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Draft Whole-Genome Sequence of the Type Strain Bacillus horikoshii DSM 8719 Ismael L. Hernández-González,
Gabriela Olmedo-Álvarez
Departamento de Ingeniería Genética, Centro de Investigaciones y Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato, Mexico
Members of the Bacillus genus have been extensively studied because of their ability to produce enzymes with high biotechnological value. Here, we report the draft of the whole-genome sequence of the type strain Bacillus horikoshii DSM 8719, an alkalitolerant strain. Received 13 May 2016 Accepted 23 May 2016 Published 14 July 2016 Citation Hernández-González IL, Olmedo-Álvarez G. 2016. Draft whole-genome sequence of the type strain Bacillus horikoshii DSM 8719. Genome Announc 4(4):e00641-16. doi:10.1128/genomeA.00641-16. Copyright © 2016 Hernández-González and Olmedo-Álvarez. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Gabriela Olmedo-Álvarez, [email protected].
T
he study of Bacillus spp. isolated from alkaline environments has taken a high importance due to their application in biotechnological processes. Species such as Bacillus horikoshii have been studied due to their ability to produce enzymes of biotechnological interest. The type strain B. horikoshii DSM 8719 has been reported as isolated from soil (1), and many bacteria identified as strains of B. horikoshii (based on the 16S rRNA sequence) have been isolated from marine environments and sometimes have been found associated with marine organisms (2). In some cases, these strains have shown the capacity to produce metabolites with antimicrobial activities. Others have the ability to produce alkaline enzymes important to industry (3, 4). The sequenced genome of the type strain B. horikoshii DSM 8719 will provide important data not only for biotechnology but also for understanding the evolution of the B. horikoshii group. The whole-genome sequencing of type strain B. horikoshii DSM 8719 was done through a hybrid strategy. The type strain was obtained from ATCC. The genome was sequenced using a 454 GS-FLX platform and Illumina mate-pair library. The raw 454 reads were processed using Newbler software, while the Illumina reads were processed by quality and length employing the FASTX toolkit package (http://hannonlab.cshl.edu/fastx_toolkit/index .html). De novo assembly was carried out using MIRA3 (5) and Velvet (6) software. The assembly produced 67 contigs (⬎1,000 bp) that comprise 4,677,891 bases with a G⫹C content of 41.3%. The genome annotation using RAST (7) identified 4,892 open reading frames (ORFs), 84 tRNAs, and 22 rRNAs. Nearly 27% of the 4,892 ORFs correspond to hypothetical proteins (1,336 ORFs). Based on the 16S rRNA sequence, the closest strain to B. horikoshii is Bacillus sp. m3-13 (ACPC01000000) (8). From the genome sequence annotated with RAST, we obtained ORFs that were screened for secondary metabolites employing antiSMASH version 3.0.4 (9). The antiSMASH software identified 7 possible gene clusters corresponding to terpene gene synthase (2 clusters), thiopeptide-lantipeptide (2 clusters), thiopeptide (1 cluster), T3pks (1 cluster), and siderophore (1 cluster). Both thiopeptideslantipeptide clusters correspond to lantipeptides of class I. Addi-
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tionally, enzymes of potential interest were readily identified, such as an alpha-amylase, one of which had been reported in another B. horikoshii strain (accession no. WP_063562491, with 93% identity) and a subtilin-related peptidase S8 (WP_063562468, with 92% identity). A large number of known and hypothetical proteases were recovered with the MEROPS database (10). In addition to its importance as a producer of compounds with biotechnological value, B. horikoshii and its relatives represent one new group inside the Bacillus genus. The knowledge obtained from the study of the genome of this organism will shed light on the evolution of the Bacillus genus. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the accession number LQXN00000000. The version described in this paper is the first version, LQXN01000000. ACKNOWLEDGMENT We acknowledge Africa Islas for technical assistance.
FUNDING INFORMATION This work, including the efforts of Gabriela Olmedo, was funded by Consejo Nacional de Ciencia y Tecnología (CONACYT) (CB-2013-01 220536). I.L.H.-G. was supported by a fellowship from CONACYT.
REFERENCES 1. Nielsen P, Fritze D, Priest FG. 1995. Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 141: 1745–1761. 2. Lu Y, Yi R. 2009. Bacillus horikoshii, a tetrodotoxin-producing bacterium isolated from the liver of puffer fish. Ann Microbiol 59:453– 458. http:// dx.doi.org/10.1007/BF03175130. 3. Thenmozhi R, Nithyanand P, Rathna J, Pandian SK. 2009. Antibiofilm activity of coral-associated bacteria against different clinical M serotypes of Streptococcus pyogenes. FEMS Immunol Med Microbiol 57:284 –294. http://dx.doi.org/10.1111/j.1574-695X.2009.00613.x. 4. Joo HS, Choi JW. 2012. Purification and characterization of a novel alkaline protease from Bacillus horikoshii. J Microbiol Biotechnol 22: 58 – 68. http://dx.doi.org/10.4014/jmb.1109.09006.
Genome Announcements
genomea.asm.org 1
Hernández-González and Olmedo-Álvarez
5. Chevreux B, Wetter T, Suhai S. 1999. Genome sequence assembly using Trace signals and additional sequence information, p. 45–56. In Computer science and biology: Proceedings of the German Conference on Bioinformatics, GCB ’99. GCB, Hannover, Germany. 6. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821– 829. http:// dx.doi.org/10.1101/gr.074492.107. 7. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. http://dx.doi.org/10.1186/1471-2164-9-75.
2 genomea.asm.org
8. Alcaraz LD, Moreno-Hagelsieb G, Eguiarte LE, Souza V, HerreraEstrella L, Olmedo G. 2010. Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics. BMC Genomics 11:332. http://dx.doi.org/10.1186/1471-2164-11-332. 9. Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W, Breitling R, Takano E, Medema MH. 2015. AntiSMASH 3.0 —a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43: W237–W243. http://dx.doi.org/10.1093/nar/gkv437. 10. Rawlings ND, Barrett AJ, Finn RD. 2016. Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res 44:D343–D350. http://dx.doi.org/10.1093/nar/ gkv1118.
Genome Announcements
July/August 2016 Volume 4 Issue 4 e00641-16
Draft Whole-Genome Sequence of the Type Strain Bacillus horikoshii DSM 8719 Ismael L. Hernández-González,
Gabriela Olmedo-Álvarez
Departamento de Ingeniería Genética, Centro de Investigaciones y Estudios Avanzados del Instituto Politécnico Nacional, Unidad Irapuato, Irapuato, Mexico
Members of the Bacillus genus have been extensively studied because of their ability to produce enzymes with high biotechnological value. Here, we report the draft of the whole-genome sequence of the type strain Bacillus horikoshii DSM 8719, an alkalitolerant strain. Received 13 May 2016 Accepted 23 May 2016 Published 14 July 2016 Citation Hernández-González IL, Olmedo-Álvarez G. 2016. Draft whole-genome sequence of the type strain Bacillus horikoshii DSM 8719. Genome Announc 4(4):e00641-16. doi:10.1128/genomeA.00641-16. Copyright © 2016 Hernández-González and Olmedo-Álvarez. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Gabriela Olmedo-Álvarez, [email protected].
T
he study of Bacillus spp. isolated from alkaline environments has taken a high importance due to their application in biotechnological processes. Species such as Bacillus horikoshii have been studied due to their ability to produce enzymes of biotechnological interest. The type strain B. horikoshii DSM 8719 has been reported as isolated from soil (1), and many bacteria identified as strains of B. horikoshii (based on the 16S rRNA sequence) have been isolated from marine environments and sometimes have been found associated with marine organisms (2). In some cases, these strains have shown the capacity to produce metabolites with antimicrobial activities. Others have the ability to produce alkaline enzymes important to industry (3, 4). The sequenced genome of the type strain B. horikoshii DSM 8719 will provide important data not only for biotechnology but also for understanding the evolution of the B. horikoshii group. The whole-genome sequencing of type strain B. horikoshii DSM 8719 was done through a hybrid strategy. The type strain was obtained from ATCC. The genome was sequenced using a 454 GS-FLX platform and Illumina mate-pair library. The raw 454 reads were processed using Newbler software, while the Illumina reads were processed by quality and length employing the FASTX toolkit package (http://hannonlab.cshl.edu/fastx_toolkit/index .html). De novo assembly was carried out using MIRA3 (5) and Velvet (6) software. The assembly produced 67 contigs (⬎1,000 bp) that comprise 4,677,891 bases with a G⫹C content of 41.3%. The genome annotation using RAST (7) identified 4,892 open reading frames (ORFs), 84 tRNAs, and 22 rRNAs. Nearly 27% of the 4,892 ORFs correspond to hypothetical proteins (1,336 ORFs). Based on the 16S rRNA sequence, the closest strain to B. horikoshii is Bacillus sp. m3-13 (ACPC01000000) (8). From the genome sequence annotated with RAST, we obtained ORFs that were screened for secondary metabolites employing antiSMASH version 3.0.4 (9). The antiSMASH software identified 7 possible gene clusters corresponding to terpene gene synthase (2 clusters), thiopeptide-lantipeptide (2 clusters), thiopeptide (1 cluster), T3pks (1 cluster), and siderophore (1 cluster). Both thiopeptideslantipeptide clusters correspond to lantipeptides of class I. Addi-
July/August 2016 Volume 4 Issue 4 e00641-16
tionally, enzymes of potential interest were readily identified, such as an alpha-amylase, one of which had been reported in another B. horikoshii strain (accession no. WP_063562491, with 93% identity) and a subtilin-related peptidase S8 (WP_063562468, with 92% identity). A large number of known and hypothetical proteases were recovered with the MEROPS database (10). In addition to its importance as a producer of compounds with biotechnological value, B. horikoshii and its relatives represent one new group inside the Bacillus genus. The knowledge obtained from the study of the genome of this organism will shed light on the evolution of the Bacillus genus. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited in DDBJ/EMBL/GenBank under the accession number LQXN00000000. The version described in this paper is the first version, LQXN01000000. ACKNOWLEDGMENT We acknowledge Africa Islas for technical assistance.
FUNDING INFORMATION This work, including the efforts of Gabriela Olmedo, was funded by Consejo Nacional de Ciencia y Tecnología (CONACYT) (CB-2013-01 220536). I.L.H.-G. was supported by a fellowship from CONACYT.
REFERENCES 1. Nielsen P, Fritze D, Priest FG. 1995. Phenetic diversity of alkaliphilic Bacillus strains: proposal for nine new species. Microbiology 141: 1745–1761. 2. Lu Y, Yi R. 2009. Bacillus horikoshii, a tetrodotoxin-producing bacterium isolated from the liver of puffer fish. Ann Microbiol 59:453– 458. http:// dx.doi.org/10.1007/BF03175130. 3. Thenmozhi R, Nithyanand P, Rathna J, Pandian SK. 2009. Antibiofilm activity of coral-associated bacteria against different clinical M serotypes of Streptococcus pyogenes. FEMS Immunol Med Microbiol 57:284 –294. http://dx.doi.org/10.1111/j.1574-695X.2009.00613.x. 4. Joo HS, Choi JW. 2012. Purification and characterization of a novel alkaline protease from Bacillus horikoshii. J Microbiol Biotechnol 22: 58 – 68. http://dx.doi.org/10.4014/jmb.1109.09006.
Genome Announcements
genomea.asm.org 1
Hernández-González and Olmedo-Álvarez
5. Chevreux B, Wetter T, Suhai S. 1999. Genome sequence assembly using Trace signals and additional sequence information, p. 45–56. In Computer science and biology: Proceedings of the German Conference on Bioinformatics, GCB ’99. GCB, Hannover, Germany. 6. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821– 829. http:// dx.doi.org/10.1101/gr.074492.107. 7. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. http://dx.doi.org/10.1186/1471-2164-9-75.
2 genomea.asm.org
8. Alcaraz LD, Moreno-Hagelsieb G, Eguiarte LE, Souza V, HerreraEstrella L, Olmedo G. 2010. Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics. BMC Genomics 11:332. http://dx.doi.org/10.1186/1471-2164-11-332. 9. Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, Lee SY, Fischbach MA, Müller R, Wohlleben W, Breitling R, Takano E, Medema MH. 2015. AntiSMASH 3.0 —a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 43: W237–W243. http://dx.doi.org/10.1093/nar/gkv437. 10. Rawlings ND, Barrett AJ, Finn RD. 2016. Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors. Nucleic Acids Res 44:D343–D350. http://dx.doi.org/10.1093/nar/ gkv1118.
Genome Announcements
July/August 2016 Volume 4 Issue 4 e00641-16
