Abstract
Enterococcus faecium is an opportunistic human pathogen, found widely in the human gastrointestinal tract, and can also be isolated from a variety of plants, animals, insects, and other environmental sources. Here, we present the fine draft genome sequence of E. faecium LCT-EF90.
GENOME ANNOUNCEMENT
Enterococci are common inhabitants of the human gastrointestinal (GI) tract (4, 9) and can also be cultivated from a variety of plants, animals, insects, and other environmental sources. For a long time, the species E. faecium was considered a harmless commensal of the mammalian GI tract and was used as a probiotic (7, 12) added to fermented foods (5); however, some strains have recently been recognized as pathogens (8, 9). E. faecium is a Gram-positive bacterium belonging to the family Enterococcaceae (10). Strain LCT-EF90 originated from an E. faecium strain (CGMCC 1.2136) that was cultured at different temperature (15°C versus 37°C) for more than 4 weeks. Cells occur singly, in pairs, or in chains. This strain has both aerobic and anaerobic cellular respiration pathways.
The genome of E. faecium was sequenced with an Illumina HiSeq 2000 instrument according to the manufacturer's instructions. High-molecular-mass genomic DNA from E. faecium was used to construct small (500-bp) and large (6-kb) random sequencing libraries. The mean read length is 90 bp for both the 500-bp and the 6,000-bp library. The reads were filtered and assembled into contigs using SOAPdenovo v1.05 (http://soap.genomics.org.cn/). Finally, 31 scaffolds consisting of 118 contigs were constructed step by step using all the paired-end information of reads with 120× and 70× genome coverage. The scaffold N50 and N90 were determined to be 1,498 kb and 108.5 kb, and the longest scaffold was 1,498 kb. The total length of the assembly was 2,773,995 bp, and the average GC content was about 38.24%.
Putative protein-coding sequences were predicted using the Glimmer 3.0 program (3). Overall, there were 2,777 predicted protein-coding sequences (CDSs) with an average gene length of 862 bp. To further verify these gene predictions, all gene functions were determined mainly by BLASTP analysis of sequences in the KEGG (6), COG, Swiss-Prot (12), TrEMBL (1), GO, and NR databases and by manual curation of the outputs of a variety of similarity searches. The results of analysis of COG database sequences showed that there were more genes clustered in the categories “Carbohydrate Transport” and “Metabolism” than in other function clusters. GO annotation analyses of the E. faecium genome revealed 20 categories, mainly containing genes for cellular components, binding, transporter activity, and catalytic activity, as well as genes for molecular functions and cellular and physiological processes.
We predicted the transposon sequences using RepeatMasker software (11) and RepeatProteinMasker software and tandem repeat sequences using TRF (Tandem Repeat Finder) (2). We identified different transposble element (TE)-related sequences, with 17 kb in total length, which occupy 0.62% of the assembly. In addition to protein-coding genes, noncoding RNA (ncRNA) sequences were also predicted, including small RNA (sRNA), rRNA, tRNA, snRNA, and micro-RNA. Genome island prediction was performed using IslandPath-DIOMB, SIGI-HMM, IslandPicker, and IslandViewer software. IslandPath-DIOMB and SIGI-HMM are prediction programs based on sequence comparison; IslandPicker is based on genome comparison, and IslandViewer is the combination of the three preceding software programs. In addition, the prophage sequences predicted by Prohinder software and the ACLAME database and CRISPRs predicted from CRISPRFinder software were carried on. Genome island sequences were also obtained, but no prophage sequences or prophage sequences were found.
Nucleotide sequence accession number.
This whole-genome sequence has been deposited at DDBJ/EMBL/GenBank under accession number AJKH00000000. The versions described in this paper are the first versions.
ACKNOWLEDGMENTS
This work was supported by the Key Pre-Research Foundation of Military Equipment of China (grant 9140A26040312JB1001), the opening foundation of the State Key Laboratory of Space Medicine Fundamentals and Application, Chinese Astronaut Research and Training Center (grant SMFA11K02), a Special Financial Grant from the China Postdoctoral Science Foundation (grant 201104776), and the National Natural Science Foundation of China (grant 81000018).
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