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Announcement
1 June 2017

Genome Sequence of Roseovarius mucosus Strain SMR3, Isolated from a Culture of the Diatom Skeletonema marinoi

ABSTRACT

We present the genome of Roseovarius mucosus strain SMR3, a marine bacterium isolated from the diatom Skeletonema marinoi strain RO5AC sampled from top layer sediments at 14 m depth. Its 4,381,426 bp genome consists of a circular chromosome and two circular plasmids and contains 4,178 coding sequences (CDSs).

GENOME ANNOUNCEMENT

Roseovarius mucosus strain SMR3 was isolated from a culture of the chain-forming diatom Skeletonema marinoi. The diatom strain (RO5AC) was established from a germinated resting cell embedded in sediment. Sediment was collected with a box corer in Öresund, Sweden (55°59.16′ N, 12°44.02′ E), in May 2010. The genome was sequenced on one single-molecule real-time (SMRT) cell using the PacBio RSII system (Pacific Biosciences, Menlo Park, CA, USA), which produced 83,546 uncorrected reads totaling 756.4 Mbp. Reads were assembled using Falcon version 1.7.5 (https://github.com/PacificBiosciences/FALCON/ [1]) with a seed read length of 7,000 bp, and circularization of contigs 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 resulting assembly contained three circular contigs totaling 4,381,426 bp, with average read coverage of 144.99×.
The chromosome is 4,170,996 bp long with a G+C content of 60.9%, plasmid pSMR3-1 is 180,135 bp (G+C 60.1%) and plasmid pSMR3-2 is 30,295 bp (G+C 58.3%). The two identical 16S rRNA sequences found in the chromosome have 99.8% identity with that of R. mucosus DSM 17069T (accession no. AONH01000000). Sequences identical to the SMR3 16S sequences were also found at three locations in Roseovarius sp. TM1035 (accession no. NZ_ABCL00000000). A phylotaxonomic analysis using PhyloPhlAn version 0.99 (3), comparing the SMR3 strain to all whole-genome sequenced strains in the family Rhodobacteraceae available at the NCBI RefSeq ftp site (ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/ ), showed it to be sister to Roseovarius sp. TM1035, and together with Roseovarius mucosus strain DSM 17069T forming a clade with 100% bootstrap support. Annotation was performed using Prokka version 1.12beta (4), which predicted 4,178 coding sequences (CDSs) (3,542 with a functional prediction and 636 hypothetical proteins), 3 pseudogenes, 46 tRNAs, 6 rRNAs, 5 noncoding RNAs (ncRNAs), and 1 tmRNA.
Roseovarius mucosus strain SMR3 contains two phosphatidylcholine synthase genes (ROSMUCSMR3_00993 and ROSMUCSMR3_02532), and both an acyl-homoserine-lactone synthase and luxR gene (ROSMUCSMR3_00613 and ROSMUCSMR3_00149, respectively; both involved in quorum sensing), all of which are suggestive of a symbiotic or pathogenic relationship with a eukaryote (reviewed in references 5 and 6). There is also evidence of interaction in the form of horizontal gene transfer between R. mucosus strain SMR3 and other bacteria within the S. marinoi microbiome. The pSMR3-2 plasmid shares 100% sequence identity, over the full length of the plasmid, with interrupted regions of a Loktanella sp. plasmid found in the same S. marinoi culture. These interruptions can primarily be accounted for by transposase genes on the Loktanella sp. plasmid.

Accession number(s).

This whole-genome project has been deposited in GenBank under the accession numbers CP020474, CP020475, and CP020476, as part of BioProject No. PRJNA380207.

ACKNOWLEDGMENTS

This work was supported by the Gordon and Betty Moore Foundation (A.K.C., M.T., A.G.; Grant 4967), the Swedish Research Council VR (A.K.C., grant 2015-04286), and the Swedish Research Council Formas (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, and Eichler EE. 2016. Long-read sequence assembly of the gorilla genome. Science352:aae0344.
2.
Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, and Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods10:563–569.
3.
Segata N, Börnigen D, Morgan XC, and Huttenhower C. 2013. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun4:2304.
4.
Seemann T. 2014. Prokka: Rapid prokaryotic genome annotation. Bioinformatics30:2068–2069.
5.
Sohlenkamp C, López-Lara IM, and Geiger O. 2003. Biosynthesis of phosphatidylcholine in bacteria. Prog Lipid Res42:115–162.
6.
Miller MB and Bassler BL. 2001. Quorum sensing in bacteria. Annu Rev Microbiol55:165–199.

Information & Contributors

Information

Published In

cover image Genome Announcements
Genome Announcements
Volume 5Number 221 June 2017
eLocator: 10.1128/genomea.00394-17

History

Received: 30 March 2017
Accepted: 11 April 2017
Published online: 1 June 2017

Contributors

Authors

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