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Draft genome sequence of Citrobacter freundii strain ST2, a γ-proteobacterium that produces N-acylhomoserine lactones.

Wang Y, Zhou J - Genom Data (2015)

Bottom Line: The results show that the genome size is 4.89 Mb with a G + C content of 51.96%. 4626 function proteins were predicted and 3647 proteins were assigned to COG functional categories.A predicted AHL-coding gene LuxR was found at contig 4 and the length was 1541 bp.LJSQ00000000.

View Article: PubMed Central - PubMed

Affiliation: Shenzhen Polytechnic, Shenzhen, Guangdong Province, PR China.

ABSTRACT
Citrobacter freundii strain ST2, isolated from the algae bloom sample, possesses an N-acylhomoserine lactone (AHL) production activity that secretes short-chain AHL molecules. In this study, we sequenced the complete genome of C. freundii strain ST2 to understand the molecular regulation of the AHL system and to search for the AHL gene in this bacterium. The results show that the genome size is 4.89 Mb with a G + C content of 51.96%. 4626 function proteins were predicted and 3647 proteins were assigned to COG functional categories. A predicted AHL-coding gene LuxR was found at contig 4 and the length was 1541 bp. The strain temporary deposited at Shenzhen Public Platform of Screening & Application of Marine Microbial Resources (Shenzhen, China), and the genome sequence can be accessed at GenBank under the accession no. LJSQ00000000.

No MeSH data available.


Related in: MedlinePlus

Function category distribution of Citrobacter freundii strain ST2 strain (based on COG function statistics).
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f0005: Function category distribution of Citrobacter freundii strain ST2 strain (based on COG function statistics).

Mentions: For the above-mentioned reasons, the draft genome sequence of C. freundii strain ST2 was determined. Genomic DNA of this bacterium was isolated using a DNA kit (Mo Bio, CA, USA) according the instructions of the manufacturer. The quality of DNA was examined using a Nanodrop spectrophotometer (Thermo Scientific, USA) and gel electrophoresis (Bio-Rad, USA). The whole-genome sequencing of C. freundii ST2 was performed using the Illumina Hiseq 2000 platform after the construction of the sequencing library using a Truseq DNA sample preparation kit, V2 (Illumina Inc. CA). After filtering the low-quality data, we assembled the short reads into a genome sequence using SOAP denovo v1.05, and the scaffolds were manually connected based on paired-end relationships. The gaps were filled using GapCloser with read mapping information. This resulted in 4,313,757 filtered reads and approximately 50-fold coverage. The filtered reads were de novo assembled with the CLC Genomic workstation v5.1, generating 21 contigs, containing 4,896,351 bp. The G + C content of this genome was 51.96%. Gene prediction was performed using prodigal (v260), and 4626 open reading frames were predicted [6]. Homologous comparisons by BLAST showed 3647 CDS involving the 21 functional COG groups and a part of the CDS involving the 34 metabolic pathway KEGG groups (Fig. 1). Annotation was performed using Blast2GO [7] against NCBI-NR sequence database [8]. One complete rRNA operon and one copy each of nine 5 s-rRNA gene, seven 16 s-rRNA gene, and six 23 s-rRNA gene were identified using RNAmmer [9]. A total of 79 tRNAs were identified using tRNAscan-SE [10]. In addition, 57 minisatellite DNAs and 3 microsatellite DNAs were determined based on the Repbase transposable elements library. The genome features of C. freundii strain ST2 were summarized in Table 1.


Draft genome sequence of Citrobacter freundii strain ST2, a γ-proteobacterium that produces N-acylhomoserine lactones.

Wang Y, Zhou J - Genom Data (2015)

Function category distribution of Citrobacter freundii strain ST2 strain (based on COG function statistics).
© Copyright Policy - CC BY-NC-ND
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664774&req=5

f0005: Function category distribution of Citrobacter freundii strain ST2 strain (based on COG function statistics).
Mentions: For the above-mentioned reasons, the draft genome sequence of C. freundii strain ST2 was determined. Genomic DNA of this bacterium was isolated using a DNA kit (Mo Bio, CA, USA) according the instructions of the manufacturer. The quality of DNA was examined using a Nanodrop spectrophotometer (Thermo Scientific, USA) and gel electrophoresis (Bio-Rad, USA). The whole-genome sequencing of C. freundii ST2 was performed using the Illumina Hiseq 2000 platform after the construction of the sequencing library using a Truseq DNA sample preparation kit, V2 (Illumina Inc. CA). After filtering the low-quality data, we assembled the short reads into a genome sequence using SOAP denovo v1.05, and the scaffolds were manually connected based on paired-end relationships. The gaps were filled using GapCloser with read mapping information. This resulted in 4,313,757 filtered reads and approximately 50-fold coverage. The filtered reads were de novo assembled with the CLC Genomic workstation v5.1, generating 21 contigs, containing 4,896,351 bp. The G + C content of this genome was 51.96%. Gene prediction was performed using prodigal (v260), and 4626 open reading frames were predicted [6]. Homologous comparisons by BLAST showed 3647 CDS involving the 21 functional COG groups and a part of the CDS involving the 34 metabolic pathway KEGG groups (Fig. 1). Annotation was performed using Blast2GO [7] against NCBI-NR sequence database [8]. One complete rRNA operon and one copy each of nine 5 s-rRNA gene, seven 16 s-rRNA gene, and six 23 s-rRNA gene were identified using RNAmmer [9]. A total of 79 tRNAs were identified using tRNAscan-SE [10]. In addition, 57 minisatellite DNAs and 3 microsatellite DNAs were determined based on the Repbase transposable elements library. The genome features of C. freundii strain ST2 were summarized in Table 1.

Bottom Line: The results show that the genome size is 4.89 Mb with a G + C content of 51.96%. 4626 function proteins were predicted and 3647 proteins were assigned to COG functional categories.A predicted AHL-coding gene LuxR was found at contig 4 and the length was 1541 bp.LJSQ00000000.

View Article: PubMed Central - PubMed

Affiliation: Shenzhen Polytechnic, Shenzhen, Guangdong Province, PR China.

ABSTRACT
Citrobacter freundii strain ST2, isolated from the algae bloom sample, possesses an N-acylhomoserine lactone (AHL) production activity that secretes short-chain AHL molecules. In this study, we sequenced the complete genome of C. freundii strain ST2 to understand the molecular regulation of the AHL system and to search for the AHL gene in this bacterium. The results show that the genome size is 4.89 Mb with a G + C content of 51.96%. 4626 function proteins were predicted and 3647 proteins were assigned to COG functional categories. A predicted AHL-coding gene LuxR was found at contig 4 and the length was 1541 bp. The strain temporary deposited at Shenzhen Public Platform of Screening & Application of Marine Microbial Resources (Shenzhen, China), and the genome sequence can be accessed at GenBank under the accession no. LJSQ00000000.

No MeSH data available.


Related in: MedlinePlus