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

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Protocol publication

[…] 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/) () 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) (). 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 (), 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 () 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 and ). Loktanella vestfoldensis strain SMR4r may also be able to digest dimethylsulfoniopropionate (DMSP), an organosulfur compound produced by many phytoplankton and used by some bacteria (); when the annotated genome of strain SMR4r was examined in Pathway Tools version 20.5 (), 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 (). These additional regions in pSMR4r-2 contain three transposase genes, two DNA invertase genes, and an additional mercuric reductase gene. […]

Pipeline specifications

Software tools PhyloPhlAn, Prokka, Pathway Tools
Databases tmRNA
Application Phylogenetics
Organisms Skeletonema marinoi