Draft Genome Sequence of Pseudomonas aeruginosa Strain ATCC 27853

Abstract

Pseudomonas aeruginosa is a common bacterium that can cause disease. The versatility of Pseudomonas aeruginosa enables the organism to infect damaged tissues or those with reduced immunity which cause inflammation and sepsis. Here we report the genome sequence of the strain ATCC 27853.

GENOME ANNOUNCEMENT

Pseudomonas aeruginosa is a common bacterium that can cause disease in animals and humans. It is found in soil, water, skin flora, and most man-made environments throughout the world. It is an opportunistic pathogen for both humans and plants (2). Pseudomonas aeruginosa ATCC 27853 is usually used to test antimicrobial activity (6). Its genome sequencing will help us to understand the pathogenesis of this pathogen. Pseudomonas aeruginosa ATCC 27853 was obtained from the China General Microbiological Culture Collection Center (CGMCC) as CGMCC 1.2387.

A total of 850 million base pairs of reads were generated using Illumina Genome Analyzer II at BGI-Shenzhen (BGI; Shenzhen, China), and 296 contigs in 124 scaffolds were assembled with the SOAPdenovo program (4) based on paired-end reads. The genome sequence of the strain ATCC 27853 was estimated to be 6.46 Mb in size based on 15Kmer analysis, while a total of 6,887,913 bp (scaffold length) were assembled and the G+C content was determined to be 66.15%. All reads provided about 111-fold coverage of the genome. Fifty-four copies of tRNA genes were predicted by the tRNAscan-SE server (5). The prediction of rRNA copies was not accurate because the short reads (average length of 100 bp) generated by Illumina technology are not suitable for its prediction. In addition, 5S, 16S, and 23S rRNAs were identified using RNAmmer (3), and the total lengths were 114 bp, 1,523 bp, and 2,888 bp, respectively. In total, 6,474 putative open reading frames were identified using Glimmer v.3.0 (1), with the length ranging from 114 bp to 13,029 bp, and the average length was 946 bp, giving a coding intensity of 88.68%. A total of 3,240 protein-coding sequences (CDSs) were located in one strand, and the other 3,243 were located in the other strand. All CDSs were translated into amino acid sequences and searched against the COG, KEGG, Swiss-Prot, TrEMBL, and NR databases.

Based on the searching results, 3,391 CDSs were classified into 22 functional COG groups, and 5,403, 2,959, 6,196, and 3,806 CDSs were assigned to the NR, Swiss-Prot, TrEMBL, and KEGG databases, respectively. Two hundred thirty-two CDSs have no annotation information in these databases at all. Comparative genomic analyses were performed using the genome sequence of Pseudomonas aeruginosa PAO1 (GenBank accession number NC_002516.2) as a reference. All reads were aligned against strain PAO1 using SOAPaligner, and the genome coverage was determined to be 95% and the genome depth was ∼120×. Accordingly, 95% of the total gene length of PAO1 was covered by our reads. All four known plasmids (GenBank accession numbers NC_008357, NC_009739, NC_010722, and NC_007100) found in Pseudomonas aeruginosa were also aligned with the reads, using SOAPaligner to determine the possible plasmid in our strain. Unfortunately, the genome coverage was less than 10% for all four plasmids. A plasmid (GenBank accession number NC_010891) derived from Pseudomonas sp. CT14 was covered more than 31%, and the covered region was composed of two fragments and the coverage was 120×, indicating that the two fragments might have originated from this plasmid and been integrated into the genome.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession number AJKG00000000. The version described in this paper is the first version, AJKG01000000.