Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3

Standards in Genomic Sciences - Tập 10 - Trang 1-8 - 2015
Shahid Manzoor1,2, Bettina Müller3, Adnan Niazi1, Anna Schnürer3, Erik Bongcam-Rudloff1
1Department of Animal Breeding and Genetics Science, Swedish University of Agricultural Science, SLU-Global Bioinformatics Centre, Uppsala, Sweden
2University of the Punjab, Lahore, Pakistan
3Department of Microbiology, Swedish University of Agricultural Sciences, BioCenter, Uppsala, Sweden

Tóm tắt

Syntrophaceticus schinkii strain Sp3 is a mesophilic syntrophic acetate oxidizing bacterium, belonging to the Clostridia class within the phylum Firmicutes, originally isolated from a mesophilic methanogenic digester. It has been shown to oxidize acetate in co-cultivation with hydrogenotrophic methanogens forming methane. The draft genome shows a total size of 3,196,921 bp, encoding 3,688 open reading frames, which includes 3,445 predicted protein-encoding genes and 55 RNA genes. Here, we are presenting assembly and annotation features as well as basic genomic properties of the type strain Sp3.

Tài liệu tham khảo

Ferry JG. Fermentation of Acetate. In: Ferry DJG, ed. Methanogenesis. Chapman & Hall Microbiology Series. Springer US; 1993:304–334. Available at: http://link.springer.com/chapter/10.1007/978-1-4615-2391-8_7. Accessed March 3, 2014. Hattori S, Kamagata Y, Hanada S, Shoun H. Thermacetogenium phaeum gen. nov., sp. nov., a strictly anaerobic, thermophilic, syntrophic acetate-oxidizing bacterium. Int. J. Syst. Evol. Microbiol. 2000;50 Pt 4:1601–1609. Petersen SP, Ahring BK. Acetate oxidation in a thermophilic anaerobic sewage-sludge digestor: the importance of non-aceticlastic methanogenesis from acetate. FEMS Microbiol. Lett. 1991;86:149–152. Schnürer A, Svensson BH, Schink B. Enzyme activities in and energetics of acetate metabolism by the mesophilic syntrophically acetate-oxidizing anaerobe Clostridium ultunense. FEMS Microbiol. Lett. 1997;154:331–336. Anna Schnürer BS. Clostridium ultunense sp. nov., a Mesophilic Bacterium Oxidizing Acetate in Syntrophic Association with a Hydrogenotrophic Methanogenic Bacterium. First Publ Int. J. Syst. Bacteriol. 1996:46(4);1145-1152. Westerholm M, Roos S, Schnürer A. Syntrophaceticus schinkii gen. nov., sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from a mesophilic anaerobic filter. FEMS Microbiol. Lett. 2010;309:100–104. Westerholm M, Roos S, Schnürer A. Tepidanaerobacter acetatoxydans sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from two ammonium-enriched mesophilic methanogenic processes. Syst. Appl. Microbiol. 2011;34:260–266. Balk M, Weijma J, Stams AJM. Thermotoga lettingae sp. nov., a novel thermophilic, methanol-degrading bacterium isolated from a thermophilic anaerobic reactor. Int. J. Syst. Evol. Microbiol. 2002;52:1361–1368. Oehler D, Poehlein A, Leimbach A, et al. Genome-guided analysis of physiological and morphological traits of the fermentative acetate oxidizer Thermacetogenium phaeum. BMC Genomics 2012;13:723. Müller B, Manzoor S, Niazi A, Bongcam-Rudloff E, Schnürer A. Genome-guided analysis of physiological capacities of Tepidanaerobacter acetatoxydans provides insights into environmental adaptations and syntrophic acetate oxidation. PloS One 2015;10:e0121237. Manzoor S, Müller B, Niazi A, Bongcam-Rudloff E, Schnürer A. Draft Genome Sequence of Clostridium ultunense Strain Esp, a Syntrophic Acetate-Oxidizing Bacterium. Genome Announc. 2013;1:e00107–13. Anon. Classifier. Available at: https://rdp.cme.msu.edu/classifier/classifier.jsp. Accessed November 2, 2015. Altschul SF, Madden TL, Schäffer AA, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. Liolios K, Mavromatis K, Tavernarakis N, Kyrpides NC. The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 2008;36:D475–D479. Anon. SciLifeLab. Available at: https://www.scilifelab.se/. Accessed November 2, 2015. Andrews S. FastQC A Quality Control tool for High Throughput Sequence Data. Available at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ Milne I, Stephen G, Bayer M, et al. Using Tablet for visual exploration of second-generation sequencing data. Brief. Bioinform. 2013;14:193–202. Darling AE, Mau B, Perna NT. ProgressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement. PLoS ONE; 2010;5:e11147. Vallenet D, Labarre L, Rouy Z, et al. MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res. 2006;34:53–65. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010;11:119. Bocs S, Cruveiller S, Vallenet D, Nuel G, Medigue C. AMIGene: Annotation of MIcrobial Genes. Nucleic Acids Res. 2003;31:3723–3726. Field D, Garrity G, Gray T, et al. The minimum information about a genome sequence (MIGS) specification. Nat. Biotechnol. 2008;26:541–547. Ludwig W, Schleifer K-H, Whitman WB. Revised road map to the phylumFirmicutes. In: Vos PD, Garrity GM, Jones D, et al., eds. Bergey’s Manual® of Systematic Bacteriology. Springer New York; 2009:1–13. Available at: http://link.springer.com/chapter/10.1007/978-0-387-68489-5_1. Accessed March 3, 2014. Wolf M, Müller T, Dandekar T, Pollack JD. Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data. Int. J. Syst. Evol. Microbiol. 2004;54:871–875. Gibbons NE, Murray RGE. Proposals Concerning the Higher Taxa of Bacteria. Int. J. Syst. Bacteriol. 1978;28:1–6. Editor L. List of new names and new combinations previously effectively, but not validly, published. List no. 132. Int. J. Syst. Evol. Microbiol. 2010;60:469–472. Rainey FA. Class II. Clostridia class nov. 2nd ed. (Vos PD, Garrity G, Jones D, et al., eds.). New York: Springer-Verlag; 2009. Wiegel J. Order III. Thermoanaerobacterales ord. nov. 2nd ed. (Vos PD, Garrity G, Jones D, et al., eds.). New York: Springer-Verlag; 2009. Wiegel J. Family I. Thermoanaerobacteraceae fam. nov. 2nd ed. (Vos PD, Garrity G, Jones D, et al., eds.). New York: Springer-Verlag; 2009. Editor L. List of new names and new combinations previously effectively, but not validly, published. Int. J. Syst. Evol. Microbiol. 2011;61:1011–1013. Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000;25:25–29. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–1797. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol. 1981;17:368–376. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) Software Version 4.0. Mol. Biol. Evol. 2007;24:1596–1599. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol. Biol. Evol. 2011;28:2731–2739. Felsenstein J. Confidence Limits on Phylogenies: An Approach Using the Bootstrap. Evolution 1985;39:783–791.