多环芳烃降解菌株矢野氏鞘氨醇单胞菌B1的基因组序列
Genome Sequence of Sphingobium yanoikuyae B1, a Polycyclic Aromatic Hydrocarbon-Degrading Strain.
作者信息
Zhao Qiang, Hu Hongbo, Wang Wei, Peng Huasong, Zhang Xuehong
机构信息
State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
出版信息
Genome Announc. 2015 Feb 5;3(1):e01522-14. doi: 10.1128/genomeA.01522-14.
Abstract
Sphingobium yanoikuyae B1 can utilize biphenyl, naphthalene, phenanthrene, toluene, and m-/p-xylene as sole sources of carbon and energy. Here, we present a 5.2-Mb assembly of its genome. An analysis of the genome can provide insights into the mechanisms of polycyclic aromatic hydrocarbon (PAH) degradation and potentially aid in bioremediation applications.
摘要
食烷鞘氨醇单胞菌B1（Sphingobium yanoikuyae B1）能够利用联苯、萘、菲、甲苯以及间二甲苯/对二甲苯作为唯一碳源和能源。在此，我们展示了该菌5.2兆碱基的基因组组装结果。对该基因组的分析能够为多环芳烃（PAH）降解机制提供深入见解，并可能有助于生物修复应用。
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本文引用的文献
1
KEGG-PATH: Kyoto encyclopedia of genes and genomes-based pathway analysis using a path analysis model.
Mol Biosyst. 2014 Jul 29;10(9):2441-7. doi: 10.1039/c4mb00287c.
2
Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data.
ISME J. 2014 Feb;8(2):398-408. doi: 10.1038/ismej.2013.153. Epub 2013 Sep 12.
3
The whole genome sequence of Sphingobium chlorophenolicum L-1: insights into the evolution of the pentachlorophenol degradation pathway.
Genome Biol Evol. 2012;4(2):184-98. doi: 10.1093/gbe/evr137. Epub 2011 Dec 16.
4
NCBI Reference Sequences: current status, policy and new initiatives.
Nucleic Acids Res. 2009 Jan;37(Database issue):D32-6. doi: 10.1093/nar/gkn721. Epub 2008 Oct 16.
5
Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Genome Res. 2008 May;18(5):821-9. doi: 10.1101/gr.074492.107. Epub 2008 Mar 18.
6
The RAST Server: rapid annotations using subsystems technology.
BMC Genomics. 2008 Feb 8;9:75. doi: 10.1186/1471-2164-9-75.
7
Identification, cloning, and characterization of a multicomponent biphenyl dioxygenase from Sphingobium yanoikuyae B1.
J Ind Microbiol Biotechnol. 2007 Sep;34(9):605-13. doi: 10.1007/s10295-007-0235-3. Epub 2007 Jul 24.
8
Structural investigations of the ferredoxin and terminal oxygenase components of the biphenyl 2,3-dioxygenase from Sphingobium yanoikuyae B1.
BMC Struct Biol. 2007 Mar 9;7:10. doi: 10.1186/1472-6807-7-10.
9
Identifying bacterial genes and endosymbiont DNA with Glimmer.
Bioinformatics. 2007 Mar 15;23(6):673-9. doi: 10.1093/bioinformatics/btm009. Epub 2007 Jan 19.
10
Effect of Sphingobium yanoikuyae B1 inoculation on bacterial community dynamics and polycyclic aromatic hydrocarbon degradation in aged and freshly PAH-contaminated soils.
Environ Pollut. 2006 Nov;144(1):228-37. doi: 10.1016/j.envpol.2005.12.026. Epub 2006 Mar 9.
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