PROKARYOTES
crossm Draft Genome Sequence of Staphylococcus succinus subsp. succinus Type Strain DSM 14617, Isolated from Plant and Soil Inclusions within 25- to 35-Million-Year-Old Dominican Amber Hairui Zhou, Zhenyu Yao, Haihong Shi, Baixin Wang, Dong Li, Jie Hou, Shuxia Ma Department of Medical School, Jiamusi University, Jiamusi, PR China
ABSTRACT Staphylococcus succinus subsp. succinus type strain DSM 14617 was iso-
lated from plant and soil inclusions within 25- to 35-million-year-old Dominican amber. The complete genome sequence of strain DSM 14617T includes a genome of 2.88 Mb (32.94% G⫹C content) without any plasmids.
S
taphylococcus succinus was first described by L. H. Lambert in 1998 (1). Members of this group are widespread in nature. Many studies have reported the frequent isolation of S. succinus from various sources, such as cheese, dry or fermented meat products, the Dead Sea, and, occasionally, humans (2–6). Type strain DSM 14617 was grown aerobically on Columbia blood agar base at 37°C for 24 h. Genomic DNA was extracted using the DNeasy blood and tissue kit (Qiagen, Germany). The quantity of DNA was measured by Cubit. Then, 10 g of DNA was sent to Zhejiang University. One DNA library was generated (422-bp insert size, with the Illumina adapter at both ends) and then sequenced using an Illumina HiSeq 2000 platform, with a 2 ⫻ 100 paired-end sequencing strategy. A total of 16.58 Mb filtered reads were assembled into scaffolds using Velvet version 1.2.07 (7); a PAGIT flow (8) was then used to prolong the initial contigs and correct sequencing errors. Predicted genes were identified using Glimmer version 3.0 (9); tRNAscan-SE version 1.21 (10) was used to find tRNA genes, and ribosomal RNAs were found by using RNAmmer version 1.2 (11). HMMER version 3.0 (12) was used to annotate the predicted genes, and the KAAS server (13) was used to assign translated amino acids to the KEGG Orthology database, following the single-directional best-hit method. Translated genes were aligned with the COG database using NCBI BLASTp. The draft genome sequence of strain DSM 14617T revealed a genome size of 2.88 Mb and a G⫹C content of 32.94% (161 scaffolds with an N50 of 241,537 bp). These scaffolds contain 2,914 coding sequences and 96 RNAs. A total of 2,315 protein-coding genes were assigned as putative functional or hypothetical proteins, and 2,089 genes were categorized into COG functional groups. Accession number(s). This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number LCSH00000000. The version described in this paper is the first version, LCSH01000000.
Received 16 November 2016 Accepted 23 November 2016 Published 26 January 2017 Citation Zhou H, Yao Z, Shi H, Wang B, Li D, Hou J, Ma S. 2017. Draft genome sequence of Staphylococcus succinus subsp. succinus type strain DSM 14617, isolated from plant and soil inclusions within 25- to 35-million-year-old Dominican amber. Genome Announc 5: e01521-16. https://doi.org/10.1128/ genomeA.01521-16. Copyright © 2017 Zhou et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Shuxia Ma, [email protected].
ACKNOWLEDGMENTS This work was supported by the State Key Clinical Department Program on Infectious Diseases from the Ministry of Health of China and by the Graduate Student Innovation Fund of Jiamusi University (lzz2015_013). Volume 5 Issue 4 e01521-16
genomea.asm.org 1
Zhou et al.
REFERENCES 1. Lambert LH, Cox T, Mitchell K, Rosselló-Mora RA, Del Cueto C, Dodge DE, Orkand P, Cano RJ. 1998. Staphylococcus succinus sp. nov., isolated from Dominican amber. Int J Syst Bacteriol 48:511–518. https://doi.org/ 10.1099/00207713-48-2-511. 2. Kesmen Z, Yetiman AE, Gulluce A, Kacmaz N, Sagdic O, Cetin B, Adiguzel A, Sahin F, Yetim H. 2012. Combination of culture-dependent and culture-independent molecular methods for the determination of lactic microbiota in sucuk. Int J Food Microbiol 153:428 – 435. https://doi.org/ 10.1016/j.ijfoodmicro.2011.12.008. 3. Place RB, Hiestand D, Burri S, Teuber M. 2002. Staphylococcus succinus subsp. casei subsp. nov., a dominant isolate from a surface ripened cheese. Syst Appl Microbiol 25:353–359. https://doi.org/10.1078/0723 -2020-00130. 4. Stabnikov V, Chu J, Jian C, Ivanov V, Li Y. 2013. Halotolerant, alkaliphilic urease-producing bacteria from different climate zones and their application for biocementation of sand. World J Microbiol Biotechnol 29: 1453–1460. https://doi.org/10.1007/s11274-013-1309-1. 5. Greppi A, Ferrocino I, La Storia A, Rantsiou K, Ercolini D, Cocolin L. 2015. Monitoring of the microbiota of fermented sausages by culture independent rRNA-based approaches. Int J Food Microbiol 212:67–75. https://doi.org/10.1016/j.ijfoodmicro.2015.01.016. 6. Nováková D, Sedlácek I, Pantu˚cek R, Stetina V, Svec P, Petrás P. 2006. Staphylococcus equorum and Staphylococcus succinus isolated from hu-
Volume 5 Issue 4 e01521-16
7.
8.
9.
10.
11.
12. 13.
man clinical specimens. J Med Microbiol 55:523–528. https://doi.org/ 10.1099/jmm.0.46246-0. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821– 829. https:// doi.org/10.1101/gr.074492.107. Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD. 2012. A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc 7:1260 –1284. https://doi.org/ 10.1038/nprot.2012.068. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673– 679. https://doi.org/10.1093/bioinformatics/btm009. Lowe TM, Eddy SR. 1997. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. https://doi.org/10.1093/nar/25.5.0955. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100 –3108. https://doi.org/10.1093/nar/ gkm160. Eddy SR. 2011. Accelerated profile HMM searches. PLoS Comput Biol 7:e1002195. https://doi.org/10.1371/journal.pcbi.1002195. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. 2007. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182–W185. https://doi.org/10.1093/nar/gkm321.
genomea.asm.org 2
crossm Draft Genome Sequence of Staphylococcus succinus subsp. succinus Type Strain DSM 14617, Isolated from Plant and Soil Inclusions within 25- to 35-Million-Year-Old Dominican Amber Hairui Zhou, Zhenyu Yao, Haihong Shi, Baixin Wang, Dong Li, Jie Hou, Shuxia Ma Department of Medical School, Jiamusi University, Jiamusi, PR China
ABSTRACT Staphylococcus succinus subsp. succinus type strain DSM 14617 was iso-
lated from plant and soil inclusions within 25- to 35-million-year-old Dominican amber. The complete genome sequence of strain DSM 14617T includes a genome of 2.88 Mb (32.94% G⫹C content) without any plasmids.
S
taphylococcus succinus was first described by L. H. Lambert in 1998 (1). Members of this group are widespread in nature. Many studies have reported the frequent isolation of S. succinus from various sources, such as cheese, dry or fermented meat products, the Dead Sea, and, occasionally, humans (2–6). Type strain DSM 14617 was grown aerobically on Columbia blood agar base at 37°C for 24 h. Genomic DNA was extracted using the DNeasy blood and tissue kit (Qiagen, Germany). The quantity of DNA was measured by Cubit. Then, 10 g of DNA was sent to Zhejiang University. One DNA library was generated (422-bp insert size, with the Illumina adapter at both ends) and then sequenced using an Illumina HiSeq 2000 platform, with a 2 ⫻ 100 paired-end sequencing strategy. A total of 16.58 Mb filtered reads were assembled into scaffolds using Velvet version 1.2.07 (7); a PAGIT flow (8) was then used to prolong the initial contigs and correct sequencing errors. Predicted genes were identified using Glimmer version 3.0 (9); tRNAscan-SE version 1.21 (10) was used to find tRNA genes, and ribosomal RNAs were found by using RNAmmer version 1.2 (11). HMMER version 3.0 (12) was used to annotate the predicted genes, and the KAAS server (13) was used to assign translated amino acids to the KEGG Orthology database, following the single-directional best-hit method. Translated genes were aligned with the COG database using NCBI BLASTp. The draft genome sequence of strain DSM 14617T revealed a genome size of 2.88 Mb and a G⫹C content of 32.94% (161 scaffolds with an N50 of 241,537 bp). These scaffolds contain 2,914 coding sequences and 96 RNAs. A total of 2,315 protein-coding genes were assigned as putative functional or hypothetical proteins, and 2,089 genes were categorized into COG functional groups. Accession number(s). This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number LCSH00000000. The version described in this paper is the first version, LCSH01000000.
Received 16 November 2016 Accepted 23 November 2016 Published 26 January 2017 Citation Zhou H, Yao Z, Shi H, Wang B, Li D, Hou J, Ma S. 2017. Draft genome sequence of Staphylococcus succinus subsp. succinus type strain DSM 14617, isolated from plant and soil inclusions within 25- to 35-million-year-old Dominican amber. Genome Announc 5: e01521-16. https://doi.org/10.1128/ genomeA.01521-16. Copyright © 2017 Zhou et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Shuxia Ma, [email protected].
ACKNOWLEDGMENTS This work was supported by the State Key Clinical Department Program on Infectious Diseases from the Ministry of Health of China and by the Graduate Student Innovation Fund of Jiamusi University (lzz2015_013). Volume 5 Issue 4 e01521-16
genomea.asm.org 1
Zhou et al.
REFERENCES 1. Lambert LH, Cox T, Mitchell K, Rosselló-Mora RA, Del Cueto C, Dodge DE, Orkand P, Cano RJ. 1998. Staphylococcus succinus sp. nov., isolated from Dominican amber. Int J Syst Bacteriol 48:511–518. https://doi.org/ 10.1099/00207713-48-2-511. 2. Kesmen Z, Yetiman AE, Gulluce A, Kacmaz N, Sagdic O, Cetin B, Adiguzel A, Sahin F, Yetim H. 2012. Combination of culture-dependent and culture-independent molecular methods for the determination of lactic microbiota in sucuk. Int J Food Microbiol 153:428 – 435. https://doi.org/ 10.1016/j.ijfoodmicro.2011.12.008. 3. Place RB, Hiestand D, Burri S, Teuber M. 2002. Staphylococcus succinus subsp. casei subsp. nov., a dominant isolate from a surface ripened cheese. Syst Appl Microbiol 25:353–359. https://doi.org/10.1078/0723 -2020-00130. 4. Stabnikov V, Chu J, Jian C, Ivanov V, Li Y. 2013. Halotolerant, alkaliphilic urease-producing bacteria from different climate zones and their application for biocementation of sand. World J Microbiol Biotechnol 29: 1453–1460. https://doi.org/10.1007/s11274-013-1309-1. 5. Greppi A, Ferrocino I, La Storia A, Rantsiou K, Ercolini D, Cocolin L. 2015. Monitoring of the microbiota of fermented sausages by culture independent rRNA-based approaches. Int J Food Microbiol 212:67–75. https://doi.org/10.1016/j.ijfoodmicro.2015.01.016. 6. Nováková D, Sedlácek I, Pantu˚cek R, Stetina V, Svec P, Petrás P. 2006. Staphylococcus equorum and Staphylococcus succinus isolated from hu-
Volume 5 Issue 4 e01521-16
7.
8.
9.
10.
11.
12. 13.
man clinical specimens. J Med Microbiol 55:523–528. https://doi.org/ 10.1099/jmm.0.46246-0. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 18:821– 829. https:// doi.org/10.1101/gr.074492.107. Swain MT, Tsai IJ, Assefa SA, Newbold C, Berriman M, Otto TD. 2012. A post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs. Nat Protoc 7:1260 –1284. https://doi.org/ 10.1038/nprot.2012.068. Delcher AL, Bratke KA, Powers EC, Salzberg SL. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673– 679. https://doi.org/10.1093/bioinformatics/btm009. Lowe TM, Eddy SR. 1997. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. https://doi.org/10.1093/nar/25.5.0955. Lagesen K, Hallin P, Rødland EA, Staerfeldt H-H, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100 –3108. https://doi.org/10.1093/nar/ gkm160. Eddy SR. 2011. Accelerated profile HMM searches. PLoS Comput Biol 7:e1002195. https://doi.org/10.1371/journal.pcbi.1002195. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. 2007. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 35:W182–W185. https://doi.org/10.1093/nar/gkm321.
genomea.asm.org 2
