PROKARYOTES
crossm Draft Genome Sequence of Thalassospira xiamenensis Strain MCCC 1A03042T Meiqing Li, Shuo Yang, Qiliang Lai, Zongze Shao State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of State Oceanic Administration, Collaborative Innovation Center for Development and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
Thalassospira xiamenensis strain MCCC 1A03042T was isolated from deepsea sediment of the Indian Ocean, and it was characterized with heavy-metal arsenic tolerance. Here, we present the draft genome of strain MCCC 1A03042T, which contains 4,786,207 bp with a G⫹C content of 52.6% and 4,359 protein-coding genes. ABSTRACT
T
he species Thalassospira xiamenensis was first proposed by Liu et al. (1). Members of the T. xiamenensis species are non-spore-forming, Gram-negative, curved rods that are motile by means of one polar flagellum. T. xiamenensis strain MCCC 1A03042T is closely related to T. xiamenensis strain M-5T, which was the type strain, and the similarity was 99.716%. Strain MCCC 1A03042T was isolated from deep-sea sediment of the Indian Ocean, plated directly on 2216E agar (2) and incubated at 22°C. We found that it was characterized with heavy-metal arsenic tolerance and grew in the medium with an arsenic concentration of 10 mM. Genomic DNA was purified from T. xiamenensis MCCC 1A03042T with an AxyPrep bacterial genomic DNA miniprep kit (Axygen) according to the manufacturer’s instructions. The genome sequence was determined by Shanghai Majorbio Bio-pharm Technology Co., Ltd. (Shanghai, China) using Solexa paired-end sequencing technology. A total of 500 Mb of clean data (500-bp library) were generated to reach about 100-fold depth of coverage with an Illumina/Solexa Genome Analyzer IIx (Illumina, San Diego, CA, USA). The genome of T. xiamenensis MCCC 1A03042T consists of 72 contigs of 4,786,207 bp with an average G⫹C content of 52.6%. Gene prediction and annotation of the draft genome were carried out using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (http://www.ncbi.nlm.nih.gov/ genomes/static/Pipeline.html) (3). In total, 4,470 genes, 4,359 of which are protein-coding genes, and 50 tRNAs were predicted; 59 pseudogenes were also identified. Genome annotation and analysis were also done using the RAST server (http://rast.nmpdr.org) (4). Four genes (ars) for arsenate reduction were found in the annotations. A previous study demonstrated that an initial step in arsenic metabolism is the reduction of arsenate (5). In addition, the presence of an arsenic transporter was also noticed. Accession number(s). The draft genome sequence of T. xiamenensis MCCC 1A03042T has been deposited at GenBank under the accession number LPXM00000000. The version described in this paper is the first version, LPXM01000000.
Received 15 December 2016 Accepted 23 December 2016 Published 2 March 2017 Citation Li M, Yang S, Lai Q, Shao Z. 2017. Draft genome sequence of Thalassospira xiamenensis strain MCCC 1A03042T. Genome Announc 5: e01702-16. https://doi.org/10.1128/ genomeA.01702-16. Copyright © 2017 Li et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Zongze Shao, [email protected].
ACKNOWLEDGMENTS This work was financially supported by the COMRA program (no. DY125-15-R-01) and by the National Infrastructure of Natural Resources for Science and Technology Program of China (no. NIMR-2016-9). REFERENCES 1. Liu C, Wu Y, Li L, Ma Y, Shao Z. 2007. Thalassospira xiamenensis sp. nov. and Thalassospira profundimaris sp. nov. Int J Syst Evol Microbiol 57: 316 –320. https://doi.org/10.1099/ijs.0.64544-0. Volume 5 Issue 9 e01702-16
2. ZoBell CE. 1941. Studies on marine bacteria. I. The cultural requirements of heterotrophic aerobes. J Mar Res 4:42–75. 3. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira genomea.asm.org 1
Li et al.
CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O. 2008. Toward an online repository of standard operating procedures (SOPs) for (meta) genomic annotation. OMICS 12:137–141. https:// doi.org/10.1089/omi.2008.0017. 4. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R.
Volume 5 Issue 9 e01702-16
2014. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:D206 –D214. https:// doi.org/10.1093/nar/gkt1226. 5. Mukhopadhyay R, Rosen BP. 2002. Arsenate reductases in prokaryotes and eukaryotes. Environ Health Perspect 110(suppl 5):745–748. https:// doi.org/10.1289/ehp.02110s5745.
genomea.asm.org 2
crossm Draft Genome Sequence of Thalassospira xiamenensis Strain MCCC 1A03042T Meiqing Li, Shuo Yang, Qiliang Lai, Zongze Shao State Key Laboratory Breeding Base of Marine Genetic Resources, Key Laboratory of Marine Genetic Resources, Third Institute of State Oceanic Administration, Collaborative Innovation Center for Development and Utilization of Marine Biological Resources, Key Laboratory of Marine Genetic Resources of Fujian Province, Xiamen, China
Thalassospira xiamenensis strain MCCC 1A03042T was isolated from deepsea sediment of the Indian Ocean, and it was characterized with heavy-metal arsenic tolerance. Here, we present the draft genome of strain MCCC 1A03042T, which contains 4,786,207 bp with a G⫹C content of 52.6% and 4,359 protein-coding genes. ABSTRACT
T
he species Thalassospira xiamenensis was first proposed by Liu et al. (1). Members of the T. xiamenensis species are non-spore-forming, Gram-negative, curved rods that are motile by means of one polar flagellum. T. xiamenensis strain MCCC 1A03042T is closely related to T. xiamenensis strain M-5T, which was the type strain, and the similarity was 99.716%. Strain MCCC 1A03042T was isolated from deep-sea sediment of the Indian Ocean, plated directly on 2216E agar (2) and incubated at 22°C. We found that it was characterized with heavy-metal arsenic tolerance and grew in the medium with an arsenic concentration of 10 mM. Genomic DNA was purified from T. xiamenensis MCCC 1A03042T with an AxyPrep bacterial genomic DNA miniprep kit (Axygen) according to the manufacturer’s instructions. The genome sequence was determined by Shanghai Majorbio Bio-pharm Technology Co., Ltd. (Shanghai, China) using Solexa paired-end sequencing technology. A total of 500 Mb of clean data (500-bp library) were generated to reach about 100-fold depth of coverage with an Illumina/Solexa Genome Analyzer IIx (Illumina, San Diego, CA, USA). The genome of T. xiamenensis MCCC 1A03042T consists of 72 contigs of 4,786,207 bp with an average G⫹C content of 52.6%. Gene prediction and annotation of the draft genome were carried out using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (http://www.ncbi.nlm.nih.gov/ genomes/static/Pipeline.html) (3). In total, 4,470 genes, 4,359 of which are protein-coding genes, and 50 tRNAs were predicted; 59 pseudogenes were also identified. Genome annotation and analysis were also done using the RAST server (http://rast.nmpdr.org) (4). Four genes (ars) for arsenate reduction were found in the annotations. A previous study demonstrated that an initial step in arsenic metabolism is the reduction of arsenate (5). In addition, the presence of an arsenic transporter was also noticed. Accession number(s). The draft genome sequence of T. xiamenensis MCCC 1A03042T has been deposited at GenBank under the accession number LPXM00000000. The version described in this paper is the first version, LPXM01000000.
Received 15 December 2016 Accepted 23 December 2016 Published 2 March 2017 Citation Li M, Yang S, Lai Q, Shao Z. 2017. Draft genome sequence of Thalassospira xiamenensis strain MCCC 1A03042T. Genome Announc 5: e01702-16. https://doi.org/10.1128/ genomeA.01702-16. Copyright © 2017 Li et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Zongze Shao, [email protected].
ACKNOWLEDGMENTS This work was financially supported by the COMRA program (no. DY125-15-R-01) and by the National Infrastructure of Natural Resources for Science and Technology Program of China (no. NIMR-2016-9). REFERENCES 1. Liu C, Wu Y, Li L, Ma Y, Shao Z. 2007. Thalassospira xiamenensis sp. nov. and Thalassospira profundimaris sp. nov. Int J Syst Evol Microbiol 57: 316 –320. https://doi.org/10.1099/ijs.0.64544-0. Volume 5 Issue 9 e01702-16
2. ZoBell CE. 1941. Studies on marine bacteria. I. The cultural requirements of heterotrophic aerobes. J Mar Res 4:42–75. 3. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D, Garrity G, Kodira genomea.asm.org 1
Li et al.
CD, Kyrpides N, Madupu R, Markowitz V, Tatusova T, Thomson N, White O. 2008. Toward an online repository of standard operating procedures (SOPs) for (meta) genomic annotation. OMICS 12:137–141. https:// doi.org/10.1089/omi.2008.0017. 4. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, Edwards RA, Gerdes S, Parrello B, Shukla M, Vonstein V, Wattam AR, Xia F, Stevens R.
Volume 5 Issue 9 e01702-16
2014. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 42:D206 –D214. https:// doi.org/10.1093/nar/gkt1226. 5. Mukhopadhyay R, Rosen BP. 2002. Arsenate reductases in prokaryotes and eukaryotes. Environ Health Perspect 110(suppl 5):745–748. https:// doi.org/10.1289/ehp.02110s5745.
genomea.asm.org 2
