Draft Genome Sequence of Pseudoalteromonas sp. Strain R3, a Red-Pigmented l-Amino Acid Oxidase-Producing Bacterium.

Here, we report a draft 5.58-Mb genome sequence of Pseudoalteromonas sp. strain R3, isolated from an intertidal-zone sludge sample, which has l-amino acid oxidase activity. The genomics information of this strain will facilitate the study of l-amino acid oxidase, quorum sensing, and the relationship of the two.

GENOME ANNOUNCEMENT

Members of the genus Pseudoalteromonas (Gammaproteobacteria, Alteromonadales, Pseudoalteromonadaceae) have been isolated from different niches around the globe, including seawater (1), sediment (2), sea ice (3), and tidal flats (4). Pseudoalteromonas is increasingly recognized as ecologically and biologically important microbe due to its influence on biofilms and its ability to synthesize bioactive molecules (5). Pseudoalteromonas sp. strain R3 was isolated from an intertidal-zone sludge sample (30.03°N, 122.11°E) located at Dinghai, Zhoushan, China, and it has been found to have l-amino acid oxidase activity, which can catalyze the oxidative deamination of l-amino acids to the corresponding α-keto acids with a release of ammonia and hydrogen peroxide (6). Pseudoalteromonas sp. R3 can also produce a red pigment and form a biofilm, which is probably regulated by quorum sensing (7). We sequenced its whole genome in order to find out whether the l-amino acid oxidase activity is regulated by quorum sensing.

The genome of Pseudoalteromonas sp. R3 was sequenced with an Illumina HiSeq 2500 platform by Nextomics Biosciences Co., Ltd. (Wuhan, China). A paired-end library with a fragment length of 300 to 500 bp, generating a total of 17,346,435 high-quality paired reads, with an average coverage of approximately 364.1×, was used. The genome was assembled by SOAPdenovo version 2.04 (http://soap.genomics.org.cn/) with multiple k-mer parameters. GapCloser version 1.12 software was subsequently applied to fill the remaining local inner gaps and correct the single-base polymorphism for the final assembly result. Glimmer version 3.02 (http://www.cbcb.umd.edu/software/glimmer/) was used to predict protein-coding open reading frames (ORFs). For RNA predictions, tRNAs were predicted by tRNAscan-SE version 1.3.1 (8), and rRNAs were predicted by RNAmmer-1.2 (9). The NCBI nonredundant (NR), Swiss-Prot (http://Uniprot.org), KEGG (http://www.genome.jp/kegg), and Clusters of Orthologous Group (COG) (http://www.ncbi.nlm.nih.gov/COG) databases were used for functional annotation.

The draft genome is estimated to 5.58 Mb, with a G+C content of 47.63% and 5,429 putative ORFs, with an average size of 944 bp. Approximately 87.8% of nucleotides were predicted to be ORFs. Furthermore, strain R3 contains 13 rRNA operons and a total of 115 tRNA genes. The genome analysis confirms the presence of the l-amino acid oxidase gene and genes related to quorum sensing.

Nucleotide sequence accession numbers.

The Pseudoalteromonas sp. R3 whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number LJDF00000000. The version described in this paper is the first version, LJDF01000000.