138 results on '"Chertkov O"'
Search Results
2. Nuclear Genome Assembly of the Microalga Nannochloropsis salina CCMP1776
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Ohan, J. A., primary, Hovde, B. T., additional, Zhang, X. L., additional, Davenport, K. W., additional, Chertkov, O., additional, Han, C., additional, Twary, S. N., additional, and Starkenburg, S. R., additional
- Published
- 2019
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3. Dual Active Site in the Endolytic Transglycosylase gp144 of Bacteriophage phiKZ
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Chertkov, O. V., primary, Armeev, G. A., additional, Uporov, I. V., additional, Legotsky, S. A., additional, Sykilinda, N. N., additional, Shaytan, A. K., additional, Klyachko, N. L., additional, and Miroshnikov, K. A., additional
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- 2017
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4. Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds
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Hwang, C., primary, Copeland, A., additional, Lucas, S., additional, Lapidus, A., additional, Barry, K., additional, Detter, J. C., additional, Glavina del Rio, T., additional, Hammon, N., additional, Israni, S., additional, Dalin, E., additional, Tice, H., additional, Pitluck, S., additional, Chertkov, O., additional, Brettin, T., additional, Bruce, D., additional, Han, C., additional, Schmutz, J., additional, Larimer, F., additional, Land, M. L., additional, Hauser, L., additional, Kyrpides, N., additional, Mikhailova, N., additional, Ye, Q., additional, Zhou, J., additional, Richardson, P., additional, and Fields, M. W., additional
- Published
- 2016
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5. Complete Genome Assembly of Escherichia coli ATCC 25922, a Serotype O6 Reference Strain
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Minogue, T. D., primary, Daligault, H. A., additional, Davenport, K. W., additional, Bishop-Lilly, K. A., additional, Broomall, S. M., additional, Bruce, D. C., additional, Chain, P. S., additional, Chertkov, O., additional, Coyne, S. R., additional, Freitas, T., additional, Frey, K. G., additional, Gibbons, H. S., additional, Jaissle, J., additional, Redden, C. L., additional, Rosenzweig, C. N., additional, Xu, Y., additional, and Johnson, S. L., additional
- Published
- 2014
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6. Complete Genome Assembly of Streptococcus pyogenes ATCC 19615, a Group A β-Hemolytic Reference Strain
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Minogue, T. D., primary, Daligault, H. A., additional, Davenport, K. W., additional, Bishop-Lilly, K. A., additional, Broomall, S. M., additional, Bruce, D. C., additional, Chain, P. S., additional, Chertkov, O., additional, Coyne, S. R., additional, Freitas, T., additional, Frey, K. G., additional, Gibbons, H. S., additional, Jaissle, J., additional, Redden, C. L., additional, Rosenzweig, C. N., additional, Xu, Y., additional, and Johnson, S. L., additional
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- 2014
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7. Complete Genome Assembly of Enterococcus faecalis 29212, a Laboratory Reference Strain
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Minogue, T. D., primary, Daligault, H. E., additional, Davenport, K. W., additional, Broomall, S. M., additional, Bruce, D. C., additional, Chain, P. S., additional, Coyne, S. R., additional, Chertkov, O., additional, Freitas, T., additional, Gibbons, H. S., additional, Jaissle, J., additional, Koroleva, G. I., additional, Ladner, J. T., additional, Palacios, G. F., additional, Rosenzweig, C. N., additional, Xu, Y., additional, and Johnson, S. L., additional
- Published
- 2014
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8. Draft Genome Assembly of Pseudomonas aeruginosa Quality Control Reference Strain Boston 41501
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Minogue, T. D., primary, Daligault, H. E., additional, Davenport, K. W., additional, Broomall, S. M., additional, Bruce, D. C., additional, Chain, P. S., additional, Coyne, S. R., additional, Gibbons, H. S., additional, Jaissle, J., additional, Chertkov, O., additional, Freitas, T., additional, Rosenzweig, C. N., additional, Xu, Y., additional, and Johnson, S. L., additional
- Published
- 2014
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9. Full-Genome Assembly of Reference Strain Providencia stuartii ATCC 33672
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Frey, K. G., primary, Bishop-Lilly, K. A., additional, Daligault, H. E., additional, Davenport, K. W., additional, Bruce, D. C., additional, Chain, P. S., additional, Coyne, S. R., additional, Chertkov, O., additional, Freitas, T., additional, Jaissle, J., additional, Koroleva, G. I., additional, Ladner, J. T., additional, Minogue, T. D., additional, Palacios, G. F., additional, Redden, C. L., additional, Xu, Y., additional, and Johnson, S. L., additional
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- 2014
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10. Whole-Genome Sequences of 24 Brucella Strains
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Minogue, T. D., primary, Daligault, H. A., additional, Davenport, K. W., additional, Bishop-Lilly, K. A., additional, Broomall, S. M., additional, Bruce, D. C., additional, Chain, P. S., additional, Chertkov, O., additional, Coyne, S. R., additional, Frey, K. G., additional, Gibbons, H. S., additional, Jaissle, J., additional, Koroleva, G. I., additional, Ladner, J. T., additional, Lo, C.-C., additional, Palacios, G. F., additional, Redden, C. L., additional, Rosenzweig, C. N., additional, Scholz, M. B., additional, Xu, Y., additional, and Johnson, S. L., additional
- Published
- 2014
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11. Draft Genome Assemblies of Proteus mirabilis ATCC 7002 and Proteus vulgaris ATCC 49132
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Minogue, T. D., primary, Daligault, H. E., additional, Davenport, K. W., additional, Bishop-Lilly, K. A., additional, Bruce, D. C., additional, Chain, P. S., additional, Coyne, S. R., additional, Chertkov, O., additional, Freitas, T., additional, Frey, K. G., additional, Jaissle, J., additional, Koroleva, G. I., additional, Ladner, J. T., additional, Palacios, G. F., additional, Redden, C. L., additional, Xu, Y., additional, and Johnson, S. L., additional
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- 2014
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12. Draft Genome Assemblies of Enterobacter aerogenes CDC 6003-71, Enterobacter cloacae CDC 442-68, and Pantoea agglomerans UA 0804-01
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Minogue, T. D., primary, Daligault, H. E., additional, Davenport, K. W., additional, Bishop-Lilly, K. A., additional, Bruce, D. C., additional, Chain, P. S., additional, Coyne, S. R., additional, Chertkov, O., additional, Freitas, T., additional, Frey, K. G., additional, Jaissle, J., additional, Koroleva, G. I., additional, Ladner, J. T., additional, Palacios, G. F., additional, Redden, C. L., additional, Xu, Y., additional, and Johnson, S. L., additional
- Published
- 2014
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13. Complete Genome Assembly of Reference Strain Ochrobactrum anthropi ATCC 49687
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Minogue, T. D., primary, Daligault, H. A., additional, Davenport, K. W., additional, Bishop-Lilly, K. A., additional, Bruce, D. C., additional, Chain, P. S., additional, Chertkov, O., additional, Coyne, S. R., additional, Freitas, T., additional, Frey, K. G., additional, Jaissle, J., additional, Koroleva, G. I., additional, Ladner, J. T., additional, Palacios, G. F., additional, Redden, C. L., additional, Xu, Y., additional, and Johnson, S. L., additional
- Published
- 2014
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14. Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Enteritidis Strain SEJ
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Bishop-Lilly, K. A., primary, Frey, K. G., additional, Daligault, H. E., additional, Davenport, K. W., additional, Bruce, D. C., additional, Chain, P. S., additional, Coyne, S. R., additional, Chertkov, O., additional, Freitas, T., additional, Jaissle, J., additional, Koroleva, G. I., additional, Ladner, J. T., additional, Minogue, T. D., additional, Palacios, G. F., additional, Redden, C. L., additional, Xu, Y., additional, and Johnson, S. L., additional
- Published
- 2014
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15. Draft Genome Assembly of Neisseria lactamica Type Strain A7515
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Minogue, T. D., primary, Daligault, H. A., additional, Davenport, K. W., additional, Bishop-Lilly, K. A., additional, Bruce, D. C., additional, Chain, P. S., additional, Chertkov, O., additional, Coyne, S. R., additional, Freitas, T., additional, Frey, K. G., additional, Jaissle, J., additional, Koroleva, G. I., additional, Ladner, J. T., additional, Palacios, G. F., additional, Redden, C. L., additional, Xu, Y., additional, and Johnson, S. L., additional
- Published
- 2014
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16. Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271T)
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Nandasena, K., Yates, R., Tiwari, R., O’Hara, G., Howieson, J., Ninawi, M., Chertkov, O., Detter, C., Tapia, R., Han, S., Woyke, T., Pitluck, S., Nolan, M., Land, M., Liolios, K., Pati, A., Copeland, A., Kyrpides, N., Ivanova, N., Goodwin, L., Meenakshi, U., Reeve, W., Nandasena, K., Yates, R., Tiwari, R., O’Hara, G., Howieson, J., Ninawi, M., Chertkov, O., Detter, C., Tapia, R., Han, S., Woyke, T., Pitluck, S., Nolan, M., Land, M., Liolios, K., Pati, A., Copeland, A., Kyrpides, N., Ivanova, N., Goodwin, L., Meenakshi, U., and Reeve, W.
- Abstract
Mesorhizobium ciceri bv. biserrulae strain WSM1271T was isolated from root nodules of the pasture legume Biserrula pelecinus growing in the Mediterranean basin. Previous studies have shown this aerobic, motile, Gram negative, non-spore-forming rod preferably nodulates B. pelecinus – a legume with many beneficial agronomic attributes for sustainable agriculture in Australia. We describe the genome of Mesorhizobium ciceri bv. biserrulae strain WSM1271T consisting of a 6,264,489 bp chromosome and a 425,539 bp plasmid that together encode 6,470 protein-coding genes and 61 RNA-only encoding genes.
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- 2013
17. Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075T
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Reeve, W., Nandasena, K., Yates, R., Tiwari, R., O’Hara, G., Ninawi, M., Chertkov, O., Goodwin, L., Bruce, D., Detter, C., Tapia, R., Han, S., Woyke, T., Pitluck, S., Nolan, M., Land, M., Copeland, A., Liolios, K., Pati, A., Mavromatis, K., Markowitz, V., Kyrpides, N., Ivanova, N., Meenakshi, U., Howieson, J., Reeve, W., Nandasena, K., Yates, R., Tiwari, R., O’Hara, G., Ninawi, M., Chertkov, O., Goodwin, L., Bruce, D., Detter, C., Tapia, R., Han, S., Woyke, T., Pitluck, S., Nolan, M., Land, M., Copeland, A., Liolios, K., Pati, A., Mavromatis, K., Markowitz, V., Kyrpides, N., Ivanova, N., Meenakshi, U., and Howieson, J.
- Abstract
Mesorhizobium opportunistum strain WSM2075T was isolated in Western Australia in 2000 from root nodules of the pasture legume Biserrula pelecinus that had been inoculated with M. ciceri bv. biserrulae WSM1271. WSM2075T is an aerobic, motile, Gram negative, non-spore-forming rod that has gained the ability to nodulate B. pelecinus but is completely ineffective in N2 fixation with this host. This report reveals that the genome of M. opportunistum strain WSM2075T contains a chromosome of size 6,884,444 bp, encoding 6,685 protein-coding genes and 62 RNA-only encoding genes. The genome contains no plasmids, but does harbor a 455.7 kb genomic island from Mesorhizobium ciceri bv. biserrulae WSM1271 that has been integrated into a phenylalanine-tRNA gene.
- Published
- 2013
18. Genome sequence of Nitrosomonas sp. AL212, an ammonia-oxidizing bacterium sensitive to high-levels of ammonia
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Yuichi, S., Norton, J.M., Bollmann, A., Klotz, M.G., Stein, L.Y., Laanbroek, H.J., Arp, D.J., Goodwin, L.A., Chertkov, O., Held, B., Bruce, D., Detter, J.Ch., Detter, J.C., Tapia, R., Han, C.S., Yuichi, S., Norton, J.M., Bollmann, A., Klotz, M.G., Stein, L.Y., Laanbroek, H.J., Arp, D.J., Goodwin, L.A., Chertkov, O., Held, B., Bruce, D., Detter, J.Ch., Detter, J.C., Tapia, R., and Han, C.S.
- Abstract
Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic ammonia-oxidizing bacterium (AOB) that was originally isolated in 1997 by Yuichi Suwa and colleagues. This organism belongs to Nitrosomonas cluster 6A characterized by sensitivity to high ammonia concentrations, higher substrate affinity (lower Km), and lower maximum growth rates in comparison to strains in Nitrosomonas cluster 7 that includes Nitrosomonas europaea and Nitrosomonas eutropha. Genome-informed studies of this ammonia-sensitive cohort of AOB are needed as they are found in freshwater environments, drinking water supplies, wastewater treatment systems and soils worldwide., Nitrosomonas sp. strain AL212 is an obligate chemolithotrophic ammonia-oxidizing bacterium (AOB) that was originally isolated in 1997 by Yuichi Suwa and colleagues. This organism belongs to Nitrosomonas cluster 6A characterized by sensitivity to high ammonia concentrations, higher substrate affinity (lower Km), and lower maximum growth rates in comparison to strains in Nitrosomonas cluster 7 that includes Nitrosomonas europaea and Nitrosomonas eutropha. Genome-informed studies of this ammonia-sensitive cohort of AOB are needed as they are found in freshwater environments, drinking water supplies, wastewater treatment systems and soils worldwide.
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- 2011
19. Whole genome sequences of two Xylella fastidiosa strains (M12 and M23) causing almond leaf scorch disease in California
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Chen, J., Xie, G., Han, S., Chertkov, O., Sims, D., and Civerolo, E.L.
- Subjects
Nucleotide sequencing -- Methods ,Proteobacteria -- Genetic aspects ,Almond -- Diseases and pests ,Bacterial diseases of plants -- Genetic aspects ,Biological sciences - Abstract
Xylella fastidiosa is a Gram-negative plant-pathogenic bacterium causing many economically important diseases, including almond leaf scorch disease (ALSD) in California. Genome information greatly facilitates research on this nutritionally fastidious organism. Here we report the complete genome sequences of two ALSD strains of this bacterium, M12 and M23. doi: 10.1128/JB.00651-10
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- 2010
20. Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1
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Rhee, Mun Su, primary, Moritz, Brélan E., additional, Xie, Gary, additional, Glavina del Rio, T., additional, Dalin, E., additional, Tice, H., additional, Bruce, D., additional, Goodwin, L., additional, Chertkov, O., additional, Brettin, T., additional, Han, C., additional, Detter, C., additional, Pitluck, S., additional, Land, Miriam L., additional, Patel, Milind, additional, Ou, Mark, additional, Harbrucker, Roberta, additional, Ingram, Lonnie O., additional, and Shanmugam, K. T., additional
- Published
- 2011
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21. Genome Sequence of the Mercury-Methylating Strain Desulfovibrio desulfuricans ND132
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Brown, S. D., primary, Gilmour, C. C., additional, Kucken, A. M., additional, Wall, J. D., additional, Elias, D. A., additional, Brandt, C. C., additional, Podar, M., additional, Chertkov, O., additional, Held, B., additional, Bruce, D. C., additional, Detter, J. C., additional, Tapia, R., additional, Han, C. S., additional, Goodwin, L. A., additional, Cheng, J.-F., additional, Pitluck, S., additional, Woyke, T., additional, Mikhailova, N., additional, Ivanova, N. N., additional, Han, J., additional, Lucas, S., additional, Lapidus, A. L., additional, Land, M. L., additional, Hauser, L. J., additional, and Palumbo, A. V., additional
- Published
- 2011
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22. DNA sequencing using differential extension with nucleotide subsets (DENS)
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Raja, M. C., primary, Zevin-Sonkin, D., additional, Shwartzburd, J., additional, Rozovskaya, T. A., additional, Sobolev, I. A., additional, Chertkov, O., additional, Ramanathan, V., additional, Lvovsky, L., additional, and Ulanovsky, L. E., additional
- Published
- 1997
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23. The genome of Pelobacter carbinolicus reveals surprising metabolic capabilities and physiological features
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Aklujkar Muktak, Haveman Shelley A, DiDonato Raymond, Chertkov Olga, Han Cliff S, Land Miriam L, Brown Peter, and Lovley Derek R
- Subjects
Pelobacter ,Genome ,Metabolism ,Physiology ,Geobacter ,2,3-butanediol ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background The bacterium Pelobacter carbinolicus is able to grow by fermentation, syntrophic hydrogen/formate transfer, or electron transfer to sulfur from short-chain alcohols, hydrogen or formate; it does not oxidize acetate and is not known to ferment any sugars or grow autotrophically. The genome of P. carbinolicus was sequenced in order to understand its metabolic capabilities and physiological features in comparison with its relatives, acetate-oxidizing Geobacter species. Results Pathways were predicted for catabolism of known substrates: 2,3-butanediol, acetoin, glycerol, 1,2-ethanediol, ethanolamine, choline and ethanol. Multiple isozymes of 2,3-butanediol dehydrogenase, ATP synthase and [FeFe]-hydrogenase were differentiated and assigned roles according to their structural properties and genomic contexts. The absence of asparagine synthetase and the presence of a mutant tRNA for asparagine encoded among RNA-active enzymes suggest that P. carbinolicus may make asparaginyl-tRNA in a novel way. Catabolic glutamate dehydrogenases were discovered, implying that the tricarboxylic acid (TCA) cycle can function catabolically. A phosphotransferase system for uptake of sugars was discovered, along with enzymes that function in 2,3-butanediol production. Pyruvate:ferredoxin/flavodoxin oxidoreductase was identified as a potential bottleneck in both the supply of oxaloacetate for oxidation of acetate by the TCA cycle and the connection of glycolysis to production of ethanol. The P. carbinolicus genome was found to encode autotransporters and various appendages, including three proteins with similarity to the geopilin of electroconductive nanowires. Conclusions Several surprising metabolic capabilities and physiological features were predicted from the genome of P. carbinolicus, suggesting that it is more versatile than anticipated.
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- 2012
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24. Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses
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Siddaramappa Shivakumara, Challacombe Jean F, Duncan Alison J, Gillaspy Allison F, Carson Matthew, Gipson Jenny, Orvis Joshua, Zaitshik Jeremy, Barnes Gentry, Bruce David, Chertkov Olga, Detter J Chris, Han Cliff S, Tapia Roxanne, Thompson Linda S, Dyer David W, and Inzana Thomas J
- Subjects
Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Pneumonia and myocarditis are the most commonly reported diseases due to Histophilus somni, an opportunistic pathogen of the reproductive and respiratory tracts of cattle. Thus far only a few genes involved in metabolic and virulence functions have been identified and characterized in H. somni using traditional methods. Analyses of the genome sequences of several Pasteurellaceae species have provided insights into their biology and evolution. In view of the economic and ecological importance of H. somni, the genome sequence of pneumonia strain 2336 has been determined and compared to that of commensal strain 129Pt and other members of the Pasteurellaceae. Results The chromosome of strain 2336 (2,263,857 bp) contained 1,980 protein coding genes, whereas the chromosome of strain 129Pt (2,007,700 bp) contained only 1,792 protein coding genes. Although the chromosomes of the two strains differ in size, their average GC content, gene density (total number of genes predicted on the chromosome), and percentage of sequence (number of genes) that encodes proteins were similar. The chromosomes of these strains also contained a number of discrete prophage regions and genomic islands. One of the genomic islands in strain 2336 contained genes putatively involved in copper, zinc, and tetracycline resistance. Using the genome sequence data and comparative analyses with other members of the Pasteurellaceae, several H. somni genes that may encode proteins involved in virulence (e.g., filamentous haemaggutinins, adhesins, and polysaccharide biosynthesis/modification enzymes) were identified. The two strains contained a total of 17 ORFs that encode putative glycosyltransferases and some of these ORFs had characteristic simple sequence repeats within them. Most of the genes/loci common to both the strains were located in different regions of the two chromosomes and occurred in opposite orientations, indicating genome rearrangement since their divergence from a common ancestor. Conclusions Since the genome of strain 129Pt was ~256,000 bp smaller than that of strain 2336, these genomes provide yet another paradigm for studying evolutionary gene loss and/or gain in regard to virulence repertoire and pathogenic ability. Analyses of the complete genome sequences revealed that bacteriophage- and transposon-mediated horizontal gene transfer had occurred at several loci in the chromosomes of strains 2336 and 129Pt. It appears that these mobile genetic elements have played a major role in creating genomic diversity and phenotypic variability among the two H. somni strains.
- Published
- 2011
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25. Complete genome sequence of the filamentous anoxygenic phototrophic bacterium Chloroflexus aurantiacus
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Larimer Frank W, Lapidus Alla, Land Miriam L, Karbach Lauren E, Honchak Barbara M, Hauser Loren J, Han Cliff S, Dalin Eileen, Chertkov Olga, Barry Kerrie, Tang Kuo-Hsiang, Mikhailova Natalia, Pitluck Samuel, Pierson Beverly K, and Blankenship Robert E
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Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Chloroflexus aurantiacus is a thermophilic filamentous anoxygenic phototrophic (FAP) bacterium, and can grow phototrophically under anaerobic conditions or chemotrophically under aerobic and dark conditions. According to 16S rRNA analysis, Chloroflexi species are the earliest branching bacteria capable of photosynthesis, and Cfl. aurantiacus has been long regarded as a key organism to resolve the obscurity of the origin and early evolution of photosynthesis. Cfl. aurantiacus contains a chimeric photosystem that comprises some characters of green sulfur bacteria and purple photosynthetic bacteria, and also has some unique electron transport proteins compared to other photosynthetic bacteria. Methods The complete genomic sequence of Cfl. aurantiacus has been determined, analyzed and compared to the genomes of other photosynthetic bacteria. Results Abundant genomic evidence suggests that there have been numerous gene adaptations/replacements in Cfl. aurantiacus to facilitate life under both anaerobic and aerobic conditions, including duplicate genes and gene clusters for the alternative complex III (ACIII), auracyanin and NADH:quinone oxidoreductase; and several aerobic/anaerobic enzyme pairs in central carbon metabolism and tetrapyrroles and nucleic acids biosynthesis. Overall, genomic information is consistent with a high tolerance for oxygen that has been reported in the growth of Cfl. aurantiacus. Genes for the chimeric photosystem, photosynthetic electron transport chain, the 3-hydroxypropionate autotrophic carbon fixation cycle, CO2-anaplerotic pathways, glyoxylate cycle, and sulfur reduction pathway are present. The central carbon metabolism and sulfur assimilation pathways in Cfl. aurantiacus are discussed. Some features of the Cfl. aurantiacus genome are compared with those of the Roseiflexus castenholzii genome. Roseiflexus castenholzii is a recently characterized FAP bacterium and phylogenetically closely related to Cfl. aurantiacus. According to previous reports and the genomic information, perspectives of Cfl. aurantiacus in the evolution of photosynthesis are also discussed. Conclusions The genomic analyses presented in this report, along with previous physiological, ecological and biochemical studies, indicate that the anoxygenic phototroph Cfl. aurantiacus has many interesting and certain unique features in its metabolic pathways. The complete genome may also shed light on possible evolutionary connections of photosynthesis.
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- 2011
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26. Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2(T), a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes.
- Author
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Melton ED, Sorokin DY, Overmars L, Chertkov O, Clum A, Pillay M, Ivanova N, Shapiro N, Kyrpides NC, Woyke T, Lapidus AL, and Muyzer G
- Abstract
Desulfurivibrio alkaliphilus strain AHT2(T) is a strictly anaerobic sulfidogenic haloalkaliphile isolated from a composite sediment sample of eight hypersaline alkaline lakes in the Wadi al Natrun valley in the Egyptian Libyan Desert. D. alkaliphilus AHT2(T) is Gram-negative and belongs to the family Desulfobulbaceae within the Deltaproteobacteria. Here we report its genome sequence, which contains a 3.10 Mbp chromosome. D. alkaliphilus AHT2(T) is adapted to survive under highly alkaline and moderately saline conditions and therefore, is relevant to the biotechnology industry and life under extreme conditions. For these reasons, D. alkaliphilus AHT2(T) was sequenced by the DOE Joint Genome Institute as part of the Community Science Program.
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- 2016
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27. Genome sequencing of 18 francisella strains to aid in assay development and testing.
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Johnson SL, Daligault HE, Davenport KW, Coyne SR, Frey KG, Koroleva GI, Broomall SM, Bishop-Lilly KA, Bruce DC, Chertkov O, Freitas T, Jaissle J, Ladner JT, Rosenzweig CN, Gibbons HS, Palacios GF, Redden CL, Xu Y, Minogue TD, and Chain PS
- Abstract
Francisella tularensis is a highly infectious bacterium with the potential to cause high fatality rates if infections are untreated. To aid in the development of rapid and accurate detection assays, we have sequenced and annotated the genomes of 18 F. tularensis and Francisella philomiragia strains., (Copyright © 2015 Johnson et al.)
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- 2015
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28. High-Quality Draft Genome Sequence of Desulfovibrio carbinoliphilus FW-101-2B, an Organic Acid-Oxidizing Sulfate-Reducing Bacterium Isolated from Uranium(VI)-Contaminated Groundwater.
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Ramsay BD, Hwang C, Woo HL, Carroll SL, Lucas S, Han J, Lapidus AL, Cheng JF, Goodwin LA, Pitluck S, Peters L, Chertkov O, Held B, Detter JC, Han CS, Tapia R, Land ML, Hauser LJ, Kyrpides NC, Ivanova NN, Mikhailova N, Pagani I, Woyke T, Arkin AP, Dehal P, Chivian D, Criddle CS, Wu W, Chakraborty R, Hazen TC, and Fields MW
- Abstract
Desulfovibrio carbinoliphilus subsp. oakridgensis FW-101-2B is an anaerobic, organic acid/alcohol-oxidizing, sulfate-reducing δ-proteobacterium. FW-101-2B was isolated from contaminated groundwater at The Field Research Center at Oak Ridge National Lab after in situ stimulation for heavy metal-reducing conditions. The genome will help elucidate the metabolic potential of sulfate-reducing bacteria during uranium reduction., (Copyright © 2015 Ramsay et al.)
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- 2015
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29. Complete genome sequence of DSM 30083(T), the type strain (U5/41(T)) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy.
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Meier-Kolthoff JP, Hahnke RL, Petersen J, Scheuner C, Michael V, Fiebig A, Rohde C, Rohde M, Fartmann B, Goodwin LA, Chertkov O, Reddy T, Pati A, Ivanova NN, Markowitz V, Kyrpides NC, Woyke T, Göker M, and Klenk HP
- Abstract
Although Escherichia coli is the most widely studied bacterial model organism and often considered to be the model bacterium per se, its type strain was until now forgotten from microbial genomics. As a part of the G enomic E ncyclopedia of B acteria and A rchaea project, we here describe the features of E. coli DSM 30083(T) together with its genome sequence and annotation as well as novel aspects of its phenotype. The 5,038,133 bp containing genome sequence includes 4,762 protein-coding genes and 175 RNA genes as well as a single plasmid. Affiliation of a set of 250 genome-sequenced E. coli strains, Shigella and outgroup strains to the type strain of E. coli was investigated using digital DNA:DNA-hybridization (dDDH) similarities and differences in genomic G+C content. As in the majority of previous studies, results show Shigella spp. embedded within E. coli and in most cases forming a single subgroup of it. Phylogenomic trees also recover the proposed E. coli phylotypes as monophyla with minor exceptions and place DSM 30083(T) in phylotype B2 with E. coli S88 as its closest neighbor. The widely used lab strain K-12 is not only genomically but also physiologically strongly different from the type strain. The phylotypes do not express a uniform level of character divergence as measured using dDDH, however, thus an alternative arrangement is proposed and discussed in the context of bacterial subspecies. Analyses of the genome sequences of a large number of E. coli strains and of strains from > 100 other bacterial genera indicate a value of 79-80% dDDH as the most promising threshold for delineating subspecies, which in turn suggests the presence of five subspecies within E. coli.
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- 2014
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30. The mitochondrial and chloroplast genomes of the haptophyte Chrysochromulina tobin contain unique repeat structures and gene profiles.
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Hovde BT, Starkenburg SR, Hunsperger HM, Mercer LD, Deodato CR, Jha RK, Chertkov O, Monnat RJ Jr, and Cattolico RA
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- Chromosome Mapping, Conserved Sequence, Membrane Transport Proteins genetics, Models, Molecular, Open Reading Frames, Operon, Phylogeny, Repetitive Sequences, Nucleic Acid, Ribosomal Proteins genetics, Sequence Analysis, DNA, Signal Transduction, Structural Homology, Protein, Genome, Chloroplast, Genome, Mitochondrial, Haptophyta genetics
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Background: Haptophytes are widely and abundantly distributed in both marine and freshwater ecosystems. Few genomic analyses of representatives within this taxon have been reported, despite their early evolutionary origins and their prominent role in global carbon fixation., Results: The complete mitochondrial and chloroplast genome sequences of the haptophyte Chrysochromulina tobin (Prymnesiales) provide insight into the architecture and gene content of haptophyte organellar genomes. The mitochondrial genome (~34 kb) encodes 21 protein coding genes and contains a complex, 9 kb tandem repeat region. Similar to other haptophytes and rhodophytes, but not cryptophytes or stramenopiles, the mitochondrial genome has lost the nad7, nad9 and nad11 genes. The ~105 kb chloroplast genome encodes 112 protein coding genes, including ycf39 which has strong structural homology to NADP-binding nitrate transcriptional regulators; a divergent 'CheY-like' two-component response regulator (ycf55) and Tic/Toc (ycf60 and ycf80) membrane transporters. Notably, a zinc finger domain has been identified in the rpl36 ribosomal protein gene of all chloroplasts sequenced to date with the exception of haptophytes and cryptophytes--algae that have gained (via lateral gene transfer) an alternative rpl36 lacking the zinc finger motif. The two C. tobin chloroplast ribosomal RNA operon spacer regions differ in tRNA content. Additionally, each ribosomal operon contains multiple single nucleotide polymorphisms (SNPs)--a pattern observed in rhodophytes and cryptophytes, but few stramenopiles. Analysis of small (<200 bp) chloroplast encoded tandem and inverted repeats in C. tobin and 78 other algal chloroplast genomes show that repeat type, size and location are correlated with gene identity and taxonomic clade., Conclusion: The Chrysochromulina tobin organellar genomes provide new insight into organellar function and evolution. These are the first organellar genomes to be determined for the prymnesiales, a taxon that is present in both oceanic and freshwater systems and represents major primary photosynthetic producers and contributors to global ecosystem stability.
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- 2014
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31. A pangenomic analysis of the Nannochloropsis organellar genomes reveals novel genetic variations in key metabolic genes.
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Starkenburg SR, Kwon KJ, Jha RK, McKay C, Jacobs M, Chertkov O, Twary S, Rocap G, and Cattolico RA
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- ATP Synthetase Complexes chemistry, ATP Synthetase Complexes genetics, ATP Synthetase Complexes metabolism, Amino Acid Sequence, Chloroplasts genetics, Genome, Mitochondrial, Mitochondria genetics, Molecular Sequence Annotation, Molecular Sequence Data, Multigene Family, Protein Structure, Secondary, Sequence Alignment, Sequence Analysis, DNA, Transcriptome, Genome, Stramenopiles genetics
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Background: Microalgae in the genus Nannochloropsis are photosynthetic marine Eustigmatophytes of significant interest to the bioenergy and aquaculture sectors due to their ability to efficiently accumulate biomass and lipids for utilization in renewable transportation fuels, aquaculture feed, and other useful bioproducts. To better understand the genetic complement that drives the metabolic processes of these organisms, we present the assembly and comparative pangenomic analysis of the chloroplast and mitochondrial genomes from Nannochloropsis salina CCMP1776., Results: The chloroplast and mitochondrial genomes of N. salina are 98.4% and 97% identical to their counterparts in Nannochloropsis gaditana. Comparison of the Nannochloropsis pangenome to other algae within and outside of the same phyla revealed regions of significant genetic divergence in key genes that encode proteins needed for regulation of branched chain amino synthesis (acetohydroxyacid synthase), carbon fixation (RuBisCO activase), energy conservation (ATP synthase), protein synthesis and homeostasis (Clp protease, ribosome)., Conclusions: Many organellar gene modifications in Nannochloropsis are unique and deviate from conserved orthologs found across the tree of life. Implementation of secondary and tertiary structure prediction was crucial to functionally characterize many proteins and therefore should be implemented in automated annotation pipelines. The exceptional similarity of the N. salina and N. gaditana organellar genomes suggests that N. gaditana be reclassified as a strain of N. salina.
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- 2014
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32. Genome sequence and emended description of Leisingera nanhaiensis strain DSM 24252(T) isolated from marine sediment.
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Breider S, Teshima H, Petersen J, Chertkov O, Dalingault H, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Tindall BJ, Kyrpides NC, Woyke T, Simon M, Göker M, Klenk HP, and Brinkhoff T
- Abstract
Leisingera nanhaiensis DSM 24252(T) is a Gram-negative, motile, rod-shaped marine Alphaproteobacterium, isolated from sandy marine sediments. Here we present the non-contiguous genome sequence and annotation together with a summary of the organism's phenotypic features. The 4,948,550 bp long genome with its 4,832 protein-coding and 64 RNA genes consists of one chromosome and six extrachromosomal elements with lengths of 236 kb, 92 kb, 61 kb, 58 kb, 56 kb, and 35 kb, respectively. The analysis of the genome showed that DSM 24252(T) possesses all genes necessary for dissimilatory nitrite reduction, and the strain was shown to be facultatively anaerobic, a deviation from the original description that calls for an emendation of the species. Also present in the genome are genes coding for a putative prophage, for gene-transfer agents and for the utilization of methylated amines. Phylogenetic analysis and intergenomic distances indicate that L. nanhaiensis might not belong to the genus Leisingera.
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- 2014
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33. Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271(T)).
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Nandasena K, Yates R, Tiwari R, O'Hara G, Howieson J, Ninawi M, Chertkov O, Detter C, Tapia R, Han S, Woyke T, Pitluck S, Nolan M, Land M, Liolios K, Pati A, Copeland A, Kyrpides N, Ivanova N, Goodwin L, Meenakshi U, and Reeve W
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Mesorhizobium ciceri bv. biserrulae strain WSM1271(T) was isolated from root nodules of the pasture legume Biserrula pelecinus growing in the Mediterranean basin. Previous studies have shown this aerobic, motile, Gram negative, non-spore-forming rod preferably nodulates B. pelecinus - a legume with many beneficial agronomic attributes for sustainable agriculture in Australia. We describe the genome of Mesorhizobium ciceri bv. biserrulae strain WSM1271(T) consisting of a 6,264,489 bp chromosome and a 425,539 bp plasmid that together encode 6,470 protein-coding genes and 61 RNA-only encoding genes.
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- 2013
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34. Complete Genome Sequence of Bacillus thuringiensis Serovar Israelensis Strain HD-789.
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Doggett NA, Stubben CJ, Chertkov O, Bruce DC, Detter JC, Johnson SL, and Han CS
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Bacillus thuringiensis is an important microbial insecticide for controlling agricultural pests. We report the finished genome sequence of Bacillus thuringiensis serovar israelensis strain HD-789, which contains genes encoding 7 parasporal crystals consisting of Cry4Aa3, Cry4Ba5 (2 genes), Cry10Aa3, Cry11Aa3, Cry60Ba3, and Cry60Aa3, plus 3 Cyt toxin genes and 1 hemagglutinin gene.
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- 2013
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35. Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075(T.).
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Reeve W, Nandasena K, Yates R, Tiwari R, O'Hara G, Ninawi M, Chertkov O, Goodwin L, Bruce D, Detter C, Tapia R, Han S, Woyke T, Pitluck S, Nolan M, Land M, Copeland A, Liolios K, Pati A, Mavromatis K, Markowitz V, Kyrpides N, Ivanova N, Goodwin L, Meenakshi U, and Howieson J
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Mesorhizobium opportunistum strain WSM2075(T) was isolated in Western Australia in 2000 from root nodules of the pasture legume Biserrula pelecinus that had been inoculated with M. ciceri bv. biserrulae WSM1271. WSM2075(T) is an aerobic, motile, Gram negative, non-spore-forming rod that has gained the ability to nodulate B. pelecinus but is completely ineffective in N2 fixation with this host. This report reveals that the genome of M. opportunistum strain WSM2075(T) contains a chromosome of size 6,884,444 bp, encoding 6,685 protein-coding genes and 62 RNA-only encoding genes. The genome contains no plasmids, but does harbor a 455.7 kb genomic island from Mesorhizobium ciceri bv. biserrulae WSM1271 that has been integrated into a phenylalanine-tRNA gene.
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- 2013
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36. Complete genome sequence of Enterobacter sp. IIT-BT 08: A potential microbial strain for high rate hydrogen production.
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Khanna N, Ghosh AK, Huntemann M, Deshpande S, Han J, Chen A, Kyrpides N, Mavrommatis K, Szeto E, Markowitz V, Ivanova N, Pagani I, Pati A, Pitluck S, Nolan M, Woyke T, Teshima H, Chertkov O, Daligault H, Davenport K, Gu W, Munk C, Zhang X, Bruce D, Detter C, Xu Y, Quintana B, Reitenga K, Kunde Y, Green L, Erkkila T, Han C, Brambilla EM, Lang E, Klenk HP, Goodwin L, Chain P, and Das D
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Enterobacter sp. IIT-BT 08 belongs to Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Enterobacteriales, Family: Enterobacteriaceae. The organism was isolated from the leaves of a local plant near the Kharagpur railway station, Kharagpur, West Bengal, India. It has been extensively studied for fermentative hydrogen production because of its high hydrogen yield. For further enhancement of hydrogen production by strain development, complete genome sequence analysis was carried out. Sequence analysis revealed that the genome was linear, 4.67 Mbp long and had a GC content of 56.01%. The genome properties encode 4,393 protein-coding and 179 RNA genes. Additionally, a putative pathway of hydrogen production was suggested based on the presence of formate hydrogen lyase complex and other related genes identified in the genome. Thus, in the present study we describe the specific properties of the organism and the generation, annotation and analysis of its genome sequence as well as discuss the putative pathway of hydrogen production by this organism.
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- 2013
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37. Complete genome sequence of the marine methyl-halide oxidizing Leisingera methylohalidivorans type strain (DSM 14336(T)), a representative of the Roseobacter clade.
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Buddruhs N, Chertkov O, Petersen J, Fiebig A, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Gronow S, Kyrpides NC, Woyke T, Göker M, Brinkhoff T, and Klenk HP
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Leisingera methylohalidivorans Schaefer et al. 2002 emend. Vandecandelaere et al. 2008 is the type species of the genus Leisingera. The genus belongs to the Roseobacter clade (Rhodobacteraceae, Alphaproteobacteria), a widely distributed lineage in marine environments. Leisingera and particularly L. methylohalidivorans strain MB2(T) is of special interest due to its methylotrophy. Here we describe the complete genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. The 4,650,996 bp long genome with its 4,515 protein-coding and 81 RNA genes consists of three replicons, a single chromosome and two extrachromosomal elements with sizes of 221 kb and 285 kb.
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- 2013
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38. Genome sequence of Phaeobacter daeponensis type strain (DSM 23529(T)), a facultatively anaerobic bacterium isolated from marine sediment, and emendation of Phaeobacter daeponensis.
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Dogs M, Teshima H, Petersen J, Fiebig A, Chertkov O, Dalingault H, Chen A, Pati A, Goodwin LA, Chain P, Detter JC, Ivanova N, Lapidus A, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Göker M, Klenk HP, and Brinkhoff T
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TF-218(T) is the type strain of the species Phaeobacter daeponensis Yoon et al. 2007, a facultatively anaerobic Phaeobacter species isolated from tidal flats. Here we describe the draft genome sequence and annotation of this bacterium together with previously unreported aspects of its phenotype. We analyzed the genome for genes involved in secondary metabolite production and its anaerobic lifestyle, which have also been described for its closest relative Phaeobacter caeruleus. The 4,642,596 bp long genome of strain TF-218(T) contains 4,310 protein-coding genes and 78 RNA genes including four rRNA operons and consists of five replicons: one chromosome and four extrachromosomal elements with sizes of 276 kb, 174 kb, 117 kb and 90 kb. Genome analysis showed that TF-218(T) possesses all of the genes for indigoidine biosynthesis, and on specific media the strain showed a blue pigmentation. We also found genes for dissimilatory nitrate reduction, gene-transfer agents, NRPS/ PKS genes and signaling systems homologous to the LuxR/I system.
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- 2013
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39. Complete Genome Sequence of Micromonospora Strain L5, a Potential Plant-Growth-Regulating Actinomycete, Originally Isolated from Casuarina equisetifolia Root Nodules.
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Hirsch AM, Alvarado J, Bruce D, Chertkov O, De Hoff PL, Detter JC, Fujishige NA, Goodwin LA, Han J, Han S, Ivanova N, Land ML, Lum MR, Milani-Nejad N, Nolan M, Pati A, Pitluck S, Tran SS, Woyke T, and Valdés M
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Micromonospora species live in diverse environments and exhibit a broad range of functions, including antibiotic production, biocontrol, and degradation of complex polysaccharides. To learn more about these versatile actinomycetes, we sequenced the genome of strain L5, originally isolated from root nodules of an actinorhizal plant growing in Mexico.
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- 2013
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40. Comparative genomics of freshwater Fe-oxidizing bacteria: implications for physiology, ecology, and systematics.
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Emerson D, Field EK, Chertkov O, Davenport KW, Goodwin L, Munk C, Nolan M, and Woyke T
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The two microaerophilic, Fe-oxidizing bacteria (FeOB) Sideroxydans ES-1 and Gallionella ES-2 have single circular chromosomes of 3.00 and 3.16 Mb that encode 3049 and 3006 genes, respectively. Multi-locus sequence analysis (MLSA) confirmed the relationship of these two organisms to one another, and indicated they may form a novel order, the Gallionellalaes, within the Betaproteobacteria. Both are adapted for chemolithoautotropy, including pathways for CO2-fixation, and electron transport pathways adapted for growth at low O2-levels, an important adaptation for growing on Fe(II). Both genomes contain Mto-genes implicated in iron-oxidation, as well as other genes that could be involved in Fe-oxidation. Nearly 10% of their genomes are devoted to environmental sensing, signal transduction, and chemotaxis, consistent with their requirement for growing in narrow redox gradients of Fe(II) and O2. There are important differences as well. Sideroxydans ES-1 is more metabolically flexible, and can utilize reduced S-compounds, including thiosulfate, for lithotrophic growth. It has a suite of genes for nitrogen fixation. Gallionella ES-2 contains additional gene clusters for exopolysaccharide production, and has more capacity to resist heavy metals. Both strains contain genes for hemerythrins and globins, but ES-1 has an especially high numbers of these genes that may be involved in oxygen homeostasis, or storage. The two strains share homology with the marine FeOB Mariprofundus ferrooxydans PV-1 in CO2 fixation genes, and respiratory genes. In addition, ES-1 shares a suite of 20 potentially redox active genes with PV-1, as well as a large prophage. Combined these genetic, morphological, and physiological differences indicate that these are two novel species, Sideroxydans lithotrophicus ES-1(T) (ATCC 700298(T); JCM 14762; DSMZ 22444; NCMA B100), and Gallionella capsiferriformans ES-2(T) (ATCC 700299(T); JCM 14763; DSMZ 22445; NCMA B101).
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- 2013
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41. Genome sequence of Phaeobacter caeruleus type strain (DSM 24564(T)), a surface-associated member of the marine Roseobacter clade.
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Beyersmann PG, Chertkov O, Petersen J, Fiebig A, Chen A, Pati A, Ivanova N, Lapidus A, Goodwin LA, Chain P, Detter JC, Rohde M, Gronow S, Kyrpides NC, Woyke T, Simon M, Göker M, Klenk HP, and Brinkhoff T
- Abstract
In 2009 Phaeobacter caeruleus was described as a novel species affiliated with the marine Roseobacter clade, which, in turn, belongs to the class Alphaproteobacteria. The genus Phaeobacter is well known for members that produce various secondary metabolites. Here we report of putative quorum sensing systems, based on the finding of six N-acyl-homoserine lactone synthetases, and show that the blue color of P. caeruleus is probably due to the production of the secondary metabolite indigoidine. Therefore, P. caeruleus might have inhibitory effects on other bacteria. In this study the genome of the type strain DSM 24564(T) was sequenced, annotated and characterized. The 5,344,419 bp long genome with its seven plasmids contains 5,227 protein-coding genes (3,904 with a predicted function) and 108 RNA genes.
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- 2013
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42. Non-contiguous finished genome sequence of plant-growth promoting Serratia proteamaculans S4.
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Neupane S, Goodwin LA, Högberg N, Kyrpides NC, Alström S, Bruce D, Quintana B, Munk C, Daligault H, Teshima H, Davenport K, Reitenga K, Green L, Chain P, Erkkila T, Gu W, Zhang X, Xu Y, Kunde Y, Chertkov O, Han J, Han C, Detter JC, Ivanova N, Pati A, Chen A, Szeto E, Mavromatis K, Huntemann M, Nolan M, Pitluck S, Deshpande S, Markowitz V, Pagani I, Klenk HP, Woyke T, and Finlay RD
- Abstract
Serratia proteamaculans S4 (previously Serratia sp. S4), isolated from the rhizosphere of wild Equisetum sp., has the ability to stimulate plant growth and to suppress the growth of several soil-borne fungal pathogens of economically important crops. Here we present the non-contiguous, finished genome sequence of S. proteamaculans S4, which consists of a 5,324,944 bp circular chromosome and a 129,797 bp circular plasmid. The chromosome contains 5,008 predicted genes while the plasmid comprises 134 predicted genes. In total, 4,993 genes are assigned as protein-coding genes. The genome consists of 22 rRNA genes, 82 tRNA genes and 58 pseudogenes. This genome is a part of the project "Genomics of four rapeseed plant growth-promoting bacteria with antagonistic effect on plant pathogens" awarded through the 2010 DOE-JGI's Community Sequencing Program.
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- 2013
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43. Genome sequence of the free-living aerobic spirochete Turneriella parva type strain (H(T)), and emendation of the species Turneriella parva.
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Stackebrandt E, Chertkov O, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mavromatis K, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Land M, Pan C, Rohde M, Gronow S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Woyke T, Kyrpides NC, and Klenk HP
- Abstract
Turneriella parva Levett et al. 2005 is the only species of the genus Turneriella which was established as a result of the reclassification of Leptospira parva Hovind-Hougen et al. 1982. Together with Leptonema and Leptospira, Turneriella constitutes the family Leptospiraceae, within the order Spirochaetales. Here we describe the features of this free-living aerobic spirochete together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the genus Turneriella and the 13(th) member of the family Leptospiraceae for which a complete or draft genome sequence is now available. The 4,409,302 bp long genome with its 4,169 protein-coding and 45 RNA genes is part of the G enomic E ncyclopedia of Bacteria and Archaea project.
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- 2013
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44. Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome.
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Fitzsimons MS, Novotny M, Lo CC, Dichosa AE, Yee-Greenbaum JL, Snook JP, Gu W, Chertkov O, Davenport KW, McMurry K, Reitenga KG, Daughton AR, He J, Johnson SL, Gleasner CD, Wills PL, Parson-Quintana B, Chain PS, Detter JC, Lasken RS, and Han CS
- Subjects
- Genomics, Humans, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Sequence Analysis, DNA methods, Bacteria genetics, Genetic Variation, Genome, Bacterial genetics, Microbiota
- Abstract
The majority of microbial genomic diversity remains unexplored. This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is amplified directly from a single cell using the whole-genome amplification technique of multiple displacement amplification (MDA). However, MDA from a single chromosome copy suffers from amplification bias and a large loss of specificity from even very small amounts of DNA contamination, which makes assembling a genome difficult and completely finishing a genome impossible except in extraordinary circumstances. Gel microdrop cultivation allows culturing of a diverse microbial community and provides hundreds to thousands of genetically identical cells as input for an MDA reaction. We demonstrate the utility of this approach by comparing sequencing results of gel microdroplets and single cells following MDA. Bias is reduced in the MDA reaction and genome sequencing, and assembly is greatly improved when using gel microdroplets. We acquired multiple near-complete genomes for two bacterial species from human oral and stool microbiome samples. A significant amount of genome diversity, including single nucleotide polymorphisms and genome recombination, is discovered. Gel microdroplets offer a powerful and high-throughput technology for assembling whole genomes from complex samples and for probing the pan-genome of naturally occurring populations.
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- 2013
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45. High-quality-draft genome sequence of the yellow-pigmented flavobacterium Joostella marina type strain (En5(T)).
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Stackebrandt E, Chertkov O, Lapidus A, Nolan M, Lucas S, Han C, Cheng JF, Tapia R, Goodwin LA, Bruce D, Pitluck S, Liolios K, Mavromatis K, Pagani I, Ivanova N, Mikhailova N, Huntemann M, Pati A, Chen A, Palaniappan K, Rohde M, Tindall BJ, Göker M, Woyke T, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, and Kyrpides NC
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At present, Joostella marina Quan et al. 2008 is the sole species with a validly published name in the genus Joostella, family Flavobacteriacae, phylum Bacteriodetes. It is a yellow-pigmented, aerobic, marine organism about which little has been reported other than the chemotaxonomic features required for initial taxonomic description. The genome of J. marina strain En5(T) complements a list of 16 Flavobacteriaceae strains for which complete genomes and draft genomes are currently available. Here we describe the features of this bacterium, together with the complete genome sequence, and annotation. This is the first member of the genus Joostella for which a complete genome sequence becomes available. The 4,508,243 bp long single replicon genome with its 3,944 protein-coding and 60 RNA genes is part of the G enomic E ncyclopedia of Bacteria and Archaea project.
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- 2013
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46. Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici.
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Lamour KH, Mudge J, Gobena D, Hurtado-Gonzales OP, Schmutz J, Kuo A, Miller NA, Rice BJ, Raffaele S, Cano LM, Bharti AK, Donahoo RS, Finley S, Huitema E, Hulvey J, Platt D, Salamov A, Savidor A, Sharma R, Stam R, Storey D, Thines M, Win J, Haas BJ, Dinwiddie DL, Jenkins J, Knight JR, Affourtit JP, Han CS, Chertkov O, Lindquist EA, Detter C, Grigoriev IV, Kamoun S, and Kingsmore SF
- Subjects
- Adaptation, Physiological, Capsicum microbiology, Chromosome Mapping, Cucurbita microbiology, Gene Expression Regulation, Genetic Linkage, Genome, Genotype, Polymorphism, Single Nucleotide, Phytophthora physiology, Plant Diseases microbiology
- Abstract
The oomycete vegetable pathogen Phytophthora capsici has shown remarkable adaptation to fungicides and new hosts. Like other members of this destructive genus, P. capsici has an explosive epidemiology, rapidly producing massive numbers of asexual spores on infected hosts. In addition, P. capsici can remain dormant for years as sexually recombined oospores, making it difficult to produce crops at infested sites, and allowing outcrossing populations to maintain significant genetic variation. Genome sequencing, development of a high-density genetic map, and integrative genomic or genetic characterization of P. capsici field isolates and intercross progeny revealed significant mitotic loss of heterozygosity (LOH) in diverse isolates. LOH was detected in clonally propagated field isolates and sexual progeny, cumulatively affecting >30% of the genome. LOH altered genotypes for more than 11,000 single-nucleotide variant sites and showed a strong association with changes in mating type and pathogenicity. Overall, it appears that LOH may provide a rapid mechanism for fixing alleles and may be an important component of adaptability for P. capsici.
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- 2012
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47. Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)).
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Anderson I, Chertkov O, Chen A, Saunders E, Lapidus A, Nolan M, Lucas S, Hammon N, Deshpande S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Palaniappan K, Land M, Pan C, Rohde M, Pukall R, Göker M, Detter JC, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, and Mavromatis K
- Abstract
Sulfobacillus acidophilus Norris et al. 1996 is a member of the genus Sulfobacillus which comprises five species of the order Clostridiales. Sulfobacillus species are of interest for comparison to other sulfur and iron oxidizers and also have biomining applications. This is the first completed genome sequence of a type strain of the genus Sulfobacillus, and the second published genome of a member of the species S. acidophilus. The genome, which consists of one chromosome and one plasmid with a total size of 3,557,831 bp harbors 3,626 protein-coding and 69 RNA genes, and is a part of the GenomicEncyclopedia ofBacteria andArchaea project.
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- 2012
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48. Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park.
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Mead DA, Lucas S, Copeland A, Lapidus A, Cheng JF, Bruce DC, Goodwin LA, Pitluck S, Chertkov O, Zhang X, Detter JC, Han CS, Tapia R, Land M, Hauser LJ, Chang YJ, Kyrpides NC, Ivanova NN, Ovchinnikova G, Woyke T, Brumm C, Hochstein R, Schoenfeld T, and Brumm P
- Abstract
Paenibacillus sp.Y412MC10 was one of a number of organisms isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. The isolate was initially classified as a Geobacillus sp. Y412MC10 based on its isolation conditions and similarity to other organisms isolated from hot springs at Yellowstone National Park. Comparison of 16 S rRNA sequences within the Bacillales indicated that Geobacillus sp.Y412MC10 clustered with Paenibacillus species, and the organism was most closely related to Paenibacillus lautus. Lucigen Corp. prepared genomic DNA and the genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute. The genome sequence was deposited at the NCBI in October 2009 (NC_013406). The genome of Paenibacillus sp. Y412MC10 consists of one circular chromosome of 7,121,665 bp with an average G+C content of 51.2%. Comparison to other Paenibacillus species shows the organism lacks nitrogen fixation, antibiotic production and social interaction genes reported in other paenibacilli. The Y412MC10 genome shows a high level of synteny and homology to the draft sequence of Paenibacillus sp. HGF5, an organism from the Human Microbiome Project (HMP) Reference Genomes. This, combined with genomic CAZyme analysis, suggests an intestinal, rather than environmental origin for Y412MC10.
- Published
- 2012
- Full Text
- View/download PDF
49. Complete genome sequence of Serratia plymuthica strain AS12.
- Author
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Neupane S, Finlay RD, Alström S, Goodwin L, Kyrpides NC, Lucas S, Lapidus A, Bruce D, Pitluck S, Peters L, Ovchinnikova G, Chertkov O, Han J, Han C, Tapia R, Detter JC, Land M, Hauser L, Cheng JF, Ivanova N, Pagani I, Klenk HP, Woyke T, and Högberg N
- Abstract
A plant-associated member of the family Enterobacteriaceae, Serratia plymuthica strain AS12 was isolated from rapeseed roots. It is of scientific interest because it promotes plant growth and inhibits plant pathogens. The genome of S. plymuthica AS12 comprises a 5,443,009 bp long circular chromosome, which consists of 4,952 protein-coding genes, 87 tRNA genes and 7 rRNA operons. This genome was sequenced within the 2010 DOE-JGI Community Sequencing Program (CSP2010) as part of the project entitled "Genomics of four rapeseed plant growth promoting bacteria with antagonistic effect on plant pathogens".
- Published
- 2012
- Full Text
- View/download PDF
50. Permanent draft genome sequence of the gliding predator Saprospira grandis strain Sa g1 (= HR1).
- Author
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Mavromatis K, Chertkov O, Lapidus A, Nolan M, Lucas S, Tice H, Del Rio TG, Cheng JF, Han C, Tapia R, Bruce D, Goodwin LA, Pitluck S, Huntemann M, Liolios K, Pagani I, Ivanova N, Mikhailova N, Pati A, Chen A, Palaniappan K, Land M, Brambilla EM, Rohde M, Spring S, Göker M, Detter JC, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP, and Woyke T
- Abstract
Saprospira grandis Gross 1911 is a member of the Saprospiraceae, a family in the class 'Sphingobacteria' that remains poorly characterized at the genomic level. The species is known for preying on other marine bacteria via 'ixotrophy'. S. grandis strain Sa g1 was isolated from decaying crab carapace in France and was selected for genome sequencing because of its isolated location in the tree of life. Only one type strain genome has been published so far from the Saprospiraceae, while the sequence of strain Sa g1 represents the second genome to be published from a non-type strain of S. grandis. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,495,250 bp long Improved-High-Quality draft of the genome with its 3,536 protein-coding and 62 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
- Published
- 2012
- Full Text
- View/download PDF
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