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Complete Genome Sequence of Marinifilaceae Bacterium Strain

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Marine Genomics 39 (2018) 1–2 Contents lists available at ScienceDirect Marine Genomics journal homepage: www.elsevier.com/locate/margen Complete genome sequence of Marinifilaceae bacterium strain SPP2, isolated from the Antarctic marine sediment Miho Watanabe a,b,⁎, Hisaya Kojima a, Manabu Fukui a a The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan b Postdoctoral Research Fellow of the Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-8471, Japan article info abstract Article history: Marinifilaceae bacterium strain SPP2 is a Gram-negative facultative anaerobe, isolated from the Antarctic marine Received 8 June 2017 sediment. Here, we present the complete genome sequence of Marinifilaceae bacterium strain SPP2, which con- Received in revised form 27 June 2017 sists of 5,718,991 bp with a G + C content of 35.99%. The genome data provides insights of microbial evolution Accepted 27 June 2017 and adaption in the Antarctic marine ecosystem. Available online 1 July 2017 © 2017 Elsevier B.V. All rights reserved. Keywords: Complete genome sequence Antarctica Bacteroidetes 1. Introduction quality scaffolds by using RS_HGAP_Assembly.3 (SMRT Analysis 2.3). The genome sequence was automatically annotated and analyzed Marinifilaceae bacterium strain SPP2 (=NBRC 111151) was isolated through the MiGAP pipeline (Sugawara et al., 2009). In this pipeline, from the marine sediments of Langhovde, Antarctica. Phylogenetic anal- RNAmmer (Lagesen et al., 2007) and tRNAscan-SE (Lowe and Eddy, ysis based on the 16S rRNA gene sequences showed that strain SPP2 was 1997) were used to identify rRNA and tRNA genes, respectively. classified into the family Marinifilaceae, the order Marinilabiliales and MetaGene Annotator (Noguchi et al., 2008) was used for prediction of the class Bacteroidia within the phylum Bacteroidetes (Fig. 1). This iso- open reading frames likely to encode proteins (coding sequences late showed the highest sequence similarities with Marinifilum [CDSs]), and functional annotation was performed based on reference albidiflavum (Xu et al., 2016; 93.8% sequence similarity) and databases, including Reference Sequence (RefSeq), TrEMBL, and Clus- Ancylomarina subtilis (Wu et al., 2016; 94.1%). This strain is a facultative ters of Orthologous Groups (COGs). Manual annotation was performed anaerobic, Gram-negative and weakly motile bacterium. Here, we de- using IMC-GE software (In Silico Biology; Yokohama, Japan). Putative scribe complete genome sequence and annotation of Marinifilaceae bac- CDSs possessing BLASTP matches with N70% coverage, 35% identity terium strain SPP2, which will provide further insight into microbial and E-values b 1×e−5 were considered potentially functional genes. evolution and Antarctic marine ecosystem. The CDSs were annotated as hypothetical proteins when these standard values were not satisfied. Transcription start sites of predicted proteins 2. Data description were corrected based on multiple sequence alignments. The protein- coding genes in the genome were also subjected to analysis on Strain SPP2 was grown aerobically on Marine broth 2216 (Difco) at WebMGA (Wu et al., 2016) for the COGs annotations. Transmembrane 15 °C without shaking. Genomic DNA was extracted from collected helices and signal peptides were predicted by using Phobius (Käll et cells using NucleoSpin Tissue Kit (Macherey-Nagel GmbH & Co., al., 2007). CRISPR loci were distinguished using the CRISPR Recognition Duren, Germany). Library construction and sequencing using the PacBio Tool (Bland et al., 2007). General features of Marinifilaceae bacterium RS II platform were carried out at Takara Bio Inc., Japan. A total of 81,920 strain SPP2 and the MIxS mandatory information were show in Table 1. polymerase reads (1,109,405,149 bp) were generated and filtered. The The final genome was comprised of a single 5,718,991 bp circular resulting sequences (1,108,341,501 bp) were assembled into 1 high chromosome, harboring a total of 4337 predicted protein-coding se- quences with a G + C content of 35.99% (Table 2). There were 83 tRNA genes and 22 rRNA genes predicted in the genome. Approximately 70.3% of all coding proteins were assigned to 20 COG functional catego- ⁎ Corresponding author at: The Institute of Low Temperature Science, Hokkaido University, Nishi 8, Kita 19, Kita-ku Sapporo, Hokkaido 060-0819, Japan. ries. The complete genome sequence will provide fundamental informa- E-mail address: [email protected] (M. Watanabe). tion for further research of polar microbiology. http://dx.doi.org/10.1016/j.margen.2017.06.006 1874-7787/© 2017 Elsevier B.V. All rights reserved. 2 M. Watanabe et al. / Marine Genomics 39 (2018) 1–2 Fig. 1. Phylogenetic tree showing the relationship of Marinifilaceae bacterium strain SPP2 and related representatives. The tree was constructed by the Maximum-Likelihood method with MEGA version 7.0.20 (Kumar et al., 2016) based on ClustalX version 2.1 (Larkin et al., 2007) aligned sequences of 16S rRNA gene. Bootstrap values (percentages of 1000 replications) of ≥50% are shown at nodes. Nucleotide sequence accession numbers Table 2 General genomic features of Marinifilaceae bacterium strain SPP2. The complete genome sequence of Marinifilaceae bacterium strain Attributes Value % of total SPP2 (=NBRC 111151) has been deposited at DDBJ/EMBL/GenBank Genome size (bp) 5,718,991 100.00 under the accession number of AP018042. Contig 1 100.00 DNA coding region (bp) 4,836,282 84.57 Acknowledgements DNA G + C content (bp) 2,058,548 35.99 Total genes 4436 100.00 RNA count 105 2.37 This study was supported by a grant-in-aid for Research Fellow of Ja- rRNA 22 0.50 pan Society for the Promotion Science to MW and JSPS KAKENHI Grant tRNA 83 1.87 Number 22370005 to M. Fukui. We also thank members of the 47th Ja- Protein-coding genes 4331 97.63 pan Antarctica Research Expedition (Expedition leader: K. Shiraishi, Genes with function prediction 2349 54.24 Genes assigned to COGs 3044 70.28 NIPR) for logistical assistance. Genes with peptide signals 1186 27.38 Genes with transmembrane helices 907 20.94 CRISPR repeats 3 – Table 1 General features and genome sequencing project information for Marinifilaceae bacterium strain SPP2 according to the MIGS recommendations. References Items Description Bland, C., Ramsey, T.L., Sabree, F., Lowe, M., Brown, K., Kyrpides, N.C., Hugenholtz, P., 2007. General features CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly Classification Domain Bacteria interspaced palindromic repeats. BMC Bioinf. 8, 209. Phylum Bacteroidetes Käll, L., Krogh, A., Sonnhammer, E.L.L., 2007. Advantages of combined transmembrane to- Order Bacteroidales pology and signal peptide prediction: the Phobius web server. Nucleic Acids Res. 35, Family Marinifilaceae W429–W432. Particle shape Rod Kumar, S., Stecher, G., Tamura, K., 2016. MEGA7: molecular evolutionary genetics analysis Gram stain Negative version 7.0 for bigger datasets. Mol. Biol. Evol., msw054 Temperature 0–25 °C Lagesen, K., Hallin, P., Rødland, E.A., Staerfeldt, H.H., Rognes, T., Ussery, D.W., 2007. Salinity 2–4% RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Motility Weakly motile Res. 35, 3100–3108. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., MIxS data Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., et al., 2007. Clustal W and Clustal X ver- Submitted_to_insdc AP018042 (GenBank) sion 2.0. Bioinformatics 23, 2947–2948. Investigation_type Bacteria Lowe, T.M., Eddy, S.R., 1997. tRNAscan-SE: a program for improved detection of transfer Project_name Complete genome sequence of Marinifilaceae bacterium RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964. fi strain SPP2 Noguchi, H., Taniguchi, T., Itoh, T., 2008. MetaGeneAnnotator: detecting species-speci c Geo_loc_name Langhovde, Antarctica patterns of ribosomal binding site for precise gene prediction in anonymous prokary- otic and phage genomes. DNA Res. 15, 387–396. Collection_date 27-01-2006 Sugawara, H., Ohyama, A., Mori, H., Kurokawa, K., 2009. Microbial GenomeAnnotation Lat_lon Missing Pipeline (MiGAP) for diverse users. Software Demonstrations S001-1-2L. 20th Int. Env_biome Marine sediment (ENVO: 03000033) Conf. Genome Inform. (GIW2009) Poster Software Demonstrations, Yokohama, Env_feature Polar (ENVO: 01000238) Japan. Env_ material Marine mud (ENVO:00005795) Wu, W.J., Zhao, J.X., Chen, G.J., Du, Z.J., 2016. Description of Ancylomarina subtilis gen. nov., Env_package Missing sp. nov., isolated from coastal sediment, proposal of Marinilabiliales ord. nov. and Source:mat_id NBRC 111151 transfer of Marinilabiliaceae, Prolixibacteraceae and Marinifilaceae to the order Biotic_relationship Free living Marinilabiliales. Int. J. Syst. Evol. Microbiol. 66, 4243–4249. Trophic_level Chemoorganotroph Xu, Z.X., Mu, X., Zhang, H.X., Chen, G.J., Du, Z.J., 2016. Marinifilum albidiflavum sp. nov., iso- Rel_to_oxygen Facultative anaerobic lated from coastal sediment. Int. J. Syst. Evol. Microbiol. 66, 4589–4593. Investigation_type Bacteria_archaea Seq_meth PacBio RS II (Pacific Biosciences) Assembly method RS HGAP v2.3 Finishing_strategy Complete; approximately 194 fold genome coverage Annot_source MiGAP.
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  • PDF (Supplemental Figure 9)

    PDF (Supplemental Figure 9)

    smmoC GCA 9001883 smmoC GCA 9001294 smmoC GCA 9001059 smmoC GCA 0018009 smmoC GCA 0026913 smmoC GCA 0028425 25.1 IMG-taxon 268745 smmoC GCA 0024005 75.1 IMG-taxon 269542 9001296 GCA smmoC 85.1 IMG-taxon 263416 smmoC GCA 0028139 75.1 ASM180097v1 pro 9001029 GCA smmoC smmoC GCA 9001290 smmoC GCA 9001981 smmoC GCA 90011520 GCA smmoC smmoC GCA 0021693 GCA smmoC smmoC GCA 90011229 GCA smmoC 85.1 ASM269138v1 pro 9002154 GCA smmoC 05.1 ASM284250v1 pro smmoC DGON d Bacte smmoC GCA 0026916 GCA smmoC smmoC GCA 0015161 smmoC GCA 9001776 GCA smmoC smmoC GCA 0001922 smmoC GCA 9001065 smmoC GCA 0026872 smmoC GCA 9001054 smmoC GCA 9001043 smmoC smmoC GCA 0024008 3772 annotated assem 05.1 ASM240050v1 pro smmoC GCA 90011400 9001764 GCA smmoC smmoC GCA 9001418 GCA smmoC 65.1 IMG-taxon 261727 IMG-taxon 65.1 15.1 ASM281391v1 pro smmoC GCA 0007565 6900 annotated assem 0951 annotated assem smmoC GCA 0029543 GCA smmoC 25.1 IMG-taxon 266752 IMG-taxon 25.1 05.1 IMG-taxon 258258 tein OGS74000.1 NAD smmoC GCA 9001882 smmoC GCA 0016934 smmoC GCA 0027815 9001884 GCA smmoC smmoC GCA 9001300 95.1 Tjejuense V1 prot smmoC GCA 0024013 smmoC GCA 0027464 55.1 ASM216935v1 pro ASM216935v1 55.1 65.1 IMG-taxon 272836 IMG-taxon 65.1 smmoC GCA 0015433 smmoC GCA 9001018 GCA smmoC 5.1 IMG-taxon 2636416 IMG-taxon 5.1 5.1 IMG-taxon 2619619 IMG-taxon 5.1 tein MAJ50422.1 NADH smmoC GCA 9001883 tein PKP13194.1 NADH 85.1 ASM269168v1 pro ASM269168v1 85.1 smmoC GCA 90011611 smmoC GCA 0021626 ria p Bacteroidota c Ba 45.1 41k protein KUO6 smmoC GCA 0018802 45.1 IMG-taxon 259569 IMG-taxon