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Draft Genome Sequence of Pseudoalteromonas sp. Strain ECSMB14103, Isolated from the East China Sea Xing-Pan Guo,a De-Wen Ding,b Wei-Yang Bao,c Jin-Long Yanga,b Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, Chinaa; Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration, Qingdao, Chinab; Institute of Marine Science and Technology, Yangzhou University, Yangzhou, Chinac
Received 8 March 2015 Accepted 16 March 2015 Published 23 April 2015 Citation Guo X-P, Ding D-W, Bao W-Y, Yang J-L. 2015. Draft genome sequence of Pseudoalteromonas sp. strain ECSMB14103, isolated from the East China Sea. Genome Announc 3(2):e00330-15. doi:10.1128/genomeA.00330-15. Copyright © 2015 Guo 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].
P
seudoalteromonas is a genus of Gammaproteobacteria that is widespread in the oceans of the world, from surface water to deep-sea sediments (1). Many Pseudoalteromonas species are frequently found in association with eukaryotic hosts in the marine environment and produce biologically active molecules (2). Interest in the formation of biofilms of Pseudoalteromonas, microbehost interaction, and the synthesis of molecules has been increasing since 1995. Recent research of the literature from the last 20 years on the topic “Pseudoalteromonas” yielded more than 1,400 references, and more than 1,000 of the references are from the last 10 years. Pseudoalteromonas species could affect the process of larval settlement and metamorphosis of many marine invertebrates, such as coral (3), bryozoan (4), polychete (5), mussel (6), barnacle (7), and sea urchin (8). Recently, some species of Pseudoalteromonas have also been known to promote the settlement of juveniles of the mussel Mytilus coruscus (9), an important fouling and aquaculture species in the East China Sea. Here, we present the genome sequence of Pseudoalteromonas sp. ECSMB14103 for the purpose of elucidating its particular molecular cues and mechanisms that promote the recruitment of larvae and juveniles of the mussel M. coruscus. Pseudoalteromonas sp. strain ECSMB14103 was isolated from marine biofilms developed on glass slides immersed at a depth of 0.5 to 1.0 m below the surface of the East China Sea (122°46= E, 30°43= N), and the 16S rDNA sequences of Pseudoalteromonas sp. ECSMB14103 shared 99% similarity with Pseudoalteromonas marina Mano4 (accession no. AY563031) (6). The draft genome sequences of the strain ECSMB14103 were obtained by the Shanghai Majorbio Pharm Technology Co., Ltd., (Shanghai, China) using the Illumina MiSeq platform with a pairedend library. After being trimmed and merged, the reads were de novo assembled with the GS De Novo assembler version 2.8. Open reading frames (ORFs) were predicted by using the Glimmer version 3.02 program (10). All ORFs were then annotated by comparison with the NCBI-NR and KEGG databases using BLASTp (BLAST 2/2/28⫹). The tRNA and rRNA were predicted by the tRNAscan-SE version 1.3.1 (11) and Barrnap ver-
March/April 2015 Volume 3 Issue 2 e00330-15
sion 0.4.2 (http://www.vicbioinformatics.com/software.barrnap .shtml) programs, respectively. The draft genome sequence of the ECSMB14103 strain comprises 4.11 Mb, which is assembled into 32 contigs, with the size of the largest contig being 1,079,592 bp. The N50 and N90 quality measurements of the contigs were 413,937 bp and 117,763 bp, respectively. The G⫹C content is 39.7%. The genome contains 3,675 predicted protein-coding sequences, 121 tRNA genes for 20 amino acids, and 4 rRNA genes. The availability of the genome sequence of Pseudoalteromonas sp. ECSMB14103 can provide insight into exploring the molecular cues involved in the recruitment of the mussel M. coruscus larvae and juveniles. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JWGY00000000. The version described in this paper is the first version, JWGY01000000. ACKNOWLEDGMENTS This work was supported by grants from the National Natural Science Foundation of China (41476131), the Innovation Program of Shanghai Municipal Education Commission (14ZZ143), and the Shanghai Universities First-Class Disciplines Project of Fisheries.
REFERENCES 1. Qin QL, Li Y, Zhang YJ, Zhou ZM, Zhang WX, Chen XL, Zhang XY, Zhou BC, Wang L, Zhang YZ. 2011. Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913. ISME J 5:274 –284. http://dx.doi.org/10.1038/ismej.2010.103. 2. Holmström C, Kjelleberg S. 1999. Marine Pseudoalteromonas species are associated with higher organisms and produce biologically active extracellular agents. FEMS Microbiol Ecol 30:285–293. http://dx.doi.org/10.1016/ S0168-6496(99)00063-X. 3. Sneed JM, Sharp KH, Ritchie KB, Paul VJ. 2014. The chemical cue tetrabromopyrrole from a biofilm bacterium induces settlement of multiple Caribbean corals. Proc Biol Sci 281:. http://dx.doi.org/10.1098/ rspb.2013.3086.
Genome Announcements
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Pseudoalteromonas sp. strain ECSMB14103 was isolated from marine biofilms formed on the East China Sea. The draft genome sequence comprises 4.11 Mp with a GⴙC content of 39.7%. The information from the draft genome will contribute to an understanding of bacteria-animal interaction.
Guo et al.
4. Dahms H, Dobretsov S, Qian P. 2004. The effect of bacterial and diatom biofilms on the settlement of the bryozoan Bugula Neritina. J Exp Mar Biol Ecol 313:191–209. http://dx.doi.org/10.1016/j.jembe.2004.08.005. 5. Huang Y, Callahan S, Hadfield MG. 2012. Recruitment in the sea: bacterial genes required for inducing larval settlement in a polychaete worm. Sci Rep 2:228. http://dx.doi.org/10.1038/srep00228. 6. 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. 7. Holmström C, Egan S, Franks A, McCloy S, Kjelleberg S. 2002. Antifouling activities expressed by marine surface associated Pseudoalteromonas species. FEMS Microbiol Ecol 41:47–58. http://dx.doi.org/10.1111/ j.1574-6941.2002.tb00965.x.
8. Huggett MJ, Williamson JE, de Nys R, Kjelleberg S, Steinberg PD. 2006. Larval settlement of the common Australian sea urchin Heliocidaris erythrogramma in response to bacteria from the surface of coralline algae. Oecologia 149:604 – 619. http://dx.doi.org/10.1007/s00442-006-0470-8. 9. 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. 10. 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. 11. 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.
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Genome Announcements
March/April 2015 Volume 3 Issue 2 e00330-15
Draft Genome Sequence of Pseudoalteromonas sp. Strain ECSMB14103, Isolated from the East China Sea Xing-Pan Guo,a De-Wen Ding,b Wei-Yang Bao,c Jin-Long Yanga,b Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, Chinaa; Marine Ecology Research Center, First Institute of Oceanography, State Oceanic Administration, Qingdao, Chinab; Institute of Marine Science and Technology, Yangzhou University, Yangzhou, Chinac
Received 8 March 2015 Accepted 16 March 2015 Published 23 April 2015 Citation Guo X-P, Ding D-W, Bao W-Y, Yang J-L. 2015. Draft genome sequence of Pseudoalteromonas sp. strain ECSMB14103, isolated from the East China Sea. Genome Announc 3(2):e00330-15. doi:10.1128/genomeA.00330-15. Copyright © 2015 Guo 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].
P
seudoalteromonas is a genus of Gammaproteobacteria that is widespread in the oceans of the world, from surface water to deep-sea sediments (1). Many Pseudoalteromonas species are frequently found in association with eukaryotic hosts in the marine environment and produce biologically active molecules (2). Interest in the formation of biofilms of Pseudoalteromonas, microbehost interaction, and the synthesis of molecules has been increasing since 1995. Recent research of the literature from the last 20 years on the topic “Pseudoalteromonas” yielded more than 1,400 references, and more than 1,000 of the references are from the last 10 years. Pseudoalteromonas species could affect the process of larval settlement and metamorphosis of many marine invertebrates, such as coral (3), bryozoan (4), polychete (5), mussel (6), barnacle (7), and sea urchin (8). Recently, some species of Pseudoalteromonas have also been known to promote the settlement of juveniles of the mussel Mytilus coruscus (9), an important fouling and aquaculture species in the East China Sea. Here, we present the genome sequence of Pseudoalteromonas sp. ECSMB14103 for the purpose of elucidating its particular molecular cues and mechanisms that promote the recruitment of larvae and juveniles of the mussel M. coruscus. Pseudoalteromonas sp. strain ECSMB14103 was isolated from marine biofilms developed on glass slides immersed at a depth of 0.5 to 1.0 m below the surface of the East China Sea (122°46= E, 30°43= N), and the 16S rDNA sequences of Pseudoalteromonas sp. ECSMB14103 shared 99% similarity with Pseudoalteromonas marina Mano4 (accession no. AY563031) (6). The draft genome sequences of the strain ECSMB14103 were obtained by the Shanghai Majorbio Pharm Technology Co., Ltd., (Shanghai, China) using the Illumina MiSeq platform with a pairedend library. After being trimmed and merged, the reads were de novo assembled with the GS De Novo assembler version 2.8. Open reading frames (ORFs) were predicted by using the Glimmer version 3.02 program (10). All ORFs were then annotated by comparison with the NCBI-NR and KEGG databases using BLASTp (BLAST 2/2/28⫹). The tRNA and rRNA were predicted by the tRNAscan-SE version 1.3.1 (11) and Barrnap ver-
March/April 2015 Volume 3 Issue 2 e00330-15
sion 0.4.2 (http://www.vicbioinformatics.com/software.barrnap .shtml) programs, respectively. The draft genome sequence of the ECSMB14103 strain comprises 4.11 Mb, which is assembled into 32 contigs, with the size of the largest contig being 1,079,592 bp. The N50 and N90 quality measurements of the contigs were 413,937 bp and 117,763 bp, respectively. The G⫹C content is 39.7%. The genome contains 3,675 predicted protein-coding sequences, 121 tRNA genes for 20 amino acids, and 4 rRNA genes. The availability of the genome sequence of Pseudoalteromonas sp. ECSMB14103 can provide insight into exploring the molecular cues involved in the recruitment of the mussel M. coruscus larvae and juveniles. Nucleotide sequence accession numbers. This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number JWGY00000000. The version described in this paper is the first version, JWGY01000000. ACKNOWLEDGMENTS This work was supported by grants from the National Natural Science Foundation of China (41476131), the Innovation Program of Shanghai Municipal Education Commission (14ZZ143), and the Shanghai Universities First-Class Disciplines Project of Fisheries.
REFERENCES 1. Qin QL, Li Y, Zhang YJ, Zhou ZM, Zhang WX, Chen XL, Zhang XY, Zhou BC, Wang L, Zhang YZ. 2011. Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913. ISME J 5:274 –284. http://dx.doi.org/10.1038/ismej.2010.103. 2. Holmström C, Kjelleberg S. 1999. Marine Pseudoalteromonas species are associated with higher organisms and produce biologically active extracellular agents. FEMS Microbiol Ecol 30:285–293. http://dx.doi.org/10.1016/ S0168-6496(99)00063-X. 3. Sneed JM, Sharp KH, Ritchie KB, Paul VJ. 2014. The chemical cue tetrabromopyrrole from a biofilm bacterium induces settlement of multiple Caribbean corals. Proc Biol Sci 281:. http://dx.doi.org/10.1098/ rspb.2013.3086.
Genome Announcements
genomea.asm.org 1
Downloaded from http://genomea.asm.org/ on November 14, 2015 by guest
Pseudoalteromonas sp. strain ECSMB14103 was isolated from marine biofilms formed on the East China Sea. The draft genome sequence comprises 4.11 Mp with a GⴙC content of 39.7%. The information from the draft genome will contribute to an understanding of bacteria-animal interaction.
Guo et al.
4. Dahms H, Dobretsov S, Qian P. 2004. The effect of bacterial and diatom biofilms on the settlement of the bryozoan Bugula Neritina. J Exp Mar Biol Ecol 313:191–209. http://dx.doi.org/10.1016/j.jembe.2004.08.005. 5. Huang Y, Callahan S, Hadfield MG. 2012. Recruitment in the sea: bacterial genes required for inducing larval settlement in a polychaete worm. Sci Rep 2:228. http://dx.doi.org/10.1038/srep00228. 6. 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. 7. Holmström C, Egan S, Franks A, McCloy S, Kjelleberg S. 2002. Antifouling activities expressed by marine surface associated Pseudoalteromonas species. FEMS Microbiol Ecol 41:47–58. http://dx.doi.org/10.1111/ j.1574-6941.2002.tb00965.x.
8. Huggett MJ, Williamson JE, de Nys R, Kjelleberg S, Steinberg PD. 2006. Larval settlement of the common Australian sea urchin Heliocidaris erythrogramma in response to bacteria from the surface of coralline algae. Oecologia 149:604 – 619. http://dx.doi.org/10.1007/s00442-006-0470-8. 9. 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. 10. 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. 11. 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.
Downloaded from http://genomea.asm.org/ on November 14, 2015 by guest
2 genomea.asm.org
Genome Announcements
March/April 2015 Volume 3 Issue 2 e00330-15
