MARGEN-00243; No of Pages 2 Marine Genomics xxx (2014) xxx–xxx
Contents lists available at ScienceDirect
Marine Genomics journal homepage: www.elsevier.com/locate/margen
Genomics/technical resources
Draft genome sequence of Halorubrum halophilum B8T, an extremely halophilic archaeon isolated from salt-fermented seafood Hae-Won Lee a,b, Kyung June Yim a, Hye Seon Song a, Young-Do Nam c, Hak-Jong Choi b, Myung-Ji Seo d, Kil-Nam Kim a, Daekyung Kim a, Seong Woon Roh a,⁎, Jin-Kyu Rhee e,⁎⁎ a
Jeju Center, Korea Basic Science Institute, Jeju 690-140, Republic of Korea World Institute of Kimchi, Gwangju 503-360, Republic of Korea Fermentation Research Center, Korea Food Research Institute, Sungnam 463-746, Republic of Korea d Division of Bioengineering, Incheon National University, Incheon 406-772, Republic of Korea e Western Seoul Center, Korea Basic Science Institute, Seoul 120-140, Republic of Korea b c
a r t i c l e
i n f o
Article history: Received 18 August 2014 Accepted 22 August 2014 Available online xxxx
a b s t r a c t The extremely halophilic archaeon, Halorubrum halophilum B8T (=JCM 18963T, CECT 8278T) was isolated from salt-fermented seafood. We report here the draft genome of H. halophilum B8T, containing 3,677,984 bp with a G + C content of 65.1%. The genome consists of 19 genes predicted to encode esterases. © 2014 Published by Elsevier B.V.
Keywords: Haloarchaea Extremely halophilic archaea Halorubrum halophilum Genome sequence
1. Introduction Halophiles have potentially valuable physiological properties to grow at high salt concentrations; they also produce commercially useful hydrolases that are activated in highly saline environments (Ventosa et al., 1998). The genus Halorubrum, proposed by McGenity and Grant (1995) as a member of the family Halobacteriaceae that is considered extremely halophilic archaea, currently comprises 27 species (http:// www.bacterio.net/halorubrum.html). Halorubrum halophilum B8T (= JCM 18963T, CECT 8278T), isolated from salt-fermented seafood made from shrimp, can grow at 15–30% (w/v) NaCl, with maximum growth at 25% NaCl and is an aerobic and red-pigmented haloarchaeon (Yim et al., 2014). This strain was reported to hydrolyze Tween 20, 40, and 80 under conditions of high salinity, suggesting the presence of an esterase with lipolytic activity. Esterases are used in the food industry for the production or enrichment of flavor, particularly in cheeserelated products (Choi and Lee, 2001). These esterases produce flavor by the transformation of low-value fats and oils (Panda and Gowrishankar, 2005). Moreover, esterases are used in pharmaceutical industry for the synthesis of chiral drugs (Panda and Gowrishankar, 2005). Here the genome sequence of H. halophilum is reported for the
⁎ Corresponding author. Tel.: +82 64 800 4931; fax: +82 64 805 7800. ⁎⁎ Corresponding author. Tel.: +82 2 6908 6224; fax: +82 2 6908 6215. E-mail addresses: [email protected] (S.W. Roh), [email protected] (J.-K. Rhee).
general sequence information of halophilic enzymes that may have potential applications in industry. H. halophilum B8T genomic DNA was extracted using the G-spin Genomic DNA Extraction Kit (iNtRON Biotechnology, Seongnam, Korea) and the sequence was determined using the Illumina MiSeq system (Illumina, Inc., San Diego, CA, USA) according to the manufacturer's instructions. A total of 9,978,008 reads were generated (with 570.15-fold coverage of the genome) using CLC Genomics Workbench 7.0.4 (CLC Bio, Aarhus, Denmark). The sequences were assembled into 103 contigs with an N50 contig size of approximately 98 kb and annotated using RNAmmer 1.2 (Lagesen et al., 2007), tRNA scan-SE 1.21 (Lowe and Eddy, 1997), Rapid Annotation using Subsystem Technology (RAST) pipeline (Aziz et al., 2008), and CLgenomics program (http://www. chunlab.com/genomics). The H. halophilum B8T draft genome was 3,677,984 bp in length, with a G + C content of 65.1%; the genome was predicted to include 4292 open reading frames (ORFs) and encodes 3 rRNA and 54 tRNA genes (Table 1). By functional categories based on COG (http://www.ncbi. nlm.nih.gov/COG/), a total of 98 genes were annotated as carbohydrate transport and metabolism genes and 387 were predicted to have general functions. Additionally, 19 genes were predicted to encode esterases, including phosphoesterase, phosphoesterase, glycerophosphoryl diester phosphodiesterase, pectin methylesterase, carboxylesterase, and thioesterase. The draft genome of H. halophilum B8T will provide basic information on esterases produced by Haloarchaea; a more detailed comparative analysis between H. halophilum B8T and other extremely
http://dx.doi.org/10.1016/j.margen.2014.08.005 1874-7787/© 2014 Published by Elsevier B.V.
Please cite this article as: Lee, H.-W., et al., Draft genome sequence of Halorubrum halophilum B8T, an extremely halophilic archaeon isolated from salt-fermented seafood..., Mar. Genomics (2014), http://dx.doi.org/10.1016/j.margen.2014.08.005
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H.-W. Lee et al. / Marine Genomics xxx (2014) xxx–xxx
Table 1 General features of Halorubrum halophilum B8T draft genome. Halorubrum halophilum B8T Assembly size (bp) G + C content (%) Contigs ORFs Coding sequences RNA genes tRNA genes
3,677,984 65.1 103 4292 3511 3 54
halophilic archaeal strains that have lipolytic activity is currently underway. 1.1. Nucleotide sequence accession number The genome sequences of H. halophilum B8T (=JCM 18963T, CECT 8278T) have been deposited at DDBJ/EMBL/GenBank under the accession number BBJP00000000. Acknowledgments
Basic Science Institute, and KBSI grant (T34525) to J.-K. Rhee from the Korea Basic Science Institute Western Seoul Center, and by the Basic Science Research Program through the National Research Foundation of Korea (2012R1A1A2040922). References Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., et al., 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9, 75. Choi, Y.-J., Lee, B., 2001. Culture conditions for the production of esterase from Lactobacillus casei CL96. Bioprocess Biosyst. Eng. 24, 59–63. Lagesen, K., Hallin, P., Rodland, E.A., Staerfeldt, H.H., et al., 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108. 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. McGenity, T.J., Grant, W.D., 1995. Transfer of Halobacterium saccharovorum, Halobacterium sodomense, Halobacterium trapanicum NRC 34021 and Halobacterium lacusprofundi to the genus Halorubrum gen. nov., as Halorubrum saccharovorum comb. nov., Halorubrum sodomense comb. nov., Halorubrum trapanicum comb. nov., and Halorubrum lacusprofundi comb. nov. Syst. Appl. Microbiol. 18, 237–243. Panda, T., Gowrishankar, B.S., 2005. Production and applications of esterases. Appl. Microbiol. Biotechnol. 67, 160–169. Ventosa, A., Nieto, J.J., Oren, A., 1998. Biology of moderately halophilic aerobic bacteria. Microbiol. Mol. Biol. Rev. 62, 504–544. Yim, K.J., Cha, I.T., Lee, H.W., Song, H.S., et al., 2014. Halorubrum halophilum sp. nov., an extremely halophilic archaeon isolated from a salt-fermented seafood. Antonie Van Leeuwenhoek 105, 603–612.
This research was supported in part by a project fund (C34703) to J.S. Choi from the Center for Analytical Research of Disaster Science of Korea
Please cite this article as: Lee, H.-W., et al., Draft genome sequence of Halorubrum halophilum B8T, an extremely halophilic archaeon isolated from salt-fermented seafood..., Mar. Genomics (2014), http://dx.doi.org/10.1016/j.margen.2014.08.005
Contents lists available at ScienceDirect
Marine Genomics journal homepage: www.elsevier.com/locate/margen
Genomics/technical resources
Draft genome sequence of Halorubrum halophilum B8T, an extremely halophilic archaeon isolated from salt-fermented seafood Hae-Won Lee a,b, Kyung June Yim a, Hye Seon Song a, Young-Do Nam c, Hak-Jong Choi b, Myung-Ji Seo d, Kil-Nam Kim a, Daekyung Kim a, Seong Woon Roh a,⁎, Jin-Kyu Rhee e,⁎⁎ a
Jeju Center, Korea Basic Science Institute, Jeju 690-140, Republic of Korea World Institute of Kimchi, Gwangju 503-360, Republic of Korea Fermentation Research Center, Korea Food Research Institute, Sungnam 463-746, Republic of Korea d Division of Bioengineering, Incheon National University, Incheon 406-772, Republic of Korea e Western Seoul Center, Korea Basic Science Institute, Seoul 120-140, Republic of Korea b c
a r t i c l e
i n f o
Article history: Received 18 August 2014 Accepted 22 August 2014 Available online xxxx
a b s t r a c t The extremely halophilic archaeon, Halorubrum halophilum B8T (=JCM 18963T, CECT 8278T) was isolated from salt-fermented seafood. We report here the draft genome of H. halophilum B8T, containing 3,677,984 bp with a G + C content of 65.1%. The genome consists of 19 genes predicted to encode esterases. © 2014 Published by Elsevier B.V.
Keywords: Haloarchaea Extremely halophilic archaea Halorubrum halophilum Genome sequence
1. Introduction Halophiles have potentially valuable physiological properties to grow at high salt concentrations; they also produce commercially useful hydrolases that are activated in highly saline environments (Ventosa et al., 1998). The genus Halorubrum, proposed by McGenity and Grant (1995) as a member of the family Halobacteriaceae that is considered extremely halophilic archaea, currently comprises 27 species (http:// www.bacterio.net/halorubrum.html). Halorubrum halophilum B8T (= JCM 18963T, CECT 8278T), isolated from salt-fermented seafood made from shrimp, can grow at 15–30% (w/v) NaCl, with maximum growth at 25% NaCl and is an aerobic and red-pigmented haloarchaeon (Yim et al., 2014). This strain was reported to hydrolyze Tween 20, 40, and 80 under conditions of high salinity, suggesting the presence of an esterase with lipolytic activity. Esterases are used in the food industry for the production or enrichment of flavor, particularly in cheeserelated products (Choi and Lee, 2001). These esterases produce flavor by the transformation of low-value fats and oils (Panda and Gowrishankar, 2005). Moreover, esterases are used in pharmaceutical industry for the synthesis of chiral drugs (Panda and Gowrishankar, 2005). Here the genome sequence of H. halophilum is reported for the
⁎ Corresponding author. Tel.: +82 64 800 4931; fax: +82 64 805 7800. ⁎⁎ Corresponding author. Tel.: +82 2 6908 6224; fax: +82 2 6908 6215. E-mail addresses: [email protected] (S.W. Roh), [email protected] (J.-K. Rhee).
general sequence information of halophilic enzymes that may have potential applications in industry. H. halophilum B8T genomic DNA was extracted using the G-spin Genomic DNA Extraction Kit (iNtRON Biotechnology, Seongnam, Korea) and the sequence was determined using the Illumina MiSeq system (Illumina, Inc., San Diego, CA, USA) according to the manufacturer's instructions. A total of 9,978,008 reads were generated (with 570.15-fold coverage of the genome) using CLC Genomics Workbench 7.0.4 (CLC Bio, Aarhus, Denmark). The sequences were assembled into 103 contigs with an N50 contig size of approximately 98 kb and annotated using RNAmmer 1.2 (Lagesen et al., 2007), tRNA scan-SE 1.21 (Lowe and Eddy, 1997), Rapid Annotation using Subsystem Technology (RAST) pipeline (Aziz et al., 2008), and CLgenomics program (http://www. chunlab.com/genomics). The H. halophilum B8T draft genome was 3,677,984 bp in length, with a G + C content of 65.1%; the genome was predicted to include 4292 open reading frames (ORFs) and encodes 3 rRNA and 54 tRNA genes (Table 1). By functional categories based on COG (http://www.ncbi. nlm.nih.gov/COG/), a total of 98 genes were annotated as carbohydrate transport and metabolism genes and 387 were predicted to have general functions. Additionally, 19 genes were predicted to encode esterases, including phosphoesterase, phosphoesterase, glycerophosphoryl diester phosphodiesterase, pectin methylesterase, carboxylesterase, and thioesterase. The draft genome of H. halophilum B8T will provide basic information on esterases produced by Haloarchaea; a more detailed comparative analysis between H. halophilum B8T and other extremely
http://dx.doi.org/10.1016/j.margen.2014.08.005 1874-7787/© 2014 Published by Elsevier B.V.
Please cite this article as: Lee, H.-W., et al., Draft genome sequence of Halorubrum halophilum B8T, an extremely halophilic archaeon isolated from salt-fermented seafood..., Mar. Genomics (2014), http://dx.doi.org/10.1016/j.margen.2014.08.005
2
H.-W. Lee et al. / Marine Genomics xxx (2014) xxx–xxx
Table 1 General features of Halorubrum halophilum B8T draft genome. Halorubrum halophilum B8T Assembly size (bp) G + C content (%) Contigs ORFs Coding sequences RNA genes tRNA genes
3,677,984 65.1 103 4292 3511 3 54
halophilic archaeal strains that have lipolytic activity is currently underway. 1.1. Nucleotide sequence accession number The genome sequences of H. halophilum B8T (=JCM 18963T, CECT 8278T) have been deposited at DDBJ/EMBL/GenBank under the accession number BBJP00000000. Acknowledgments
Basic Science Institute, and KBSI grant (T34525) to J.-K. Rhee from the Korea Basic Science Institute Western Seoul Center, and by the Basic Science Research Program through the National Research Foundation of Korea (2012R1A1A2040922). References Aziz, R.K., Bartels, D., Best, A.A., DeJongh, M., et al., 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9, 75. Choi, Y.-J., Lee, B., 2001. Culture conditions for the production of esterase from Lactobacillus casei CL96. Bioprocess Biosyst. Eng. 24, 59–63. Lagesen, K., Hallin, P., Rodland, E.A., Staerfeldt, H.H., et al., 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108. 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. McGenity, T.J., Grant, W.D., 1995. Transfer of Halobacterium saccharovorum, Halobacterium sodomense, Halobacterium trapanicum NRC 34021 and Halobacterium lacusprofundi to the genus Halorubrum gen. nov., as Halorubrum saccharovorum comb. nov., Halorubrum sodomense comb. nov., Halorubrum trapanicum comb. nov., and Halorubrum lacusprofundi comb. nov. Syst. Appl. Microbiol. 18, 237–243. Panda, T., Gowrishankar, B.S., 2005. Production and applications of esterases. Appl. Microbiol. Biotechnol. 67, 160–169. Ventosa, A., Nieto, J.J., Oren, A., 1998. Biology of moderately halophilic aerobic bacteria. Microbiol. Mol. Biol. Rev. 62, 504–544. Yim, K.J., Cha, I.T., Lee, H.W., Song, H.S., et al., 2014. Halorubrum halophilum sp. nov., an extremely halophilic archaeon isolated from a salt-fermented seafood. Antonie Van Leeuwenhoek 105, 603–612.
This research was supported in part by a project fund (C34703) to J.S. Choi from the Center for Analytical Research of Disaster Science of Korea
Please cite this article as: Lee, H.-W., et al., Draft genome sequence of Halorubrum halophilum B8T, an extremely halophilic archaeon isolated from salt-fermented seafood..., Mar. Genomics (2014), http://dx.doi.org/10.1016/j.margen.2014.08.005
