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Draft Genome Sequence of Pseudoalteromonas tetraodonis Strain MQS005, a Bacterium with Potential Quorum-Sensing Regulation Yonglong Pan,a Yanbo Wang,a,b Xiaoqing Yan,a Asit Mazumder,a,c Yan Lianga Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People’s Republic of Chinaa; Jilin University, Jilin, People’s Republic of Chinab; University of Victoria, Victoria, British Columbia, Canadac
We present here the draft genome sequence of Pseudoalteromonas tetraodonis strain MQS005, a bacterium possessing potential quorum-sensing regulatory activity. This strain was isolated from water from the South China Sea, People’s Republic of China. The assembly consists of 4,252,538 bp and contains 144 contigs, with a GⴙC content of 41.85%. Received 2 June 2016 Accepted 17 June 2016 Published 4 August 2016 Citation Pan Y, Wang Y, Yan X, Mazumder A, Liang Y. 2016. Draft genome sequence of Pseudoalteromonas tetraodonis strain MQS005, a bacterium with potential quorumsensing regulation. Genome Announc 4(4):e00724-16. doi:10.1128/genomeA.00724-16. Copyright © 2016 Pan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Yan Liang, [email protected].
P
seudoalteromonas tetraodonis strain MQS005 was isolated from water from the South China Sea, People’s Republic of China. P. tetraodonis, a deep-sea marine bacterium, has a symbiotic relationship with fish (e.g., pufferfish) and produces neurotoxin tetrodotoxin (1). We found that this strain could efficiently degrade the quorum-sensing (2) signaling molecules acylhomoserine lactones (AHLs) and secrete long-chain AHLs upon short-chain AHL induction. Genomic DNA of P. tetraodonis strain MQS005 was extracted using the TIANamp bacteria DNA kit (Cat. no. DP302; Tiangen Biotech Co., Ltd., Beijing, China). A paired-end library with an insert size of 350 bp was constructed and sequenced using the Illumina HiSeq platform with a PE150 strategy. Then, the highquality reads without PCR adapter sequences were assembled by SOAPdenovo (3) to generate scaffolds, and all reads were used for further gap closure. A total of 1,214 Mb of high-quality sequence data were obtained, and the resulting assembly consisted of 4,252,538 bp containing 144 contigs (longest, 221,568 bp; N50, 60,836 bp), with a G⫹C content of 41.85%. With gene prediction, up to 3,943 genes in the genome assembly of P. tetraodonis strain MQS005 were found by GeneMarkS (http://topaz.gatech.edu/) with integrated model and Heuristic model parameters. Gene annotation was performed with a Blast search (http://blast.ncbi.nlm .nih.gov/) (E value ⬍1e-5 and minimal alignment length larger than 40%) against 4 databases. A total of 3,738, 2,222, 1,977, and 2,692 functional genes were annotated from the Kyoto Encyclopedia of Genes and Genomes (KEGG) (4), Clusters of Orthologous Groups (COG) (5), Nonredundant protein (NR) databases, and Gene Ontology (GO) (6), respectively. Accession number(s). The genome sequence of P. tetraodonis strain MQS005 was deposited at DDBJ/EMBL/GenBank under the accession no. LYRQ00000000. The version described in this paper is version LYRQ01000000. ACKNOWLEDGMENTS This work was supported by the Guangdong Science and Technology Department (grant 2013B030800001), Shenzhen Science and Technology
July/August 2016 Volume 4 Issue 4 e00724-16
Project (grants JCYJ20140509174140691 and JCYJ20140417113430641), 1000 Talent Plan for High-Level Foreign Experts of China Bureau of Foreign Experts Affairs [2014] no. 49, and a CAS Adjunct Professorship (grants 2013T1G0038 and GJHS2014090100463583).
FUNDING INFORMATION This work, including the efforts of Xiaoqing Yan and Yan Liang, was funded by Shenzhen Science and Technology Project (JCYJ20140509174140691 and JCYJ20140417113430641).This work, including the efforts of Asit Mazumder, was funded by 100 Talent Plan for High-Level Foreign Experts ([2014] no. 49). This work, including the efforts of Yan Liang, was funded by CSA Adjunct Professorship (2013T1G0038 and GJHS2014090100463583). This work, including the efforts of Yan Liang, was funded by Guangdong Science and Technology Department (Science and Technology Department, Guangdong Province) (2013B030800001).
REFERENCES 1. Ivanova EP, Romanenko LA, Matté MH, Matté GR, Lysenko AM, Simidu U, Kita-Tsukamoto K, Sawabe T, Vysotskii MV, Frolova GM, Mikhailov V, Christen R, Colwell RR. 2001. Retrieval of the species Alteromonas tetraodonis Simidu et al. 1990 as Pseudoalteromonas tetraodonis comb. nov. and emendation of description. Int J Syst Evol Microbiol 51: 1071–1078. http://dx.doi.org/10.1099/00207713-51-3-1071. 2. Federle MJ, Bassler BL. 2003. Interspecies communication in bacteria. J Clin Invest 112:1291–1299. http://dx.doi.org/10.1172/JCI20195. 3. Li R, Li Y, Kristiansen K, Wang J. 2008. SOAP: Short Oligonucleotide Alignment Program. Bioinformatics 24:713–714. http://dx.doi.org/ 10.1093/bioinformatics/btn025. 4. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res 32: D277–D280. http://dx.doi.org/10.1093/nar/gkh063. 5. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41. http://dx.doi.org/10.1186/1471-2105-4-41. 6. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29.
Genome Announcements
genomea.asm.org 1
Draft Genome Sequence of Pseudoalteromonas tetraodonis Strain MQS005, a Bacterium with Potential Quorum-Sensing Regulation Yonglong Pan,a Yanbo Wang,a,b Xiaoqing Yan,a Asit Mazumder,a,c Yan Lianga Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People’s Republic of Chinaa; Jilin University, Jilin, People’s Republic of Chinab; University of Victoria, Victoria, British Columbia, Canadac
We present here the draft genome sequence of Pseudoalteromonas tetraodonis strain MQS005, a bacterium possessing potential quorum-sensing regulatory activity. This strain was isolated from water from the South China Sea, People’s Republic of China. The assembly consists of 4,252,538 bp and contains 144 contigs, with a GⴙC content of 41.85%. Received 2 June 2016 Accepted 17 June 2016 Published 4 August 2016 Citation Pan Y, Wang Y, Yan X, Mazumder A, Liang Y. 2016. Draft genome sequence of Pseudoalteromonas tetraodonis strain MQS005, a bacterium with potential quorumsensing regulation. Genome Announc 4(4):e00724-16. doi:10.1128/genomeA.00724-16. Copyright © 2016 Pan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Yan Liang, [email protected].
P
seudoalteromonas tetraodonis strain MQS005 was isolated from water from the South China Sea, People’s Republic of China. P. tetraodonis, a deep-sea marine bacterium, has a symbiotic relationship with fish (e.g., pufferfish) and produces neurotoxin tetrodotoxin (1). We found that this strain could efficiently degrade the quorum-sensing (2) signaling molecules acylhomoserine lactones (AHLs) and secrete long-chain AHLs upon short-chain AHL induction. Genomic DNA of P. tetraodonis strain MQS005 was extracted using the TIANamp bacteria DNA kit (Cat. no. DP302; Tiangen Biotech Co., Ltd., Beijing, China). A paired-end library with an insert size of 350 bp was constructed and sequenced using the Illumina HiSeq platform with a PE150 strategy. Then, the highquality reads without PCR adapter sequences were assembled by SOAPdenovo (3) to generate scaffolds, and all reads were used for further gap closure. A total of 1,214 Mb of high-quality sequence data were obtained, and the resulting assembly consisted of 4,252,538 bp containing 144 contigs (longest, 221,568 bp; N50, 60,836 bp), with a G⫹C content of 41.85%. With gene prediction, up to 3,943 genes in the genome assembly of P. tetraodonis strain MQS005 were found by GeneMarkS (http://topaz.gatech.edu/) with integrated model and Heuristic model parameters. Gene annotation was performed with a Blast search (http://blast.ncbi.nlm .nih.gov/) (E value ⬍1e-5 and minimal alignment length larger than 40%) against 4 databases. A total of 3,738, 2,222, 1,977, and 2,692 functional genes were annotated from the Kyoto Encyclopedia of Genes and Genomes (KEGG) (4), Clusters of Orthologous Groups (COG) (5), Nonredundant protein (NR) databases, and Gene Ontology (GO) (6), respectively. Accession number(s). The genome sequence of P. tetraodonis strain MQS005 was deposited at DDBJ/EMBL/GenBank under the accession no. LYRQ00000000. The version described in this paper is version LYRQ01000000. ACKNOWLEDGMENTS This work was supported by the Guangdong Science and Technology Department (grant 2013B030800001), Shenzhen Science and Technology
July/August 2016 Volume 4 Issue 4 e00724-16
Project (grants JCYJ20140509174140691 and JCYJ20140417113430641), 1000 Talent Plan for High-Level Foreign Experts of China Bureau of Foreign Experts Affairs [2014] no. 49, and a CAS Adjunct Professorship (grants 2013T1G0038 and GJHS2014090100463583).
FUNDING INFORMATION This work, including the efforts of Xiaoqing Yan and Yan Liang, was funded by Shenzhen Science and Technology Project (JCYJ20140509174140691 and JCYJ20140417113430641).This work, including the efforts of Asit Mazumder, was funded by 100 Talent Plan for High-Level Foreign Experts ([2014] no. 49). This work, including the efforts of Yan Liang, was funded by CSA Adjunct Professorship (2013T1G0038 and GJHS2014090100463583). This work, including the efforts of Yan Liang, was funded by Guangdong Science and Technology Department (Science and Technology Department, Guangdong Province) (2013B030800001).
REFERENCES 1. Ivanova EP, Romanenko LA, Matté MH, Matté GR, Lysenko AM, Simidu U, Kita-Tsukamoto K, Sawabe T, Vysotskii MV, Frolova GM, Mikhailov V, Christen R, Colwell RR. 2001. Retrieval of the species Alteromonas tetraodonis Simidu et al. 1990 as Pseudoalteromonas tetraodonis comb. nov. and emendation of description. Int J Syst Evol Microbiol 51: 1071–1078. http://dx.doi.org/10.1099/00207713-51-3-1071. 2. Federle MJ, Bassler BL. 2003. Interspecies communication in bacteria. J Clin Invest 112:1291–1299. http://dx.doi.org/10.1172/JCI20195. 3. Li R, Li Y, Kristiansen K, Wang J. 2008. SOAP: Short Oligonucleotide Alignment Program. Bioinformatics 24:713–714. http://dx.doi.org/ 10.1093/bioinformatics/btn025. 4. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. 2004. The KEGG resource for deciphering the genome. Nucleic Acids Res 32: D277–D280. http://dx.doi.org/10.1093/nar/gkh063. 5. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41. http://dx.doi.org/10.1186/1471-2105-4-41. 6. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29.
Genome Announcements
genomea.asm.org 1
