Abstract
We report here the 6.0-Mb draft genome assembly of Pseudoalteromonas luteoviolacea strain IPB1 that was isolated from the Hawaiian marine sponge Iotrochota protea. Genome mining complemented with bioassay studies will elucidate secondary metabolite biosynthetic pathways and will help explain the ecological interaction between host sponge and microorganism.
GENOME ANNOUNCEMENT
Marine sponges are known to harbor diverse microbial communities. The species composition of these microbial communities is dependent on temporal and geographic factors (1–3). Many of the associated microorganisms are capable of producing bioactive secondary metabolites, which contribute to the ecological success of the host organism (4, 5). Pseudoalteromonas luteoviolacea strain IPB1 is a Gram-negative marine bacterium that was isolated from a Hawaiian marine sponge, Iotrochota protea, found in Puhi Bay (Hilo, HI), and identified from 16S rRNA sequencing and phylogenetic analysis. To our knowledge, this is the first published genome of P. luteoviolacea found within a marine sponge host (6, 7).
Genomic DNA of strain IPB1 was isolated using the UltraClean microbial DNA isolation kit (Mo Bio Laboratories, Inc.). A genome library was prepared using a Fast DNA fragmentation and library prep set for Ion Torrent (New England BioLabs), selected to a target length of 480 bp. An Ion Torrent library quantification kit (Kapa Biosystems) and a high-sensitivity DNA kit (Agilent) were used to determine the library dilution factor and assess the library size distribution, respectively. Emulsion PCR was performed using the Ion PGM Hi-Q OT2 kit-400 on an Ion OneTouch 2 system. The percent templated Ion Sphere particles for unenriched samples was measured with the Ion Sphere quality control kit on the Qubit fluorometer 3.0. Template enrichment was performed on Ion OneTouch enrichment system. The sample was loaded into an Ion 318 Chip version 2 and sequenced using the Ion PGM Hi-Q sequencing kit on the Ion PGM system.
The sequencing yielded 5,378,737 reads, with an average read length of 306 bp, totaling 1.65 Gb. Quality assessment of with the SPAdes software assembly resulted in a final genome assembly of 91 contigs, with a total size of 6,068,981 bp (265-fold coverage), an N50 contig length of 539,200 nucleotides, and a mean G+C content of 42.7%. The draft genome was annotated by the Rapid Annotations using Subsystems Technology (RAST) server and NCBI Prokaryotic Genome Annotation Pipeline (PGAP), which predicted 4,885 gene-coding sequences and 128 RNAs (73 tRNAs and 51 rRNAs) (8, 9). Secondary metabolite gene clusters were characterized using antiSMASH and PRISM (10–14). Further genome analysis and manipulation will be performed to determine the biosynthetic pathways involved in secondary metabolite production. By understanding the function of P. luteoviolacea IPB1, it will help toward elucidating its ecological role within the Hawaiian marine sponge host, I. protea.
Accession number(s).
The annotated draft genome sequence was deposited in DDBJ/EMBL/GenBank under accession no. MAUJ00000000. The version described in this paper is version MAUJ00000000.1.
ACKNOWLEDGMENTS
This research was supported by the University of Hawaii at Hilo Evolutionary Genomics Core Facility and the U.S. National Science Foundation grant HRD 0833211.
Footnotes
Citation Sakai-Kawada FE, Yakym CJ, Helmkampf M, Hagiwara K, Ip CG, Antonio BJ, Armstrong E, Ulloa WJ, Awaya JD. 2016. Draft genome sequence of marine sponge symbiont Pseudoalteromonas luteoviolacea IPB1, isolated from Hilo, Hawaii. Genome Announc 4(5):e01002-16. doi:10.1128/genomeA.01002-16.
REFERENCES
- 1.Lee YK, Lee J, Lee HK. 2001. Microbial symbiosis in marine sponges. J Microbiol 39:254–264. [Google Scholar]
- 2.Wang X, Brandt D, Thakur NL, Wiens M, Batel R, Schröder HC, Müller WEG. 2013. Molecular cross-talk between sponge host and associated microbes. Phytochem Rev 12:369–390. doi: 10.1007/s11101-012-9226-8. [DOI] [Google Scholar]
- 3.Webster NS, Taylor MW. 2012. Marine sponges and their microbial symbionts: love and other relationships. Environ Microbiol 14:335–346. doi: 10.1111/j.1462-2920.2011.02460.x. [DOI] [PubMed] [Google Scholar]
- 4.Bowman JP. 2007. Bioactive compound synthetic capacity and ecological significance of marine bacterial genus Pseudoalteromonas. Mar Drugs 5:220–241. doi: 10.3390/md504220. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.Holmström C, Kjelleberg S. 1999. Marine Pseudoalteromonas species are associated with higher organisms and produce biologically active extracellular agents. FEMS Microbiol Ecol 30:285–293. [DOI] [PubMed] [Google Scholar]
- 6.Cress BF, Erkert KA, Barquera B, Koffas MAG. 2013. Draft genome sequence of Pseudoalteromonas luteoviolacea strain B (ATCC 29581). Genome Announc 1(2):e00048-13. doi: 10.1128/genomeA.00048-13. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 7.Asahina AY, Hadfield MG. 2015. Draft genome sequence of Pseudoalteromonas luteoviolacea HI1, determined using Roche 454 and PacBio single-molecule real-time hybrid sequencing. Genome Announc 3(1):e01590-14. doi: 10.1128/genomeA.01590-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, 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]
- 9.Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R. 2014. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:D206–D214. doi: 10.1093/nar/gkt1226. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 10.Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P, Fischbach MA, Weber T, Takano E, Breitling R. 2011. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39:W339–W346. doi: 10.1093/nar/gkr466. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 11.Steinbeck C, Han Y, Kuhn S, Horlacher O, Luttmann E, Willighagen E. 2003. The chemistry development kit (CDK): an open-source Java library for chemo- and bioinformatics. J Chem Inf Comput Sci 43:493–500. doi: 10.1021/ci025584y. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 12.Finn RD, Clements J, Eddy SR. 2011. HMMER Web server: interactive sequence similarity searching. Nucleic Acids Res 39:W29–W37. doi: 10.1093/nar/gkr367. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 13.Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic local alignment search tool. J Mol Biol 215:403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
- 14.Prlić A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh CH, Foisy S, Holland R, Rimša G, Heuer ML, Brandstätter-Müller H, Bourne PE, Willis S. 2012. BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics 28:2693–2695. doi: 10.1093/bioinformatics/bts494. [DOI] [PMC free article] [PubMed] [Google Scholar]