Draft genome sequence of Syntrophorhabdus aromaticivorans strain UI, a mesophilic aromatic compound-degrading syntroph

Genome Announcements

Volumn 2, Issue 1, 2014, Pages

  Nobu, Masaru K ^a   Narihiro, Takashi ^a,b   Tamaki, Hideyuki ^b   Qiu, Yan Ling ^c   Sekiguchi, Yuji ^b   Woyke, Tanja ^d   Goodwin, Lynne ^e   Davenport, Karen W ^e   Kamagata, Yoichi ^b,f   Liu, Wen Tso ^a  

^a University of Illinois at Urbana Champaign   (United States)

^b NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^c QINGDAO INSTITUTE OF BIOENERGY AND BIOPROCESS TECHNOLOGY   (China)

^d DOE JOINT GENOME INSTITUTE   (United States)

^e LOS ALAMOS NATIONAL LABORATORY   (United States)

^f NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84998692981     PISSN: None     EISSN: 21698287     Source Type: Journal    
DOI: 10.1128/genomeA.e01064-13     Document Type: Article

References (15)

1. Qiu YL, Hanada S, Ohashi A, Harada H, Kamagata Y, Sekiguchi Y. 2008 Syntrophorhabdus aromaticivorans gen. nov., sp. nov., the first cultured anaerobe capable of degrading phenol to acetate in obligate syntrophic associations with a hydrogenotrophic methanogen. Appl. Environ. Microbiol. 74:2051-2058. http://dx.doi.org/10.1128/AEM.02378-07.
2. Mountfort DO, Brulla WJ, Krumholz LR, Bryant MP. 1984. Syntrophus buswellii gen. nov., sp. nov.: a benzoate catabolizer from methanogenic ecosystems. Int. J. Syst. Bacteriol. 34:216-217. http://dx.doi.org/10.1099/00207713-34-2-216.
3. Wallrabenstein C, Gorny N, Springer N, Ludwig W, Schink B. 1995. Pure culture of Syntrophus buswellii, definition of its phylogenetic status, and description of Syntrophus gentianae sp. nov. Syst. Appl. Microbiol. 18:62-66. http://dx.doi.org/10.1016/S0723-2020(11)80449-2.
4. Jackson BE, Bhupathiraju VK, Tanner RS, Woese CR, McInerney MJ. 1999 Syntrophus aciditrophicus sp. nov., a new anaerobic bacterium that degrades fatty acids and benzoate in syntrophic association with hydrogen-using microorganisms. Arch. Microbiol. 171:107-114. http://dx.doi.org/10.1007/s002030050685.
5. Brauman A, Müller JA, Garcia JL, Brune A, Schink B. 1998. Fermentative degradation of 3-hydroxybenzoate in pure culture by a novel strictly anaerobic bacterium, Sporotomaculum hydroxybenzoicum gen. nov., sp. nov. Int. J. Syst. Bacteriol. 48(Pt 1):215-221. http://dx.doi.org/10.1099/0 0207713-48-1-215.
6. Qiu YL, Sekiguchi Y, Imachi H, Kamagata Y, Tseng IC, Cheng SS, Ohashi A, Harada H. 2003. Sporotomaculum syntrophicum sp. nov., a novel anaerobic, syntrophic benzoate-degrading bacterium isolated from methanogenic sludge treating wastewater from terephthalate manufacturing. Arch. Microbiol. 179:457. http://link.springer.com/article/10.1007/s00203-003-0557-0.
7. Qiu YL, Sekiguchi Y, Hanada S, Imachi H, Tseng IC, Cheng SS, Ohashi A, Harada H, Kamagata Y. 2006. Pelotomaculum terephthalicum sp. nov. and Pelotomaculum isophthalicum sp. nov.: two anaerobic bacteria that degrade phthalate isomers in syntrophic association with hydrogenotrophic methanogens. Arch. Microbiol. 185:172-182. http://dx.doi.org/10.1007/s00203-005-0081-5.
8. Bennett S. 2004. Solexa Ltd. Pharmacogenomics 5:433-438. http://dx.doi.org/10.1517/14622416.5.4.433.
9. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen ZT, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu PG, Begley RF, Rothberg JM. 2005 Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380. http://dx.doi.org/10.1038/nature03959.
10. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821-829. http://dx.doi.org/10.1101/gr.074492.107.
11. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 8:186-194.
12. Ewing B, Hillier L, Wendl MC, Green P. 1998. Base-calling of automated sequencer traces using Phred. I. Accuracy assessment. Genome Res. 8:175-185. http://dx.doi.org/10.1101/gr.8.3.175.
13. Gordon D, Abajian C, Green P. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195-202. http://dx.doi.org/10.1101/gr.8.3.195.
14. Han C, Chain P. 2006. Finishing repeat regions automatically with Dup-Finisher, p 141-146. In Arabnia HR, Valafar H (ed), Proceedings of the 2006 International Conference on Bioinformatics & Computational Biology. CSREA Press, Las Vegas, NV.
15. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Anderson I, Lykidis A, Mavromatis K, Ivanova NN, Kyrpides NC. 2010. The integrated microbial genomes system: an expanding comparative analysis resource. Nucleic Acids Res. 38:D382-D390. http://dx.doi.org/10.1093/nar/gkp887.