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Complete genome sequence of Marinifilaceae bacterium strain SPP2, isolated from the Antarctic marine sediment
MARGEN-00540; No of Pages 2 Marine Genomics xxx (2016) xxx–xxx
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 b
The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan Postdoctoral Research Fellow of the Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-8471, Japan
a r t i c l e
i n f o
Article history: Received 8 June 2017 Received in revised form 27 June 2017 Accepted 27 June 2017 Available online xxxx
a b s t r a c t Marinifilaceae bacterium strain SPP2 is a Gram-negative facultative anaerobe, isolated from the Antarctic marine sediment. Here, we present the complete genome sequence of Marinifilaceae bacterium strain SPP2, which consists of 5,718,991 bp with a G + C content of 35.99%. The genome data provides insights of microbial evolution and adaption in the Antarctic marine ecosystem. © 2016 Published by Elsevier B.V.
Keywords: Complete genome sequence Antarctica Bacteroidetes
1. Introduction Marinifilaceae bacterium strain SPP2 (=NBRC 111151) was isolated from the marine sediments of Langhovde, Antarctica. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain SPP2 was classified into the family Marinifilaceae, the order Marinilabiliales and the class Bacteroidia within the phylum Bacteroidetes (Fig. 1). This isolate showed the highest sequence similarities with Marinifilum albidiflavum (Xu et al., 2016; 93.8% sequence similarity) and Ancylomarina subtilis (Wu et al., 2016; 94.1%). This strain is a facultative anaerobic, Gram-negative and weakly motile bacterium. Here, we describe complete genome sequence and annotation of Marinifilaceae bacterium strain SPP2, which will provide further insight into microbial evolution and Antarctic marine ecosystem. 2. Data description Strain SPP2 was grown aerobically on Marine broth 2216 (Difco) at 15 °C without shaking. Genomic DNA was extracted from collected cells using NucleoSpin Tissue Kit (Macherey-Nagel GmbH & Co., Duren, Germany). Library construction and sequencing using the PacBio RS II platform were carried out at Takara Bio Inc., Japan. A total of 81,920 polymerase reads (1,109,405,149 bp) were generated and filtered. The resulting sequences (1,108,341,501 bp) were assembled into 1 high
⁎ Corresponding author at: The Institute of Low Temperature Science, Hokkaido University, Nishi 8, Kita 19, Kita-ku Sapporo, Hokkaido 060-0819, Japan. E-mail address: [email protected] (M. Watanabe).
quality scaffolds by using RS_HGAP_Assembly.3 (SMRT Analysis 2.3). The genome sequence was automatically annotated and analyzed through the MiGAP pipeline (Sugawara et al., 2009). In this pipeline, RNAmmer (Lagesen et al., 2007) and tRNAscan-SE (Lowe and Eddy, 1997) were used to identify rRNA and tRNA genes, respectively. MetaGene Annotator (Noguchi et al., 2008) was used for prediction of open reading frames likely to encode proteins (coding sequences [CDSs]), and functional annotation was performed based on reference databases, including Reference Sequence (RefSeq), TrEMBL, and Clusters of Orthologous Groups (COGs). Manual annotation was performed using IMC-GE software (In Silico Biology; Yokohama, Japan). Putative CDSs possessing BLASTP matches with N 70% coverage, 35% identity and E-values b 1 × e−5 were considered potentially functional genes. The CDSs were annotated as hypothetical proteins when these standard values were not satisfied. Transcription start sites of predicted proteins were corrected based on multiple sequence alignments. The proteincoding genes in the genome were also subjected to analysis on WebMGA (Wu et al., 2016) for the COGs annotations. Transmembrane helices and signal peptides were predicted by using Phobius (Käll et al., 2007). CRISPR loci were distinguished using the CRISPR Recognition Tool (Bland et al., 2007). General features of Marinifilaceae bacterium strain SPP2 and the MIxS mandatory information were show in Table 1. The final genome was comprised of a single 5,718,991 bp circular chromosome, harboring a total of 4337 predicted protein-coding sequences 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 categories. The complete genome sequence will provide fundamental information for further research of polar microbiology.
http://dx.doi.org/10.1016/j.margen.2017.06.006 1874-7787/© 2016 Published by Elsevier B.V.
Please cite this article as: Watanabe, M., et al., Complete genome sequence of Marinifilaceae bacterium strain SPP2, isolated from the Antarctic marine sediment, Mar. Genomics (2016), http://dx.doi.org/10.1016/j.margen.2017.06.006
2
M. Watanabe et al. / Marine Genomics xxx (2016) xxx–xxx
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 The complete genome sequence of Marinifilaceae bacterium strain SPP2 (= NBRC 111151) has been deposited at DDBJ/EMBL/GenBank under the accession number of AP018042. Acknowledgements This study was supported by a grant-in-aid for Research Fellow of Japan Society for the Promotion Science to MW and JSPS KAKENHI Grant Number 22370005 to M. Fukui. We also thank members of the 47th Japan Antarctica Research Expedition (Expedition leader: K. Shiraishi, NIPR) for logistical assistance.
Table 2 General genomic features of Marinifilaceae bacterium strain SPP2. Attributes
Value
% of total
Genome size (bp) Contig DNA coding region (bp) DNA G + C content (bp) Total genes RNA count rRNA tRNA Protein-coding genes Genes with function prediction Genes assigned to COGs Genes with peptide signals Genes with transmembrane helices CRISPR repeats
5,718,991 1 4,836,282 2,058,548 4436 105 22 83 4331 2349 3044 1186 907 3
100.00 100.00 84.57 35.99 100.00 2.37 0.50 1.87 97.63 54.24 70.28 27.38 20.94 –
Table 1 General features and genome sequencing project information for Marinifilaceae bacterium strain SPP2 according to the MIGS recommendations.
References Items General features Classification
Particle shape Gram stain Temperature Salinity Motility
Description Domain Bacteria Phylum Bacteroidetes Order Bacteroidales Family Marinifilaceae Rod Negative 0–25 °C 2–4% Weakly motile
MIxS data Submitted_to_insdc AP018042 (GenBank) Investigation_type Bacteria Project_name Complete genome sequence of Marinifilaceae bacterium strain SPP2 Geo_loc_name Langhovde, Antarctica Collection_date 27-01-2006 Lat_lon Missing Env_biome Marine sediment (ENVO: 03000033) Env_feature Polar (ENVO: 01000238) Env_ material Marine mud (ENVO:00005795) Env_package Missing Source:mat_id NBRC 111151 Biotic_relationship Free living Trophic_level Chemoorganotroph Rel_to_oxygen Facultative anaerobic 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
Bland, C., Ramsey, T.L., Sabree, F., Lowe, M., Brown, K., Kyrpides, N.C., Hugenholtz, P., 2007. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinf. 8, 209. Käll, L., Krogh, A., Sonnhammer, E.L.L., 2007. Advantages of combined transmembrane topology and signal peptide prediction: the Phobius web server. Nucleic Acids Res. 35, W429–W432. Kumar, S., Stecher, G., Tamura, K., 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol., msw054 Lagesen, K., Hallin, P., Rødland, E.A., Staerfeldt, H.H., Rognes, T., Ussery, D.W., 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., et al., 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948. Lowe, T.M., Eddy, S.R., 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964. Noguchi, H., Taniguchi, T., Itoh, T., 2008. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res. 15, 387–396. Sugawara, H., Ohyama, A., Mori, H., Kurokawa, K., 2009. Microbial GenomeAnnotation Pipeline (MiGAP) for diverse users. Software Demonstrations S001-1-2L. 20th Int. Conf. Genome Inform. (GIW2009) Poster Software Demonstrations, Yokohama, Japan. Wu, W.J., Zhao, J.X., Chen, G.J., Du, Z.J., 2016. Description of Ancylomarina subtilis gen. nov., sp. nov., isolated from coastal sediment, proposal of Marinilabiliales ord. nov. and transfer of Marinilabiliaceae, Prolixibacteraceae and Marinifilaceae to the order Marinilabiliales. Int. J. Syst. Evol. Microbiol. 66, 4243–4249. Xu, Z.X., Mu, X., Zhang, H.X., Chen, G.J., Du, Z.J., 2016. Marinifilum albidiflavum sp. nov., isolated from coastal sediment. Int. J. Syst. Evol. Microbiol. 66, 4589–4593.
Please cite this article as: Watanabe, M., et al., Complete genome sequence of Marinifilaceae bacterium strain SPP2, isolated from the Antarctic marine sediment, Mar. Genomics (2016), http://dx.doi.org/10.1016/j.margen.2017.06.006
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 b
The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan Postdoctoral Research Fellow of the Japan Society for the Promotion of Science, Chiyoda-ku, Tokyo 102-8471, Japan
a r t i c l e
i n f o
Article history: Received 8 June 2017 Received in revised form 27 June 2017 Accepted 27 June 2017 Available online xxxx
a b s t r a c t Marinifilaceae bacterium strain SPP2 is a Gram-negative facultative anaerobe, isolated from the Antarctic marine sediment. Here, we present the complete genome sequence of Marinifilaceae bacterium strain SPP2, which consists of 5,718,991 bp with a G + C content of 35.99%. The genome data provides insights of microbial evolution and adaption in the Antarctic marine ecosystem. © 2016 Published by Elsevier B.V.
Keywords: Complete genome sequence Antarctica Bacteroidetes
1. Introduction Marinifilaceae bacterium strain SPP2 (=NBRC 111151) was isolated from the marine sediments of Langhovde, Antarctica. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain SPP2 was classified into the family Marinifilaceae, the order Marinilabiliales and the class Bacteroidia within the phylum Bacteroidetes (Fig. 1). This isolate showed the highest sequence similarities with Marinifilum albidiflavum (Xu et al., 2016; 93.8% sequence similarity) and Ancylomarina subtilis (Wu et al., 2016; 94.1%). This strain is a facultative anaerobic, Gram-negative and weakly motile bacterium. Here, we describe complete genome sequence and annotation of Marinifilaceae bacterium strain SPP2, which will provide further insight into microbial evolution and Antarctic marine ecosystem. 2. Data description Strain SPP2 was grown aerobically on Marine broth 2216 (Difco) at 15 °C without shaking. Genomic DNA was extracted from collected cells using NucleoSpin Tissue Kit (Macherey-Nagel GmbH & Co., Duren, Germany). Library construction and sequencing using the PacBio RS II platform were carried out at Takara Bio Inc., Japan. A total of 81,920 polymerase reads (1,109,405,149 bp) were generated and filtered. The resulting sequences (1,108,341,501 bp) were assembled into 1 high
⁎ Corresponding author at: The Institute of Low Temperature Science, Hokkaido University, Nishi 8, Kita 19, Kita-ku Sapporo, Hokkaido 060-0819, Japan. E-mail address: [email protected] (M. Watanabe).
quality scaffolds by using RS_HGAP_Assembly.3 (SMRT Analysis 2.3). The genome sequence was automatically annotated and analyzed through the MiGAP pipeline (Sugawara et al., 2009). In this pipeline, RNAmmer (Lagesen et al., 2007) and tRNAscan-SE (Lowe and Eddy, 1997) were used to identify rRNA and tRNA genes, respectively. MetaGene Annotator (Noguchi et al., 2008) was used for prediction of open reading frames likely to encode proteins (coding sequences [CDSs]), and functional annotation was performed based on reference databases, including Reference Sequence (RefSeq), TrEMBL, and Clusters of Orthologous Groups (COGs). Manual annotation was performed using IMC-GE software (In Silico Biology; Yokohama, Japan). Putative CDSs possessing BLASTP matches with N 70% coverage, 35% identity and E-values b 1 × e−5 were considered potentially functional genes. The CDSs were annotated as hypothetical proteins when these standard values were not satisfied. Transcription start sites of predicted proteins were corrected based on multiple sequence alignments. The proteincoding genes in the genome were also subjected to analysis on WebMGA (Wu et al., 2016) for the COGs annotations. Transmembrane helices and signal peptides were predicted by using Phobius (Käll et al., 2007). CRISPR loci were distinguished using the CRISPR Recognition Tool (Bland et al., 2007). General features of Marinifilaceae bacterium strain SPP2 and the MIxS mandatory information were show in Table 1. The final genome was comprised of a single 5,718,991 bp circular chromosome, harboring a total of 4337 predicted protein-coding sequences 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 categories. The complete genome sequence will provide fundamental information for further research of polar microbiology.
http://dx.doi.org/10.1016/j.margen.2017.06.006 1874-7787/© 2016 Published by Elsevier B.V.
Please cite this article as: Watanabe, M., et al., Complete genome sequence of Marinifilaceae bacterium strain SPP2, isolated from the Antarctic marine sediment, Mar. Genomics (2016), http://dx.doi.org/10.1016/j.margen.2017.06.006
2
M. Watanabe et al. / Marine Genomics xxx (2016) xxx–xxx
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 The complete genome sequence of Marinifilaceae bacterium strain SPP2 (= NBRC 111151) has been deposited at DDBJ/EMBL/GenBank under the accession number of AP018042. Acknowledgements This study was supported by a grant-in-aid for Research Fellow of Japan Society for the Promotion Science to MW and JSPS KAKENHI Grant Number 22370005 to M. Fukui. We also thank members of the 47th Japan Antarctica Research Expedition (Expedition leader: K. Shiraishi, NIPR) for logistical assistance.
Table 2 General genomic features of Marinifilaceae bacterium strain SPP2. Attributes
Value
% of total
Genome size (bp) Contig DNA coding region (bp) DNA G + C content (bp) Total genes RNA count rRNA tRNA Protein-coding genes Genes with function prediction Genes assigned to COGs Genes with peptide signals Genes with transmembrane helices CRISPR repeats
5,718,991 1 4,836,282 2,058,548 4436 105 22 83 4331 2349 3044 1186 907 3
100.00 100.00 84.57 35.99 100.00 2.37 0.50 1.87 97.63 54.24 70.28 27.38 20.94 –
Table 1 General features and genome sequencing project information for Marinifilaceae bacterium strain SPP2 according to the MIGS recommendations.
References Items General features Classification
Particle shape Gram stain Temperature Salinity Motility
Description Domain Bacteria Phylum Bacteroidetes Order Bacteroidales Family Marinifilaceae Rod Negative 0–25 °C 2–4% Weakly motile
MIxS data Submitted_to_insdc AP018042 (GenBank) Investigation_type Bacteria Project_name Complete genome sequence of Marinifilaceae bacterium strain SPP2 Geo_loc_name Langhovde, Antarctica Collection_date 27-01-2006 Lat_lon Missing Env_biome Marine sediment (ENVO: 03000033) Env_feature Polar (ENVO: 01000238) Env_ material Marine mud (ENVO:00005795) Env_package Missing Source:mat_id NBRC 111151 Biotic_relationship Free living Trophic_level Chemoorganotroph Rel_to_oxygen Facultative anaerobic 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
Bland, C., Ramsey, T.L., Sabree, F., Lowe, M., Brown, K., Kyrpides, N.C., Hugenholtz, P., 2007. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinf. 8, 209. Käll, L., Krogh, A., Sonnhammer, E.L.L., 2007. Advantages of combined transmembrane topology and signal peptide prediction: the Phobius web server. Nucleic Acids Res. 35, W429–W432. Kumar, S., Stecher, G., Tamura, K., 2016. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol., msw054 Lagesen, K., Hallin, P., Rødland, E.A., Staerfeldt, H.H., Rognes, T., Ussery, D.W., 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108. Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., et al., 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947–2948. Lowe, T.M., Eddy, S.R., 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964. Noguchi, H., Taniguchi, T., Itoh, T., 2008. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res. 15, 387–396. Sugawara, H., Ohyama, A., Mori, H., Kurokawa, K., 2009. Microbial GenomeAnnotation Pipeline (MiGAP) for diverse users. Software Demonstrations S001-1-2L. 20th Int. Conf. Genome Inform. (GIW2009) Poster Software Demonstrations, Yokohama, Japan. Wu, W.J., Zhao, J.X., Chen, G.J., Du, Z.J., 2016. Description of Ancylomarina subtilis gen. nov., sp. nov., isolated from coastal sediment, proposal of Marinilabiliales ord. nov. and transfer of Marinilabiliaceae, Prolixibacteraceae and Marinifilaceae to the order Marinilabiliales. Int. J. Syst. Evol. Microbiol. 66, 4243–4249. Xu, Z.X., Mu, X., Zhang, H.X., Chen, G.J., Du, Z.J., 2016. Marinifilum albidiflavum sp. nov., isolated from coastal sediment. Int. J. Syst. Evol. Microbiol. 66, 4589–4593.
Please cite this article as: Watanabe, M., et al., Complete genome sequence of Marinifilaceae bacterium strain SPP2, isolated from the Antarctic marine sediment, Mar. Genomics (2016), http://dx.doi.org/10.1016/j.margen.2017.06.006