- Email: [email protected]
De novo assembly of complete genome sequence of Planococcus kocurii ATCC 43650T, a potential plant growth promoting bacterium
MARGEN-00450; No of Pages 3 Marine Genomics xxx (2016) xxx–xxx
Contents lists available at ScienceDirect
Marine Genomics journal homepage: www.elsevier.com/locate/margen
Genomics/technical resources
De novo assembly of complete genome sequence of Planococcus kocurii ATCC 43650T, a potential plant growth promoting bacterium Wah-Seng See-Too a,b, Jia Yi Tan a, Robson Ee a, Yan-Lue Lim a, Peter Convey b,c, David A. Pearce b,c,d, Wai-Fong Yin a, Kok-Gan Chan a,e,⁎ a
Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 OET, UK d Faculty of Health and Life Sciences, University of Northumbria, Newcastle Upon Tyne NE1 8ST, UK e UM Omics Centre, University of Malaya, Kuala Lumpur, Malaysia b c
a r t i c l e
i n f o
Article history: Received 19 March 2016 Received in revised form 17 April 2016 Accepted 17 April 2016 Available online xxxx
a b s t r a c t Planococcus kocurii ATCC 43650T is a halotolerant and psychrotolerant bacterium isolated from the skin of a North sea cod. Here, we present the first complete genome and annotation of P. kocurii ATCC 43650T, identifying its potential as a plant growth promoting bacterium and its capability in the biosynthesis of butanol. © 2016 Elsevier B.V. All rights reserved.
Keywords: Halotolerant Psychrotolerant Butanol biosynthesis Glutamate dehydrogenase SMRT sequencing
1. Introduction Planococcus spp. are motile, cocci-shaped, Gram-positive bacteria in the family Planococcaceae. To date, the Planococcus genus includes 12 recognized species. Predominantly isolated from cold and/or marine environments, Planococcus spp. have demonstrated various degradation capabilities including starch degradation in Planococcus donghaensis JH1T (Choi et al., 2007) and aromatic compound degradation in Planococcus sp. ZD22 and S5 (Dalal et al., 2012; Hupert-Kocurek et al., 2012; Li et al., 2006). Some Planococcus species also display remarkable heavy metal resistance and a capability to produce biosurfactants (Chowdhury et al., 2003; Nithya et al., 2011) while utilizing olive oil as the sole carbon source (Hupert-Kocurek et al., 2012). As most Planococcus species are also halotolerant and psychrotolerant, members of the genus have been proposed to be useful as potential bioremediation candidates of significant biotechnological value (Hupert-Kocurek et al., 2012).
⁎ Corresponding author at: Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia. E-mail address: [email protected] (K.-G. Chan).
Planococcus kocurii ATCC 43650T (= JCM 2569T, = HK 701T) is an understudied member of the Planococcus genus originally isolated from the skin of a North Sea cod by Hao and Komagata (1985). To date, no biotechnological evaluation has been conducted for this bacterium. Here, we explore the biotechnological potential of P. kocurii ATCC 43650T by sequencing the complete genome (3,487,770 bp, with a G + C content of 40.9%) using Single Molecule Real-Time (SMRT) sequencing technology. The functional annotation performed unraveled its potential as a plant growth promoting bacterium and in butanol biosynthesis. The availability of this complete genome will facilitate robust comparative genome analyses in this genus. 2. Data description P. kocurii ATCC 43650T was cultured aerobically for 48 h at 20 °C on seawater yeast peptone agar. Genomic DNA was extracted using the MasterPure™ Gram Positive DNA purification kit (Epicenter, WI, USA) following the manufacturer's protocols. A template library was constructed according to the “Guidelines for Preparing 20kb SMRTbell™ Templates” and sequenced in 1 SMRT cells using the PacBio RS II single-molecule real-time (SMRT) sequencing technology (Pacific Biosciences, CA, USA). An output data of 1,180,039,791 bases and 88,826
http://dx.doi.org/10.1016/j.margen.2016.04.007 1874-7787/© 2016 Elsevier B.V. All rights reserved.
Please cite this article as: See-Too, W.-S., et al., De novo assembly of complete genome sequence of Planococcus kocurii ATCC 43650T, a potential plant growth promoting bacterium, Mar. Genomics (2016), http://dx.doi.org/10.1016/j.margen.2016.04.007
2
W.-S. See-Too et al. / Marine Genomics xxx (2016) xxx–xxx
Table 1 General features of P. kocurii ATCC 43650T. Attribute
Chromosome (CP013661.1)
Plasmid (CP013660.1)
Genome size (bp) Contigs G + C content (%) Genes Protein Pseudogenes rRNA (5S, 16S, 23S) tRNA ncRNA
3,487,770 1 40.9 3328 3237 45 28 (9, 10, 9) 72 4
21,505 1 40.0 22 16 6 – – –
reads with 279.99 fold coverage was generated from the SMRT sequencing in which de novo assembly was performed using the Hierarchical Genome-Assembly Process (HGAP) version 3 in SMRT Analysis v2.3.0. The open reading frame (ORF) was subsequently predicted using Prodigal v2.6.1 (Hyatt et al., 2010) and coding DNA sequences (CDS) were translated and searched against the UniProt, Pfam and COG (Clusters of Orthologous Group) databases. Non-coding genes and miscellaneous features were predicted using RNAmmer v1.2 (Lagesen et al., 2007), tRNAscan-SE v1.21 (Lowe and Eddy, 1997), SignalP v4.1 (Petersen et al., 2011) and TMHMM v2.0 (Krogh et al., 2001). The graphical circular map of the genome was constructed and visualized using Circos v0.67 (Krzywinski et al., 2009). The complete genome of P. kocurii ATCC 43650T is made up of a single circular chromosome (3,487,770 bp, 40.9% G + C content) and a circular plasmid of (21,505 bp, 40.0% G + C content) (Table 1). Briefly, a total of 3328 genes, 3237 proteins, 45 pseudogenes and 28 rRNAs were identified in the chromosome, with a further 22 genes, 16 proteins and 6 pseudogenes identified in the plasmid. A graphical map along with the COG distribution of both the chromosome and plasmid genomes of P. kocurii ATCC 43650T are given in Fig. 1. A MIxS mandatory information of the MIxS checklist and environmental packages containing the
phenotypic, physiological and biochemical key features of P. kocurii ATCC 43650T is presented in Table 2. Two pathways involved in assimilation of ammonia were identified in the genome. The first pathway was a glutamate dehydrogenase (GDH) pathway using NAD-specific glutamate dehydrogenase (NCBI locus tag: AUO94_11260, AUO94_13090, AUO94_15260). The second was a glutamine synthetase (GS)–glutamate synthase (GOGAT) pathway which involved glutamine synthetase (NCBI locus tag: AUO94_06480; EC 6.3.1.2), glutamate synthase (NCBI locus tag: AUO94_02135, AUO94_02130; EC 1.4.1.13), serine hydroxymethyltransferase (NCBI locus tag: AUO94_03600; EC 2.1.2.1), glycine dehydrogenase (NCBI locus tag: AUO94_09395, AUO94_09400; EC 1.4.4.2) and glutamine amidotransferase (NCBI locus tag: AUO94_00170). Functional annotation also revealed 18 genes for the biosynthesis of butanol using the acetone/isopropanol butanol–ethanol (A/IBE) pathway, which included acetyl-coA acetyl transferase (NCBI locus tag: AUO94_03485, AUO94_06550, AUO94_11520, AUO94_13195, AUO94_14735), 3-hydroxybutyryl-coA-dehydrogenase (NCBI locus tag: AUO94_02245, AUO94_03490, AUO94_04680), enoyl-coA-hydrotase (NCBI locus tag: AUO94_02695, AUO94_05775, AUO94_10305, AUO94_10505, AUO94_11770, AUO94_11910), butryl-coA dehydrogenase (NCBI locus tag: AUO94_13135), acetaldehyde dehydrogenase (NCBI locus tag: AUO94_02290), alcohol dehydrogenase (NCBI locus tag: AUO94_12930), and butanol dehydrogenase (NCBI locus tag: AUO94_11255). The availability of this genome may serve as a fundamental resource to further study the full biotechnological potential of P. kocurii ATCC 43650T.
Nucleotide sequence accession number The complete genome sequence of P. kocurii ATCC 43650T (=JCM 2569T, =HK 701T) has been deposited at DDBJ/EMBL/GenBank under the accession number of CP013661.1 (chromosome) and CP013660.1 (plasmid).
Fig. 1. Graphical map of the chromosome (left) and plasmid (right) genomes of P. kocurii ATCC 43650T.
Please cite this article as: See-Too, W.-S., et al., De novo assembly of complete genome sequence of Planococcus kocurii ATCC 43650T, a potential plant growth promoting bacterium, Mar. Genomics (2016), http://dx.doi.org/10.1016/j.margen.2016.04.007
W.-S. See-Too et al. / Marine Genomics xxx (2016) xxx–xxx Table 2 MIGS mandatory information for P. kocurii ATCC 43650T. Item General feature of classification Classification
Gram stain Cell shape Motility Temperature range (°C) NaCl concentration (optimum) (%) Investigation Submitted to INSDC Investigation type Project name
Environment Geographic location (latitude and longitude) Geographic location (depth) Geographic location (country) Collection date Environment (biome) Environment (feature)
Description Domain: Bacteria Phylum: Firmicutes Class: Bacilli Order: Bacillales Family: Planococcaceae Genus: Planococcus Species: kocurii Positive Cocci Motile 5–30 °C 0–10%
Chromosome accession number: CP013661.1 Plasmid accession number: CP013660.1 MIGS BA Complete genome sequencing of Planococcus kocurii ATCC 43650T
Not collected Not collected Not collected 1st January 1957 Skin North Sea cod
MIGS/MIMS/MIMARKS extension Environmental package
Skin of the North Sea cod (host-associated)
Nucleic acid sequence source Isolation and growth conditions
Hao and Komagata (1985)
Sequencing Target gene or locus Sequencing method Sequencing platform Assembly Assemble method Assembly name Finishing strategy Coverage Assembly size (bp) Contig
Complete genome sequence of Planococcus kocurii ATCC 43650T Single Molecules Real-Time (SMRT) sequencing PacBio RS II sequencer
3
14/1, Grant No. H-50001-A000027; UMMOHE HIR Grant UM.C/625/1/ HIR/MOHE/CHAN/01, Grant No. A-000001-50001) awarded to KokGan Chan. Peter Convey is supported by NERC core funding to the British Antarctic Survey's ‘Biodiversity, Evolution and Adaptation’ Team. References Choi, J.H., Im, W.T., Liu, Q.M., Yoo, J.S., Shin, J.H., Rhee, S.K., Roh, D.H., 2007. Planococcus donghaensis sp. nov., a starch-degrading bacterium isolated from the East Sea, South Korea. Int. J. Syst. Evol. Microbiol. 57, 2645–2650. Chowdhury, R., Sen, A.K., Karak, P., Chatterjee, R., Giri, A.K., Keya, C., 2003. Isolation and characterization of an arsenic-resistant bacterium from a bore-well in West Bengal, India. Ann. Microbiol. 59, 253–258. Dalal, S., Panigrahi, D.P., Randhawa, G.S., Dubey, R.C., 2012. Molecular characterisation of high-strength polycyclic aromatic hydrocarbon (PAH)-degrading and phenoltolerant bacteria obtained from thermal power plant wastewater. Chem. Ecol. 28, 187–192. Hao, M.V., Komagata, K., 1985. A new species of Planococcus, P. kocurii isolated from fish, frozen foods, and fish curing brine. J. Gen. Appl. Microbiol. 31, 41–455. Hupert-Kocurek, K., Guzik, U., Wojcieszynska, D., 2012. Characterization of catechol 2,3dioxygenase from Planococcus sp. strain S5 induced by high phenol concentration. Acta Biochim. Pol. 59, 345–351. Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W., Hauser, L.J., 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinf. 11, 119. Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E.L., 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567–580. Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S.J., Marra, M.A., 2009. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645. Lagesen, K., Hallin, P., Rødland, E.A., Stærfeldt, H.-H., Rognes, T., Ussery, D.W., 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108. Li, H., Liu, Y.H., Luo, N., Zhang, X.Y., Luan, T.G., Hu, J.M., Wang, Z.Y., Wu, P.C., Chen, M.J., et al., 2006. Biodegradation of benzene and its derivatives by a psychrotolerant and moderately haloalkaliphilic Planococcus sp. strain ZD22. Res. Microbiol. 157, 629–636. 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. Nithya, C., Gnanalakshmi, B., Pandian, S.K., 2011. Assessment and characterization of heavy metal resistance in Palk Bay sediment bacteria. Mar. Environ. Res. 71, 283–294. Petersen, T.N., Brunak, S., von Heijne, G., Nielsen, H., 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 8, 785–786.
De novo assembly Hierarchical Genome Assembly Process (HGAP) version 3 Complete genome, finished 230.5× Chromosome: 3,487,770 bp Plasmid: 21,505 bp 2 (1 chromosome, 1 plasmid)
Acknowledgments This work was supported by the University of Malaya High Impact Research Grants (UMMOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/
Please cite this article as: See-Too, W.-S., et al., De novo assembly of complete genome sequence of Planococcus kocurii ATCC 43650T, a potential plant growth promoting bacterium, Mar. Genomics (2016), http://dx.doi.org/10.1016/j.margen.2016.04.007
Contents lists available at ScienceDirect
Marine Genomics journal homepage: www.elsevier.com/locate/margen
Genomics/technical resources
De novo assembly of complete genome sequence of Planococcus kocurii ATCC 43650T, a potential plant growth promoting bacterium Wah-Seng See-Too a,b, Jia Yi Tan a, Robson Ee a, Yan-Lue Lim a, Peter Convey b,c, David A. Pearce b,c,d, Wai-Fong Yin a, Kok-Gan Chan a,e,⁎ a
Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia National Antarctic Research Centre (NARC), Institute of Postgraduate Studies, University of Malaya, 50603 Kuala Lumpur, Malaysia British Antarctic Survey, NERC, High Cross, Madingley Road, Cambridge CB3 OET, UK d Faculty of Health and Life Sciences, University of Northumbria, Newcastle Upon Tyne NE1 8ST, UK e UM Omics Centre, University of Malaya, Kuala Lumpur, Malaysia b c
a r t i c l e
i n f o
Article history: Received 19 March 2016 Received in revised form 17 April 2016 Accepted 17 April 2016 Available online xxxx
a b s t r a c t Planococcus kocurii ATCC 43650T is a halotolerant and psychrotolerant bacterium isolated from the skin of a North sea cod. Here, we present the first complete genome and annotation of P. kocurii ATCC 43650T, identifying its potential as a plant growth promoting bacterium and its capability in the biosynthesis of butanol. © 2016 Elsevier B.V. All rights reserved.
Keywords: Halotolerant Psychrotolerant Butanol biosynthesis Glutamate dehydrogenase SMRT sequencing
1. Introduction Planococcus spp. are motile, cocci-shaped, Gram-positive bacteria in the family Planococcaceae. To date, the Planococcus genus includes 12 recognized species. Predominantly isolated from cold and/or marine environments, Planococcus spp. have demonstrated various degradation capabilities including starch degradation in Planococcus donghaensis JH1T (Choi et al., 2007) and aromatic compound degradation in Planococcus sp. ZD22 and S5 (Dalal et al., 2012; Hupert-Kocurek et al., 2012; Li et al., 2006). Some Planococcus species also display remarkable heavy metal resistance and a capability to produce biosurfactants (Chowdhury et al., 2003; Nithya et al., 2011) while utilizing olive oil as the sole carbon source (Hupert-Kocurek et al., 2012). As most Planococcus species are also halotolerant and psychrotolerant, members of the genus have been proposed to be useful as potential bioremediation candidates of significant biotechnological value (Hupert-Kocurek et al., 2012).
⁎ Corresponding author at: Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia. E-mail address: [email protected] (K.-G. Chan).
Planococcus kocurii ATCC 43650T (= JCM 2569T, = HK 701T) is an understudied member of the Planococcus genus originally isolated from the skin of a North Sea cod by Hao and Komagata (1985). To date, no biotechnological evaluation has been conducted for this bacterium. Here, we explore the biotechnological potential of P. kocurii ATCC 43650T by sequencing the complete genome (3,487,770 bp, with a G + C content of 40.9%) using Single Molecule Real-Time (SMRT) sequencing technology. The functional annotation performed unraveled its potential as a plant growth promoting bacterium and in butanol biosynthesis. The availability of this complete genome will facilitate robust comparative genome analyses in this genus. 2. Data description P. kocurii ATCC 43650T was cultured aerobically for 48 h at 20 °C on seawater yeast peptone agar. Genomic DNA was extracted using the MasterPure™ Gram Positive DNA purification kit (Epicenter, WI, USA) following the manufacturer's protocols. A template library was constructed according to the “Guidelines for Preparing 20kb SMRTbell™ Templates” and sequenced in 1 SMRT cells using the PacBio RS II single-molecule real-time (SMRT) sequencing technology (Pacific Biosciences, CA, USA). An output data of 1,180,039,791 bases and 88,826
http://dx.doi.org/10.1016/j.margen.2016.04.007 1874-7787/© 2016 Elsevier B.V. All rights reserved.
Please cite this article as: See-Too, W.-S., et al., De novo assembly of complete genome sequence of Planococcus kocurii ATCC 43650T, a potential plant growth promoting bacterium, Mar. Genomics (2016), http://dx.doi.org/10.1016/j.margen.2016.04.007
2
W.-S. See-Too et al. / Marine Genomics xxx (2016) xxx–xxx
Table 1 General features of P. kocurii ATCC 43650T. Attribute
Chromosome (CP013661.1)
Plasmid (CP013660.1)
Genome size (bp) Contigs G + C content (%) Genes Protein Pseudogenes rRNA (5S, 16S, 23S) tRNA ncRNA
3,487,770 1 40.9 3328 3237 45 28 (9, 10, 9) 72 4
21,505 1 40.0 22 16 6 – – –
reads with 279.99 fold coverage was generated from the SMRT sequencing in which de novo assembly was performed using the Hierarchical Genome-Assembly Process (HGAP) version 3 in SMRT Analysis v2.3.0. The open reading frame (ORF) was subsequently predicted using Prodigal v2.6.1 (Hyatt et al., 2010) and coding DNA sequences (CDS) were translated and searched against the UniProt, Pfam and COG (Clusters of Orthologous Group) databases. Non-coding genes and miscellaneous features were predicted using RNAmmer v1.2 (Lagesen et al., 2007), tRNAscan-SE v1.21 (Lowe and Eddy, 1997), SignalP v4.1 (Petersen et al., 2011) and TMHMM v2.0 (Krogh et al., 2001). The graphical circular map of the genome was constructed and visualized using Circos v0.67 (Krzywinski et al., 2009). The complete genome of P. kocurii ATCC 43650T is made up of a single circular chromosome (3,487,770 bp, 40.9% G + C content) and a circular plasmid of (21,505 bp, 40.0% G + C content) (Table 1). Briefly, a total of 3328 genes, 3237 proteins, 45 pseudogenes and 28 rRNAs were identified in the chromosome, with a further 22 genes, 16 proteins and 6 pseudogenes identified in the plasmid. A graphical map along with the COG distribution of both the chromosome and plasmid genomes of P. kocurii ATCC 43650T are given in Fig. 1. A MIxS mandatory information of the MIxS checklist and environmental packages containing the
phenotypic, physiological and biochemical key features of P. kocurii ATCC 43650T is presented in Table 2. Two pathways involved in assimilation of ammonia were identified in the genome. The first pathway was a glutamate dehydrogenase (GDH) pathway using NAD-specific glutamate dehydrogenase (NCBI locus tag: AUO94_11260, AUO94_13090, AUO94_15260). The second was a glutamine synthetase (GS)–glutamate synthase (GOGAT) pathway which involved glutamine synthetase (NCBI locus tag: AUO94_06480; EC 6.3.1.2), glutamate synthase (NCBI locus tag: AUO94_02135, AUO94_02130; EC 1.4.1.13), serine hydroxymethyltransferase (NCBI locus tag: AUO94_03600; EC 2.1.2.1), glycine dehydrogenase (NCBI locus tag: AUO94_09395, AUO94_09400; EC 1.4.4.2) and glutamine amidotransferase (NCBI locus tag: AUO94_00170). Functional annotation also revealed 18 genes for the biosynthesis of butanol using the acetone/isopropanol butanol–ethanol (A/IBE) pathway, which included acetyl-coA acetyl transferase (NCBI locus tag: AUO94_03485, AUO94_06550, AUO94_11520, AUO94_13195, AUO94_14735), 3-hydroxybutyryl-coA-dehydrogenase (NCBI locus tag: AUO94_02245, AUO94_03490, AUO94_04680), enoyl-coA-hydrotase (NCBI locus tag: AUO94_02695, AUO94_05775, AUO94_10305, AUO94_10505, AUO94_11770, AUO94_11910), butryl-coA dehydrogenase (NCBI locus tag: AUO94_13135), acetaldehyde dehydrogenase (NCBI locus tag: AUO94_02290), alcohol dehydrogenase (NCBI locus tag: AUO94_12930), and butanol dehydrogenase (NCBI locus tag: AUO94_11255). The availability of this genome may serve as a fundamental resource to further study the full biotechnological potential of P. kocurii ATCC 43650T.
Nucleotide sequence accession number The complete genome sequence of P. kocurii ATCC 43650T (=JCM 2569T, =HK 701T) has been deposited at DDBJ/EMBL/GenBank under the accession number of CP013661.1 (chromosome) and CP013660.1 (plasmid).
Fig. 1. Graphical map of the chromosome (left) and plasmid (right) genomes of P. kocurii ATCC 43650T.
Please cite this article as: See-Too, W.-S., et al., De novo assembly of complete genome sequence of Planococcus kocurii ATCC 43650T, a potential plant growth promoting bacterium, Mar. Genomics (2016), http://dx.doi.org/10.1016/j.margen.2016.04.007
W.-S. See-Too et al. / Marine Genomics xxx (2016) xxx–xxx Table 2 MIGS mandatory information for P. kocurii ATCC 43650T. Item General feature of classification Classification
Gram stain Cell shape Motility Temperature range (°C) NaCl concentration (optimum) (%) Investigation Submitted to INSDC Investigation type Project name
Environment Geographic location (latitude and longitude) Geographic location (depth) Geographic location (country) Collection date Environment (biome) Environment (feature)
Description Domain: Bacteria Phylum: Firmicutes Class: Bacilli Order: Bacillales Family: Planococcaceae Genus: Planococcus Species: kocurii Positive Cocci Motile 5–30 °C 0–10%
Chromosome accession number: CP013661.1 Plasmid accession number: CP013660.1 MIGS BA Complete genome sequencing of Planococcus kocurii ATCC 43650T
Not collected Not collected Not collected 1st January 1957 Skin North Sea cod
MIGS/MIMS/MIMARKS extension Environmental package
Skin of the North Sea cod (host-associated)
Nucleic acid sequence source Isolation and growth conditions
Hao and Komagata (1985)
Sequencing Target gene or locus Sequencing method Sequencing platform Assembly Assemble method Assembly name Finishing strategy Coverage Assembly size (bp) Contig
Complete genome sequence of Planococcus kocurii ATCC 43650T Single Molecules Real-Time (SMRT) sequencing PacBio RS II sequencer
3
14/1, Grant No. H-50001-A000027; UMMOHE HIR Grant UM.C/625/1/ HIR/MOHE/CHAN/01, Grant No. A-000001-50001) awarded to KokGan Chan. Peter Convey is supported by NERC core funding to the British Antarctic Survey's ‘Biodiversity, Evolution and Adaptation’ Team. References Choi, J.H., Im, W.T., Liu, Q.M., Yoo, J.S., Shin, J.H., Rhee, S.K., Roh, D.H., 2007. Planococcus donghaensis sp. nov., a starch-degrading bacterium isolated from the East Sea, South Korea. Int. J. Syst. Evol. Microbiol. 57, 2645–2650. Chowdhury, R., Sen, A.K., Karak, P., Chatterjee, R., Giri, A.K., Keya, C., 2003. Isolation and characterization of an arsenic-resistant bacterium from a bore-well in West Bengal, India. Ann. Microbiol. 59, 253–258. Dalal, S., Panigrahi, D.P., Randhawa, G.S., Dubey, R.C., 2012. Molecular characterisation of high-strength polycyclic aromatic hydrocarbon (PAH)-degrading and phenoltolerant bacteria obtained from thermal power plant wastewater. Chem. Ecol. 28, 187–192. Hao, M.V., Komagata, K., 1985. A new species of Planococcus, P. kocurii isolated from fish, frozen foods, and fish curing brine. J. Gen. Appl. Microbiol. 31, 41–455. Hupert-Kocurek, K., Guzik, U., Wojcieszynska, D., 2012. Characterization of catechol 2,3dioxygenase from Planococcus sp. strain S5 induced by high phenol concentration. Acta Biochim. Pol. 59, 345–351. Hyatt, D., Chen, G.L., Locascio, P.F., Land, M.L., Larimer, F.W., Hauser, L.J., 2010. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinf. 11, 119. Krogh, A., Larsson, B., von Heijne, G., Sonnhammer, E.L., 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305, 567–580. Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S.J., Marra, M.A., 2009. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645. Lagesen, K., Hallin, P., Rødland, E.A., Stærfeldt, H.-H., Rognes, T., Ussery, D.W., 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108. Li, H., Liu, Y.H., Luo, N., Zhang, X.Y., Luan, T.G., Hu, J.M., Wang, Z.Y., Wu, P.C., Chen, M.J., et al., 2006. Biodegradation of benzene and its derivatives by a psychrotolerant and moderately haloalkaliphilic Planococcus sp. strain ZD22. Res. Microbiol. 157, 629–636. 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. Nithya, C., Gnanalakshmi, B., Pandian, S.K., 2011. Assessment and characterization of heavy metal resistance in Palk Bay sediment bacteria. Mar. Environ. Res. 71, 283–294. Petersen, T.N., Brunak, S., von Heijne, G., Nielsen, H., 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 8, 785–786.
De novo assembly Hierarchical Genome Assembly Process (HGAP) version 3 Complete genome, finished 230.5× Chromosome: 3,487,770 bp Plasmid: 21,505 bp 2 (1 chromosome, 1 plasmid)
Acknowledgments This work was supported by the University of Malaya High Impact Research Grants (UMMOHE HIR Grant UM.C/625/1/HIR/MOHE/CHAN/
Please cite this article as: See-Too, W.-S., et al., De novo assembly of complete genome sequence of Planococcus kocurii ATCC 43650T, a potential plant growth promoting bacterium, Mar. Genomics (2016), http://dx.doi.org/10.1016/j.margen.2016.04.007