Draft Genome Sequences and Annotation of Enterococcus faecium Strain LCT-EF20 De Chang,a Yuanfang Zhu,b Jiapeng Chen,b Xiangqun Fang,a Tianzhi Li,a Junfeng Wang,a Yinghua Guo,a Longxiang Su,a Guogang Xu,a Yajuan Wang,a Zhenhong Chen,a Changting Liua Nanlou Respiratory Diseases Department, Chinese PLA General Hospital, Beijing, Chinaa; BGI-Shenzhen, Shenzhen, People’s Republic of Chinab D.C. and Y.Z. contributed equally to this article
The space environment is reported to cause biological alterations in microorganisms, such as growth, drug resistance, and virulence. Here, we present the model of Enterococcus faecium to investigate the effects of space conditions on the microbe and on the whole-genome sequences of the strain LCT-EF20 after being exposed to space flight. Received 1 November 2012 Accepted 12 November 2012 Published 24 January 2013 Citation Chang D, Zhu Y, Chen J, Fang X, Li T, Wang J, Guo Y, Su L, Xu G, Wang Y, Chen Z, Liu C. 2013. Draft genome sequences and annotation of Enterococcus faecium strain LCT-EF20. Genome Announc. 1(1):e00083-12. doi:10.1128/genomeA.00083-12. Copyright © 2013 Chang et al. This is an open-access article distributed under the terms of the Attribution 3.0 Unported Creative Commons License. Address correspondence to Changting Liu,
[email protected].
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revious studies have suggested that space flight may alter the effectiveness of antibiotics against microbes (1, 2). The inhibition of bacterial growth in space requires higher concentrations of various drugs due to the reduced efficacy of the drugs and increased bacterial resistance (3, 4). In addition, bacteria exposed to space flight displayed increased virulence as discovered through murine infection assays (5, 6). Enterococcus faecium is a ubiquitous opportunistic pathogen grown in human and animal intestines (7). Since E. faecium coexists in human intestines, it is necessary to assess the behavior and genome of E. faecium under space flight conditions. Therefore, in order to prevent astronauts from infectious disease in space and to provide insight into the identification of candidate targets for refractory infections on the ground, the genome of E. faecium (LCT-EF20) under space flight conditions was sequenced and analyzed. The clustering of shotgun reads and manual finishing of the assembly resulted in 111 contiguous sequences (contigs) with an N50 of 73,148 bp and 120⫻ average genome coverage. The combined contig length was 2,718,930 bp, connected to 34 scaffolds (⬎500 bp each), with total length of 2,809,068 bp containing 90,138-bp gap regions. The G⫹C content of the overall assembly was 38%. The assembly contains 2,807 genes with a length of 2,431,857 bp consisting of 86.57% in the genome. The transposon sequences were predicted using RepeatMasker and RepeatProteinMasker software programs, and tandem repeat sequences were predicted using Tandem Repeats Finder (TRF) (8). Finally, 313-kb different transposable element (TE)-related sequences consisting of 0.44% in the genome were found. Protein-coding sequences were retrieved from the chromosomes of E. faecium strain LCT-EF20. The gene functions were annotated using BLASTP to identify all coding protein sequences comparing the Kyoto Encyclopedia of Genes and Genomes (KEGG) (9), Clusters of Orthologous Groups (COG), Swiss-Prot, TrEMBL, Gene Ontology (GO), and nonredundant (NR) databases. Homologous proteins were identified by BLASTP with the criteria of an e value cutoff of 1e⫺5 and a minimum aligned sequence length coverage of 50% of a query sequence. Similarly, using the above criteria, 1,896 protein fami-
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lies were yielded, with 1,885 single-copy protein families. Genome island prediction, prophage sequences, and clustered regularly interspaced short palindromic repeats (CRISPRs) were also predicted separately, but no sequence was found. Nucleotide sequence accession number. This whole genome sequence of E. faecium LCT-EF20 has been deposited at DDBJ/ EMBL/GenBank under the accession no. ANAI00000000. ACKNOWLEDGMENTS This work was supported by the Key Pre-Research Foundation of Military Equipment of China (grant no. 9140A17040312JB1001); the Special Financial Grant from the China Postdoctoral Science Foundation (no. 201104776); the opening foundation of the State Key Laboratory of Space Medicine Fundamentals and Application, Chinese Astronaut Research, and Training Center (no. SMFA11K02); and the National Natural Science Foundation of China (no. 81000018).
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Chang et al.
Richter E, Sarker S, Barrila J, Porwollik S, Cheng P, McClelland M, Tsaprallis G, Radabaugh T, Hunt A, Shah M, Nelman-Gonzalez M, Hing S, Parra M, Dumars P, Norwood K, Bober R, Devich J, Ruggles A, CdeBaca A, Narayan S, Benjamin J, Goulart C, Rupert M, Catella L, Schurr MJ, Buchanan K, Morici L, McCracken J, Porter MD, Pierson DL, Smith SM, Mergeay M, Leys N, Stefanyshyn-Piper HM, Gorie D, Nickerson CA. 2008. Media ion composition controls regulatory and virulence response of salmonella in spaceflight. PLoS One 3:e3923.
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