT
Photobacterium is one of the major genera of the family Vibrionaceae and is widespread in marine environments. Previously, the name Photobacterium phosphoreum was used to refer to various species. Recent multilocus fine-scale phylogenetic analysis has resolved three distinct species in the P. phosphoreum group: Photobacterium phosphoreum, Photobacterium iliopiscarium, and Photobacterium kishitanii (1). Among them, P. phosphoreum and P. kishitanii are luminous, and P. kishitanii is the only species found in the light organs of deep-sea fishes. None of the P. iliopiscarium strains analyzed emit light. P. phosphoreum ANT-2200 is a piezophilic species isolated from the Mediterranean Sea at a depth of 2,200 m (2, 3). To gain insight into the genetic traits underlying the differences among the three closely related species of the P. phosphoreum group dwelling in different environments, we sequenced the genome of P. phosphoreum ANT-2200.
The ANT-2200 whole-genome shotgun sequence was obtained using the Illumina technology. Mate-paired (MP) and paired-end (PE) libraries were created with 8-kb and 350-bp insert sizes, respectively. The sequencing was performed on a MiSeq instrument with paired read lengths of 150, leading to 90- and 180-fold coverage for the MP and PE data, respectively. These data were assembled using Velvet 1.0 (http://www.ebi.ac.uk/~zerbino/velvet), and to reduce the number of undetermined bases, GapCloser (http://soap.genomics.org.cn/soapdenovo.html) was used on the scaffold sequences, with the PE reads. The annotation was performed using the MicroScope platform (https://www.genoscope.cns.fr/agc/microscope/home/index.php) (4).
The whole-genome draft of P. phosphoreum ANT-2200 consists of 25 contigs assembled into 19 scaffolds, for a total of 5,107,216 bp with 38.89% G+C content. A total of 4,667 coding DNA sequences were predicted, as well as 36 miscellaneous RNAs, 6 disrupted rRNA operons, and 168 tRNA genes.
Among the NCBI genomic reference sequences, the top 11 that were homologous to the P. phosphoreum ANT-2200 genome are from 6 Photobacterium genomes with decreasing E values, in the following order: P. leiognathi subsp. mandapamensis svers.1.1 (accession no. NZ_DF093598.1), P. leiognathi lrivu.4.1 (accession no. NZ_DF196819.1), P. angustum S14 (accession no. NZ_CH902602.1), P. profundum SS9 (accession no. NC_006370.1), Photobacterium sp. strain SKA34 (accession no. NZ_CH724145.1), P. angustum S14 (accession no. NZ_CH902604.1), P. leiognathi subsp. mandapamensis svers.1.1 (accession no. NZ_DF093594.1), P. leiognathi lrivu.4.1 (accession no. NZ_DF196811.1), Photobacterium sp. SKA34 (accession no. NZ_CH724147.1), P. angustum S14 (accession no. NZ_CH902603.1), and P. profundum 3TCK (accession no. NZ_CH724136.1). A synton of the luxLCDABFEG-ribEBHA luminous genes was found in the ANT-2200 genome and is perfectly conserved in the genome of P. leiognathi subsp. mandapamensis svers.1.1. As a trait of adaptation to the deep-sea habitat, the genome of the piezophilic P. profundum strain SS9 contains 2 sets of flagellar genes functioning under different pressures and viscosities (5). ANT-2200 bears two sets of flagellar genes that are highly conserved compared to those from SS9. Furthermore, SS9 has multiple torA genes encoding trimethylamine N-oxide reductases, one of them being upregulated by high hydrostatic pressure (6). Interestingly, the genome of P. phosphoreum ANT-2200 has four copies of torA, including the counterpart of the pressure-upregulated torA. The genome of P. phosphoreum ANT-2200 will be used as the first representative of the P. phosphoreum group in studies of the evolution of luminous bacteria and adaptation of bacteria to the deep-sea habitats.
Nucleotide sequence accession numbers.
The genome sequence of P. phosphoreum ANT-2200 was deposited in EMBL under accession no. CCAR010000001 to CCAR010000025 .
ACKNOWLEDGMENTS
This work was supported by grant SIDSSE-201307 and the Strategic Priority Research Program grant XDB06010200 from the Chinese Academy of Sciences, a grant for LIA-BioMNSL from the Centre National de la Recherche Scientifique, the grant DY125-15-R-03 from the China Ocean Mineral Resources R & D Association (COMRA) Special Foundation, the grant NSFC 41306161 from the National Science Foundation of China, and a grant from the Mt. Tai Scholar Construction Engineering Special Foundation of Shandong Province. D. Murat was supported by a grant from the Fondation pour la Recherche Médicale, SPF20110421349.
We thank France Genomique for the support for this sequencing project.
Footnotes
Citation Zhang S-D, Barbe V, Garel M, Zhang W-J, Chen H, Santini C-L, Murat D, Jing H, Zhao Y, Lajus A, Martini S, Pradel N, Tamburini C, Wu L-F. 2014. Genome sequence of luminous piezophile Photobacterium phosphoreum ANT-2200. Genome Announc. 2(2):e00096-14. doi:10.1128/genomeA.00096-14.
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