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Announcement
22 March 2018

Complete Genome Sequence of Loktanella vestfoldensis Strain SMR4r, a Novel Strain Isolated from a Culture of the Chain-Forming Diatom Skeletonema marinoi

ABSTRACT

We report here the genome sequence of Loktanella vestfoldensis strain SMR4r, isolated from the marine diatom Skeletonema marinoi strain RO5AC. Its 3,987,360-bp genome consists of a circular chromosome and two circular plasmids, one of which appears to be shared with an S. marinoi-associated Roseovarius species.

GENOME ANNOUNCEMENT

The chain-forming diatom Skeletonema marinoi strain RO5AC associates with a large number of bacterial species, and efforts are ongoing to determine their roles in the diatom-microbe holobiont. Loktanella vestfoldensis strain SMR4r is one such bacterium which has been found as a result. The diatom strain was established from a germinated resting cell embedded in top-layer sediment, collected from 14 m depth with a box corer in May 2010 from Öresund, Sweden (55°59.16′N, 12°44.02′E). The bacterial genome was sequenced using PacBio RS II technology (Pacific Biosciences, Menlo Park, CA, USA) on one single-molecule real-time (SMRT) cell, producing 81,585 uncorrected reads totaling 845.4 Mbp. Falcon version 1.7.5 (https://github.com/PacificBiosciences/FALCON/) (1) was used to assemble the reads (seed read length, 17,100 bp), and contig circularization was confirmed by joining the corresponding ends and realigning the reads using the RS_Resequencing.1 protocol on SMRT Portal version 2.3.0 (Pacific Biosciences) (2). The final assembly contained three circular contigs totaling 3,987,360 bp (average read coverage, 177.86×).
The chromosome is 3,836,950 bp long, with a G+C content of 60.8%; plasmid pSMR4r-1 is 111,030 bp (G+C content, 57.4%), and plasmid pSMR4r-2 is 39,380 bp (G+C content, 58.2%). Strain SMR4r’s two identical 16S rRNA sequences have 99.8% identity with the three 16S sequences of L. vestfoldensis strain DSM 16212T (GenBank accession number NZ_ARNL00000000). A phylotaxonomic analysis using PhyloPhlAn version 0.99 (3), comparing strain SMR4r to all whole-genome-sequenced Rhodobacteraceae strains on NCBI’s RefSeq site (ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/), showed it to be a sister to L. vestfoldensis strain DSM 16212T (100% bootstrap support). Annotation using Prokka version 1.12beta (4) predicted 3,936 coding sequences (CDSs; with 3,267 proteins having a functional prediction and 669 labeled as hypothetical), 8 pseudogenes, 45 tRNAs, 6 rRNAs, 19 noncoding RNAs (ncRNAs), and 1 transfer-messenger RNA (tmRNA).
Loktanella vestfoldensis strain SMR4r contains genes for both phosphatidylcholine synthase (LOKVESSMR4R_00456) and acyl-homoserine-lactone synthase (LOKVESSMR4R_01736, involved in quorum sensing), suggesting interaction with a eukaryote (reviewed in references 5 and 6). Loktanella vestfoldensis strain SMR4r may also be able to digest dimethylsulfoniopropionate (DMSP), an organosulfur compound produced by many phytoplankton and used by some bacteria (7); when the annotated genome of strain SMR4r was examined in Pathway Tools version 20.5 (8), three of the five enzymes in the DMSP degradation superpathway were found, two of which, dmdA (LOKVESSMR4R_00811) and dmdC (LOKVESSMR4R_00511 and LOKVESSMR4R_02869), are noted by Pathway Tools as being unique to this pathway.
There is also evidence that strain SMR4r interacts with another S. marinoi-associated bacterial species. Plasmid pSMR4r-2 contains interrupted regions accounting for the entirety of the Roseovarius mucosus strain SMR3 plasmid pSMR3-2 (GenBank accession number CP020476), with 100% sequence identity (9). These additional regions in pSMR4r-2 contain three transposase genes, two DNA invertase genes, and an additional mercuric reductase gene.

Accession number(s).

This whole-genome project has been deposited in GenBank under the accession numbers CP021431, CP021432, and CP021433, as part of BioProject number PRJNA380207.

ACKNOWLEDGMENTS

This work was supported by the Gordon and Betty Moore Foundation (to M.T., A.G., and A.K.C., grant 4967), the Swedish Research Council VR (to A.K.C., grant 2015-04286), and the Swedish Research Council Formas (to A.G., grant 219-2012–2070).
We thank the Linnéus Center for Marine Evolutionary Biology (CeMEB; http://cemeb.science.gu.se/) for support.
All bioinformatics analyses were run on the Albiorix computer cluster (http://albiorix.bioenv.gu.se/) at the Department of Marine Sciences, University of Gothenburg.

REFERENCES

1.
Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, Shendure J, Wilson RK, Haussler D, Chin C-S, Eichler EE. 2016. Long-read sequence assembly of the gorilla genome. Science 352:aae0344.
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Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569.
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Segata N, Börnigen D, Morgan XC, Huttenhower C. 2013. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 4:2304.
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Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069.
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Sohlenkamp C, López-Lara IM, Geiger O. 2003. Biosynthesis of phosphatidylcholine in bacteria. Prog Lipid Res 42:115–162.
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Miller MB, Bassler BL. 2001. Quorum sensing in bacteria. Annu Rev Microbiol 55:165–199.
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Reisch CR, Moran MA, Whitman WB. 2011. Bacterial catabolism of dimethylsulfoniopropionate (DMSP). Front Microbiol 2:172.
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Karp PD, Paley S, Romero P. 2002. The Pathway Tools software. Bioinformatics 18:S225–S232.
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Töpel M, Pinder MIM, Johansson ON, Kourtchenko O, Godhe A, Clarke AK. 2017. Genome sequence of Roseovarius mucosus strain SMR3, isolated from a culture of the diatom Skeletonema marinoi. Genome Announc 5:e00394-17.

Information & Contributors

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Published In

cover image Genome Announcements
Genome Announcements
Volume 6Number 1222 March 2018
eLocator: e01558-17
PubMed: 29567748

History

Received: 13 December 2017
Accepted: 23 February 2018
Published online: 22 March 2018

Contributors

Authors

Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
Matthew I. M. Pinder
Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
Oskar N. Johansson
Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
Olga Kourtchenko
Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
Anna Godhe
Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
Adrian K. Clarke
Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden

Notes

Address correspondence to Mats Töpel, [email protected].
M.T. and M.I.M.P. contributed equally to this work.

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