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Draft Genome Sequence of Shewanella sp. ECSMB14101, Isolated from the East China Sea Jin-Long Yang,a,b Xing-Pan Guo,a De-Wen Dingb Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, Chinaa; Marine Ecology Research Center, the First Institute of Oceanography, State Oceanic Administration, Qingdao, Chinab
Shewanella sp. ECSMB14101 was isolated from marine biofilms formed on the East China Sea. The draft genome sequence comprises 4,272,451 bp with a GⴙC content of 49.82%. Information on this draft genome will contribute to the understanding of bacterium-animal interactions.
Citation Yang J-L, Guo X-P, Ding D-W. 2015. Draft genome sequence of Shewanella sp. ECSMB14101, isolated from the East China Sea. Genome Announc 3(1):e01388-14. doi: 10.1128/genomeA.01388-14. Copyright © 2015 Yang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Jin-Long Yang, [email protected].
M
embers of the genus Shewanella compose a diverse group of facultative anaerobic bacteria widely distributed in marine and freshwater environments (1). Given their widespread distribution in environments where organic matter is actively degraded, members of the genus Shewanella may be viewed as useful model organisms for obtaining systems-level insight into the carbon-cycling process (2). In addition, Shewanella sp. ECSMB14101 is just one of a host of biofouling microorganisms that can be found in marine biofilms, and can induce the settlement of larvae (3) and plantigrades (4) of the mussel Mytilus coruscus, an important fouling and aquaculture species in the East China Sea (5). More than 40 Shewanella genomes have been fully sequenced to data, and 25 strains have complete whole-genome sequences. In order to understand the interaction between the role of Shewanella sp. ECSMB14101 and the settlement mechanism of the mussel Mytilus coruscus, the draft genome of Shewanella sp. ECSMB14101 was sequenced. The strain of Shewanella sp. ECSMB14101 was isolated from marine biofilms formed on the East China Sea (122°46=E; 30°43=N, water depth of 0.5 m), and the 16S rRNA sequences of Shewanella sp. ECSMB14101 shared 100% similarity with Shewanella marisflavi (accession no. AY485224) (3). Here, we present the draft genome sequence of the strain ECSMB14101, generated using the Illumina MiSeq platform by Shanghai Majorbio Pharm Technology Co., Ltd. (Shanghai, China) with a paired-end library. After trimmed and merged, the reads were de novo assembled with GS De Novo Assembler v2.8. Open reading frames (ORFs) were predicted using the program Glimmer 3.02 (6). All ORFs were then annotated by comparison with NCBI-NR and KEGG using BLASTp (BLAST 2/2/28⫹). The tRNA and rRNA were predicted by the program tRNAscan-SE v1.3.1 and Barrnap 0.4.2 (http://www.vicbioinformatics.com /software.barrnap.shtml), respectively (7). The draft genome sequence of the strain ECSMB14101 consists of 81 contigs (⬎200 bp) of 4,272,451 bp, and the largest contig assembled is 587,120 bp. The N50 and N90 quality measurement of the contigs were 159,739 bp and 43,702 bp, respectively. The draft genome sequence has a G⫹C content of 49.82%. The genome contains 3,647 predicted protein-coding sequences, 90 tRNA genes for 20 amino acids, and 4 rRNA genes. The genome sequence of
January/February 2015 Volume 3 Issue 1 e01388-14
Shewanella sp. ECSMB14101 will provide a starting point for understanding the relationship between the settlement-associated contractile structure genes and the settlement process of the mussel M. coruscus. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. JSFF00000000. The version described in this paper is the first version, JSFF01000000. ACKNOWLEDGMENTS This work was supported by grants from the National Natural Science Foundation of China (41476131), the Shanghai Municipal Science and Technology Commission (12230502100), the Innovation Program of Shanghai Municipal Education Commission (14ZZ143), and Shanghai Universities First-class Disciplines Project of Fisheries.
REFERENCES 1. Hau HH, Gralnick JA. 2007. Ecology and biotechnology of the genus Shewanella. Annu Rev Microbiol 61:237–258. http://dx.doi.org/10.1146/ annurev.micro.61.080706.093257. 2. Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JL, Saffarini DA, Serres MH, Spormann AM, Zhulin IB, Tiedje JM. 2008. Towards environmental systems biology of Shewanella. Nat Rev Microbiol 6:592– 603. http://dx.doi.org/10.1038/nrmicro1947. 3. Yang JL, Shen PJ, Liang X, Li YF, Bao WY, Li JL. 2013. Larval settlement and metamorphosis of the mussel Mytilus coruscus in response to monospecific bacterial biofilms. Biofouling 29:247–259. http://dx.doi.org/ 10.1080/08927014.2013.764412. 4. Li YF, Guo XP, Yang JL, Liang X, Bao WY, Shen PJ, Shi ZY, Li JL. 2014. Effects of bacterial biofilms on settlement of plantigrades of the mussel Mytilus coruscus. Aquaculture 433:434 – 441. http://dx.doi.org/10.1016/ j.aquaculture.2014.06.031. 5. Wang C, Bao WY, Gu ZQ, Li YF, Liang X, Ling Y, Cai SL, Shen HD, Yang JL. 2012. Larval settlement and metamorphosis of the mussel Mytilus coruscus in response to natural biofilms. Biofouling 28:249 –256. http:// dx.doi.org/10.1080/08927014.2012.671303. 6. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27: 4636 – 4641. http://dx.doi.org/10.1093/nar/27.23.4636. 7. 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. http://dx.doi.org/10.1093/nar/25.5.0955.
Genome Announcements
genomea.asm.org 1
Downloaded from http://genomea.asm.org/ on November 15, 2015 by guest
Received 24 November 2014 Accepted 2 December 2014 Published 15 January 2015
Draft Genome Sequence of Shewanella sp. ECSMB14101, Isolated from the East China Sea Jin-Long Yang,a,b Xing-Pan Guo,a De-Wen Dingb Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, Chinaa; Marine Ecology Research Center, the First Institute of Oceanography, State Oceanic Administration, Qingdao, Chinab
Shewanella sp. ECSMB14101 was isolated from marine biofilms formed on the East China Sea. The draft genome sequence comprises 4,272,451 bp with a GⴙC content of 49.82%. Information on this draft genome will contribute to the understanding of bacterium-animal interactions.
Citation Yang J-L, Guo X-P, Ding D-W. 2015. Draft genome sequence of Shewanella sp. ECSMB14101, isolated from the East China Sea. Genome Announc 3(1):e01388-14. doi: 10.1128/genomeA.01388-14. Copyright © 2015 Yang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license. Address correspondence to Jin-Long Yang, [email protected].
M
embers of the genus Shewanella compose a diverse group of facultative anaerobic bacteria widely distributed in marine and freshwater environments (1). Given their widespread distribution in environments where organic matter is actively degraded, members of the genus Shewanella may be viewed as useful model organisms for obtaining systems-level insight into the carbon-cycling process (2). In addition, Shewanella sp. ECSMB14101 is just one of a host of biofouling microorganisms that can be found in marine biofilms, and can induce the settlement of larvae (3) and plantigrades (4) of the mussel Mytilus coruscus, an important fouling and aquaculture species in the East China Sea (5). More than 40 Shewanella genomes have been fully sequenced to data, and 25 strains have complete whole-genome sequences. In order to understand the interaction between the role of Shewanella sp. ECSMB14101 and the settlement mechanism of the mussel Mytilus coruscus, the draft genome of Shewanella sp. ECSMB14101 was sequenced. The strain of Shewanella sp. ECSMB14101 was isolated from marine biofilms formed on the East China Sea (122°46=E; 30°43=N, water depth of 0.5 m), and the 16S rRNA sequences of Shewanella sp. ECSMB14101 shared 100% similarity with Shewanella marisflavi (accession no. AY485224) (3). Here, we present the draft genome sequence of the strain ECSMB14101, generated using the Illumina MiSeq platform by Shanghai Majorbio Pharm Technology Co., Ltd. (Shanghai, China) with a paired-end library. After trimmed and merged, the reads were de novo assembled with GS De Novo Assembler v2.8. Open reading frames (ORFs) were predicted using the program Glimmer 3.02 (6). All ORFs were then annotated by comparison with NCBI-NR and KEGG using BLASTp (BLAST 2/2/28⫹). The tRNA and rRNA were predicted by the program tRNAscan-SE v1.3.1 and Barrnap 0.4.2 (http://www.vicbioinformatics.com /software.barrnap.shtml), respectively (7). The draft genome sequence of the strain ECSMB14101 consists of 81 contigs (⬎200 bp) of 4,272,451 bp, and the largest contig assembled is 587,120 bp. The N50 and N90 quality measurement of the contigs were 159,739 bp and 43,702 bp, respectively. The draft genome sequence has a G⫹C content of 49.82%. The genome contains 3,647 predicted protein-coding sequences, 90 tRNA genes for 20 amino acids, and 4 rRNA genes. The genome sequence of
January/February 2015 Volume 3 Issue 1 e01388-14
Shewanella sp. ECSMB14101 will provide a starting point for understanding the relationship between the settlement-associated contractile structure genes and the settlement process of the mussel M. coruscus. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. JSFF00000000. The version described in this paper is the first version, JSFF01000000. ACKNOWLEDGMENTS This work was supported by grants from the National Natural Science Foundation of China (41476131), the Shanghai Municipal Science and Technology Commission (12230502100), the Innovation Program of Shanghai Municipal Education Commission (14ZZ143), and Shanghai Universities First-class Disciplines Project of Fisheries.
REFERENCES 1. Hau HH, Gralnick JA. 2007. Ecology and biotechnology of the genus Shewanella. Annu Rev Microbiol 61:237–258. http://dx.doi.org/10.1146/ annurev.micro.61.080706.093257. 2. Fredrickson JK, Romine MF, Beliaev AS, Auchtung JM, Driscoll ME, Gardner TS, Nealson KH, Osterman AL, Pinchuk G, Reed JL, Rodionov DA, Rodrigues JL, Saffarini DA, Serres MH, Spormann AM, Zhulin IB, Tiedje JM. 2008. Towards environmental systems biology of Shewanella. Nat Rev Microbiol 6:592– 603. http://dx.doi.org/10.1038/nrmicro1947. 3. Yang JL, Shen PJ, Liang X, Li YF, Bao WY, Li JL. 2013. Larval settlement and metamorphosis of the mussel Mytilus coruscus in response to monospecific bacterial biofilms. Biofouling 29:247–259. http://dx.doi.org/ 10.1080/08927014.2013.764412. 4. Li YF, Guo XP, Yang JL, Liang X, Bao WY, Shen PJ, Shi ZY, Li JL. 2014. Effects of bacterial biofilms on settlement of plantigrades of the mussel Mytilus coruscus. Aquaculture 433:434 – 441. http://dx.doi.org/10.1016/ j.aquaculture.2014.06.031. 5. Wang C, Bao WY, Gu ZQ, Li YF, Liang X, Ling Y, Cai SL, Shen HD, Yang JL. 2012. Larval settlement and metamorphosis of the mussel Mytilus coruscus in response to natural biofilms. Biofouling 28:249 –256. http:// dx.doi.org/10.1080/08927014.2012.671303. 6. Delcher AL, Harmon D, Kasif S, White O, Salzberg SL. 1999. Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27: 4636 – 4641. http://dx.doi.org/10.1093/nar/27.23.4636. 7. 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. http://dx.doi.org/10.1093/nar/25.5.0955.
Genome Announcements
genomea.asm.org 1
Downloaded from http://genomea.asm.org/ on November 15, 2015 by guest
Received 24 November 2014 Accepted 2 December 2014 Published 15 January 2015
