Abstract
Here, we present the draft genome sequence of Pseudoalteromonas tetraodonis UCD-SED8, a marine bacterium normally associated with the production of tetrodotoxin in pufferfish. This strain was isolated from sediment samples surrounding Zostera marina roots collected from Bodega Marine, California. The assembly consists of 4,017,727 bp contained in 35 contigs.
GENOME ANNOUNCEMENT
Pseudoalteromonas tetraodonis UCD-SED8 was isolated from sediment samples surrounding common eelgrass (Zostera marina) roots grown at Bodega Marine Laboratory (Bodega, Bay, California, USA). The eelgrass sampling site was located north of Westshore Park, California, USA (38°19′10.0″N, 123°03′13.8″W). P. tetraodonis is a deep-sea marine bacterium that normally produces the neurotoxin tetrodotoxin, in association with pufferfish (Fugu poecilonotus) (1). It was originally described as Alteromonas tetraodonis (2); recent phylogenetic analysis, however, has confirmed its taxonomic association with the phylum Gammaproteobacteria. As a result, its identity was emended to Pseudoalteromonas tetraodonis (1).
Serial dilutions of sediment of 1:100 and 1:1,000 were made and spread on an altered seawater nutrient agar medium (ATCC Medium 2205, using InstantOcean in place of synthetic seawater), grown at room temperature for 24 h, and individual colonies were dilution-streaked onto seawater nutrient agar petri plates. DNA was extracted from a fresh 5-mL overnight culture using a Wizard Genomic DNA purification kit (Promega). Sanger sequencing was performed on the PCR-amplified 16S rRNA product (27F and 1391R PCR primers). BLAST and phylogenetic analyses (3) were used to identify this isolate.
A Nextera DNA sample prep kit (Illumina) was used to make a paired-end library (Illumina). Libraries were sequenced on an Illumina MiSeq platform, at a read length of 300 bp. A total of 3,029,779 high-quality paired-end reads were processed by the A5 assembly pipeline (4). This pipeline automates error correction, data cleaning, contig assembly, scaffolding, and quality control. The resulting assembly consisted of 35 contigs (longest: 921,029 bp; N50: 499,738) that were submitted to GenBank. This final assembly had 4,017,727 bp with a GC content of 40.0% and an overall coverage estimate of ~380×. Genome completeness was assessed using the PhyloSift software (5), which searches for a list of 37 highly conserved, single-copy marker genes (6), of which all 37 were found in this assembly.
The RAST server was used to perform an automated annotation (7). P. tetraodonis UCD-SED8 contains 3,627 predicted protein-coding sequences and 118 predicted noncoding RNAs.
Nucleotide sequence accession numbers.
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number LITK00000000. The version described in this paper is the first version, LITK01000000.
ACKNOWLEDGMENTS
Illumina sequencing was performed at the DNA Technologies Core facility in the Genome Center at the UC Davis, Davis, California, USA. This work was funded by a grant from the Gordon and Betty Moore Foundation (GBMF3330) “Investigating the co-evolutionary relationships between seagrasses and their microbial symbionts” to J.E.
We thank Qingyi “John” Zhang for his help with the Illumina library preparation.
Footnotes
Citation Lee RD, Jospin G, Lang JM, Eisen JA, Coil DA. 2015. Draft genome sequence of Pseudoalteromonas tetraodonis strain UCD-SED8 (phylum Gammaproteobacteria). Genome Announc 3(6):e01276-15. doi:10.1128/genomeA.01276-15.
REFERENCES
- 1.Ivanova EP, Romanenko LA, Matte MH, Matte GR, Lysenko AM, Simidu U, Kita-Tsukamoto K, Sawabe T, Vysotskii MV, Frolova GM, Mikhailov V, Christen R, Colwell RR. 2001. Retrieval of the species Alteromonas tetraodonis Simidu et al. 1990 as Pseudoalteromonas tetraodonis comb. nov. and emendation of description. Int J Syst Evol Microbiol 51:1071–1078. doi: 10.1099/00207713-51-3-1071. [DOI] [PubMed] [Google Scholar]
- 2.Simidu U, Kita-Tsukamoto K, Yasumoto T, Yotsu M. 1990. Taxonomy of four marine bacterial strains that produce tetrodotoxin. Int J Syst Bacteriol 40:331–336. doi: 10.1099/00207713-40-4-331. [DOI] [PubMed] [Google Scholar]
- 3.Dunitz MI, Lang JM, Jospin G, Darling AE, Eisen JA, Coil DA. 2015. Swabs to genomes: a comprehensive workflow. PeerJ 3:e453v452. doi: 10.7717/peerj.960. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Tritt A, Eisen JA, Facciotti MT, Darling AE. 2012. An integrated pipeline for de novo assembly of microbial genomes. PLoS One 7:e42304. doi: 10.1371/journal.pone.0042304. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Darling AE, Jospin G, Lowe E, Matsen IV FA, Bik HM, Eisen JA. 2014. PhyloSift: phylogenetic analysis of genomes and metagenomes. PeerJ 2:e243. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.Wu D, Jospin G, Eisen J. 2013. Systematic identification of gene families for use as “markers” for phylogenetic and phylogeny-driven ecological studies of bacteria and archaea and their major subgroups. PLoS One 8:e77033. doi: 10.1371/journal.pone.0077033. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Aziz RK, Bartels D, Best AA, Disz T, Edwards R, Formsma K, Gerdes S, Glass E, Kubal M, Meyer F, Olsen G, Olsen R, Osterman A, Overbeek R, McNeil L, Paarmann D, Paczian T, Parrello B, Pusch G, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]