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Whole Genome Sequencing of Thermus oshimai JL-2 and Thermus thermophilus JL-18, Incomplete Denitrifiers from the United States Great Basin
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abstract
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The strains Thermus oshimai JL-2 and Thermus thermophilus JL-18 each have a circular chromosome, 2.07 Mb and 1.9 Mb in size, respectively, and each has two plasmids ranging from 0.27 Mb to 57.2 kb. The megaplasmid of each strain contains a gene cluster for the reduction of nitrate to nitrous oxide, consistent with their incomplete denitrification phenotypes.
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The strains Thermus oshimai JL-2 and Thermus thermophilus JL-18 each have a circular chromosome, 2.07 Mb and 1.9 Mb in size, respectively, and each has two plasmids ranging from 0.27 Mb to 57.2 kb. The megaplasmid of each strain contains a gene cluster for the reduction of nitrate to nitrous oxide, consistent with their incomplete denitrification phenotypes.
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GENOME ANNOUNCEMENT
The genus Thermus comprises >15 species of thermophilic bacteria, including the biotechnologically exalted Thermus aquaticus and the genetically tractable Thermus thermophilus. We reported previously the isolation of a large number of Thermus strains from the Great Boiling Spring system in the U.S. Great Basin, typified by Thermus oshimai JL-2 and Thermus thermophilus JL-18, and described their roles in incomplete denitrification in situ (1, 2).
The genomes of T. oshimai JL-2 and T. thermophilus JL-18 were sequenced using 454-GS-FLX Titanium and Illumina GA II (2 × 75 bp) methodologies, were assembled using Newbler version 2.3 (prerelease), and were annotated using Prodigal version 1.4, Gene Prediction Improvement Pipeline (GenePRIMP) at the Joint Genome Institute (JGI) in Walnut Creek, CA. The data are available at the Joint Genome Institute (JGI) Integrated Microbial Genomes (IMG) website (3). T. oshimai JL-2 contains a 2.07-Mb circular chromosome carrying 2,205 predicted genes; a circular megaplasmid, pTHEOS01 (0.27 Mb, 268 predicted genes); and a smaller circular plasmid, pTHEOS02 (57.2 kb, 75 predicted genes). T. thermophilus JL-18 has a 1.9-Mb circular chromosome carrying 2,057 predicted genes; a circular megaplasmid, pTTJL1801 (0.26 Mb, 279 predicted genes); and a smaller circular plasmid, pTTJL1802 (0.14 Mb, 172 predicted genes).
The chromosome of T. thermophilus JL-18 was similar to those of T. thermophilus HB8 and T. thermophilus HB27, apart from a few chromosomal rearrangements (4). However, extensive rearrangements were observed in the T. thermophilus JL-18 megaplasmid pTTJL1801 when compared to the T. thermophilus HB8 and HB27 megaplasmids; this is consistent with the elevated plasticity reported previously for Thermus megaplasmids (5). The chromosome and megaplasmid of T. oshimai JL-2 pTHEOS01 exhibit little or no synteny with any of the complete Thermus genomes.
The megaplasmids of both species include a complete nitrate reductase operon (narGHJIK). T. oshimai JL-2 possesses two nitrate/nitrite transporters (narK1 and narK2), which is similar to T. thermophilus HB8 (6), whereas T. thermophilus JL-18 possesses a single copy of narK. Genes encoding nitrite reductase (nirS and nirK in T. oshimai JL-2 and nirS in T. thermophilus JL-18) and nitric oxide reductase (norB and norC) were also identified in close proximity to the narGHIJK operon in the megaplasmids of both T. thermophilus JL-18 and T. oshimai JL-2. However, nitrous oxide reductase (nos) genes, which are needed for the conversion of nitrous oxide to dinitrogen, are absent, concurrent with the incomplete denitrification phenotype of these strains and the high flux of nitrous oxide reported at Great Boiling Spring (2). Both megaplasmids also possess genes encoding a DNA repair system that is proposed to impart thermophily in T. thermophilus HB8 and HB27 (5). A sox gene cluster that includes a sulfite dehydrogenase gene (soxCD) essential for the chemotrophic growth of Paracoccus pantotrophus (7) was identified in T. oshimai JL-2 and T. thermophilus JL-18 chromosomes, suggesting that these organisms can carry out sulfur oxidation.
Nucleotide sequence accession numbers.
The genome sequences from this study are available from GenBank under the following accession no: CP003249.1 (T. oshimai JL-2 chromosome), CP003250.1 (T. oshimai JL-2 megaplasmid pTHEOS01), CP003251.1 (T. oshimai JL-2 plasmid pTHEOS02), CP003252.1 (T. thermophilus JL-18 chromosome), CP003253.1 (T. thermophilus JL-18 plasmid pTTJL1801), and CP003254.1 (T. thermophilus JL-18 plasmid pTTJL1802).
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GENOME ANNOUNCEMENT
The genus Thermus comprises >15 species of thermophilic bacteria, including the biotechnologically exalted Thermus aquaticus and the genetically tractable Thermus thermophilus. We reported previously the isolation of a large number of Thermus strains from the Great Boiling Spring system in the U.S. Great Basin, typified by Thermus oshimai JL-2 and Thermus thermophilus JL-18, and described their roles in incomplete denitrification in situ (1, 2).
The genomes of T. oshimai JL-2 and T. thermophilus JL-18 were sequenced using 454-GS-FLX Titanium and Illumina GA II (2 × 75 bp) methodologies, were assembled using Newbler version 2.3 (prerelease), and were annotated using Prodigal version 1.4, Gene Prediction Improvement Pipeline (GenePRIMP) at the Joint Genome Institute (JGI) in Walnut Creek, CA. The data are available at the Joint Genome Institute (JGI) Integrated Microbial Genomes (IMG) website (3). T. oshimai JL-2 contains a 2.07-Mb circular chromosome carrying 2,205 predicted genes; a circular megaplasmid, pTHEOS01 (0.27 Mb, 268 predicted genes); and a smaller circular plasmid, pTHEOS02 (57.2 kb, 75 predicted genes). T. thermophilus JL-18 has a 1.9-Mb circular chromosome carrying 2,057 predicted genes; a circular megaplasmid, pTTJL1801 (0.26 Mb, 279 predicted genes); and a smaller circular plasmid, pTTJL1802 (0.14 Mb, 172 predicted genes).
The chromosome of T. thermophilus JL-18 was similar to those of T. thermophilus HB8 and T. thermophilus HB27, apart from a few chromosomal rearrangements (4). However, extensive rearrangements were observed in the T. thermophilus JL-18 megaplasmid pTTJL1801 when compared to the T. thermophilus HB8 and HB27 megaplasmids; this is consistent with the elevated plasticity reported previously for Thermus megaplasmids (5). The chromosome and megaplasmid of T. oshimai JL-2 pTHEOS01 exhibit little or no synteny with any of the complete Thermus genomes.
The megaplasmids of both species include a complete nitrate reductase operon (narGHJIK). T. oshimai JL-2 possesses two nitrate/nitrite transporters (narK1 and narK2), which is similar to T. thermophilus HB8 (6), whereas T. thermophilus JL-18 possesses a single copy of narK. Genes encoding nitrite reductase (nirS and nirK in T. oshimai JL-2 and nirS in T. thermophilus JL-18) and nitric oxide reductase (norB and norC) were also identified in close proximity to the narGHIJK operon in the megaplasmids of both T. thermophilus JL-18 and T. oshimai JL-2. However, nitrous oxide reductase (nos) genes, which are needed for the conversion of nitrous oxide to dinitrogen, are absent, concurrent with the incomplete denitrification phenotype of these strains and the high flux of nitrous oxide reported at Great Boiling Spring (2). Both megaplasmids also possess genes encoding a DNA repair system that is proposed to impart thermophily in T. thermophilus HB8 and HB27 (5). A sox gene cluster that includes a sulfite dehydrogenase gene (soxCD) essential for the chemotrophic growth of Paracoccus pantotrophus (7) was identified in T. oshimai JL-2 and T. thermophilus JL-18 chromosomes, suggesting that these organisms can carry out sulfur oxidation.
Nucleotide sequence accession numbers.
The genome sequences from this study are available from GenBank under the following accession no: CP003249.1 (T. oshimai JL-2 chromosome), CP003250.1 (T. oshimai JL-2 megaplasmid pTHEOS01), CP003251.1 (T. oshimai JL-2 plasmid pTHEOS02), CP003252.1 (T. thermophilus JL-18 chromosome), CP003253.1 (T. thermophilus JL-18 plasmid pTTJL1801), and CP003254.1 (T. thermophilus JL-18 plasmid pTTJL1802).
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GENOME ANNOUNCEMENT
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The genus Thermus comprises >15 species of thermophilic bacteria, including the biotechnologically exalted Thermus aquaticus and the genetically tractable Thermus thermophilus. We reported previously the isolation of a large number of Thermus strains from the Great Boiling Spring system in the U.S. Great Basin, typified by Thermus oshimai JL-2 and Thermus thermophilus JL-18, and described their roles in incomplete denitrification in situ (1, 2).
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p
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The genomes of T. oshimai JL-2 and T. thermophilus JL-18 were sequenced using 454-GS-FLX Titanium and Illumina GA II (2 × 75 bp) methodologies, were assembled using Newbler version 2.3 (prerelease), and were annotated using Prodigal version 1.4, Gene Prediction Improvement Pipeline (GenePRIMP) at the Joint Genome Institute (JGI) in Walnut Creek, CA. The data are available at the Joint Genome Institute (JGI) Integrated Microbial Genomes (IMG) website (3). T. oshimai JL-2 contains a 2.07-Mb circular chromosome carrying 2,205 predicted genes; a circular megaplasmid, pTHEOS01 (0.27 Mb, 268 predicted genes); and a smaller circular plasmid, pTHEOS02 (57.2 kb, 75 predicted genes). T. thermophilus JL-18 has a 1.9-Mb circular chromosome carrying 2,057 predicted genes; a circular megaplasmid, pTTJL1801 (0.26 Mb, 279 predicted genes); and a smaller circular plasmid, pTTJL1802 (0.14 Mb, 172 predicted genes).
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The chromosome of T. thermophilus JL-18 was similar to those of T. thermophilus HB8 and T. thermophilus HB27, apart from a few chromosomal rearrangements (4). However, extensive rearrangements were observed in the T. thermophilus JL-18 megaplasmid pTTJL1801 when compared to the T. thermophilus HB8 and HB27 megaplasmids; this is consistent with the elevated plasticity reported previously for Thermus megaplasmids (5). The chromosome and megaplasmid of T. oshimai JL-2 pTHEOS01 exhibit little or no synteny with any of the complete Thermus genomes.
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p
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The megaplasmids of both species include a complete nitrate reductase operon (narGHJIK). T. oshimai JL-2 possesses two nitrate/nitrite transporters (narK1 and narK2), which is similar to T. thermophilus HB8 (6), whereas T. thermophilus JL-18 possesses a single copy of narK. Genes encoding nitrite reductase (nirS and nirK in T. oshimai JL-2 and nirS in T. thermophilus JL-18) and nitric oxide reductase (norB and norC) were also identified in close proximity to the narGHIJK operon in the megaplasmids of both T. thermophilus JL-18 and T. oshimai JL-2. However, nitrous oxide reductase (nos) genes, which are needed for the conversion of nitrous oxide to dinitrogen, are absent, concurrent with the incomplete denitrification phenotype of these strains and the high flux of nitrous oxide reported at Great Boiling Spring (2). Both megaplasmids also possess genes encoding a DNA repair system that is proposed to impart thermophily in T. thermophilus HB8 and HB27 (5). A sox gene cluster that includes a sulfite dehydrogenase gene (soxCD) essential for the chemotrophic growth of Paracoccus pantotrophus (7) was identified in T. oshimai JL-2 and T. thermophilus JL-18 chromosomes, suggesting that these organisms can carry out sulfur oxidation.
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Nucleotide sequence accession numbers.
The genome sequences from this study are available from GenBank under the following accession no: CP003249.1 (T. oshimai JL-2 chromosome), CP003250.1 (T. oshimai JL-2 megaplasmid pTHEOS01), CP003251.1 (T. oshimai JL-2 plasmid pTHEOS02), CP003252.1 (T. thermophilus JL-18 chromosome), CP003253.1 (T. thermophilus JL-18 plasmid pTTJL1801), and CP003254.1 (T. thermophilus JL-18 plasmid pTTJL1802).
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Nucleotide sequence accession numbers.
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The genome sequences from this study are available from GenBank under the following accession no: CP003249.1 (T. oshimai JL-2 chromosome), CP003250.1 (T. oshimai JL-2 megaplasmid pTHEOS01), CP003251.1 (T. oshimai JL-2 plasmid pTHEOS02), CP003252.1 (T. thermophilus JL-18 chromosome), CP003253.1 (T. thermophilus JL-18 plasmid pTTJL1801), and CP003254.1 (T. thermophilus JL-18 plasmid pTTJL1802).
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Citation Murugapiran SK, Huntemann M, Wei C-L, Han J, Detter JC, Han CS, Erkkila TH, Teshima H, Chen A, Kyrpides N, Mavrommatis K, Markowitz V, Szeto E, Ivanova N, Pagani I, Lam J, McDonald AI, Dodsworth JA, Pati A, Goodwin L, Peters L, Pitluck S, Woyke T, Hedlund BP. 2013. Whole genome sequencing of Thermus oshimai JL-2 and Thermus thermophilus JL-18, incomplete denitrifiers from the United States Great Basin. Genome Announc. 1(1):e00106-12. doi:10.1128/genomeA.00106-12.
ACKNOWLEDGMENTS
The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. Additional support was provided by NSF grant no. MCB-0546865 and EPS-9977809. We are also grateful for support from Greg Fullmer through the University of Nevada Las Vegas (UNLV) Foundation.
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footnote
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Citation Murugapiran SK, Huntemann M, Wei C-L, Han J, Detter JC, Han CS, Erkkila TH, Teshima H, Chen A, Kyrpides N, Mavrommatis K, Markowitz V, Szeto E, Ivanova N, Pagani I, Lam J, McDonald AI, Dodsworth JA, Pati A, Goodwin L, Peters L, Pitluck S, Woyke T, Hedlund BP. 2013. Whole genome sequencing of Thermus oshimai JL-2 and Thermus thermophilus JL-18, incomplete denitrifiers from the United States Great Basin. Genome Announc. 1(1):e00106-12. doi:10.1128/genomeA.00106-12.
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Citation Murugapiran SK, Huntemann M, Wei C-L, Han J, Detter JC, Han CS, Erkkila TH, Teshima H, Chen A, Kyrpides N, Mavrommatis K, Markowitz V, Szeto E, Ivanova N, Pagani I, Lam J, McDonald AI, Dodsworth JA, Pati A, Goodwin L, Peters L, Pitluck S, Woyke T, Hedlund BP. 2013. Whole genome sequencing of Thermus oshimai JL-2 and Thermus thermophilus JL-18, incomplete denitrifiers from the United States Great Basin. Genome Announc. 1(1):e00106-12. doi:10.1128/genomeA.00106-12.
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ACKNOWLEDGMENTS
The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. Additional support was provided by NSF grant no. MCB-0546865 and EPS-9977809. We are also grateful for support from Greg Fullmer through the University of Nevada Las Vegas (UNLV) Foundation.
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ACKNOWLEDGMENTS
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The work conducted by the U.S. Department of Energy Joint Genome Institute is supported by the Office of Science of the U.S. Department of Energy under contract no. DE-AC02-05CH11231. Additional support was provided by NSF grant no. MCB-0546865 and EPS-9977809. We are also grateful for support from Greg Fullmer through the University of Nevada Las Vegas (UNLV) Foundation.
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