Abstract
Pseudomonas aeruginosa AH16 is a virulent strain isolated from a patient with chronic pneumonia in China. Here, we present a 6.8-Mb (G+C content, 66.13%) assembly of its genome with 6,332 putative coding sequences, which may provide insights into the genomic basis of activity of the clinical P. aeruginosa strain in China.
GENOME ANNOUNCEMENT
Pseudomonas aeruginosa is a Gram-negative human pathogen and a ubiquitous environmental bacterium found in soil and water (5). P. aeruginosa is an important nosocomial infection pathogen (1) and community-acquired pathogen (8) in China. The genome of P. aeruginosa is formed by a conserved core genome and diversity accessory genome consisting of genomic islands, prophages, transposons, and insert sequences (5). However, no genome sequence information on the clinical P. aeruginosa strain isolated in China is available. Strain AH16 was isolated from a sputum sample from a patient with chronic pneumonia in Anhui Province, China. It is more virulent and produces more biofilm than the laboratory P. aeruginosa strain. Therefore, the genome sequence of strain AH16 will help us to understand the pathogenesis and genome evolution of this pathogen.
The genome of P. aeruginosa AH16 was sequenced using the 454 Genome Sequencer FLXPlus platform (Roche) to generate 250,644 reads and approximately 120 Mb of raw data. The reads were assembled into 130 contigs (larger than 500 bp) using the Newbler software. In the assembled contigs, the average, maximum, and minimum lengths are 52,040 bp, 537,227 bp, and 517 bp, respectively. The open reading frames (ORFs) were predicted using Glimmer 3.02 (2) and Zcurve (4). The ORF of strain AH16 was annotated by searching the NR database (11) and SEED database (http://www.theseed.org/). The rRNA and tRNA genes were identified by RNAmmer 1.2 (6) and tRNAscan-SE (9), respectively. The metabolic pathways were examined through KAAS (KEGG Automatic Annotation Server) (10). The insert sequence (IS) and clustered regularly interspaced short palindromic repeats (CRISPRs) were predicted by IS Finder (http://www-is.biotoul.fr/) and CRISPRFinder (3), respectively. Comparative genome analysis was performed with mGenomeSubtractor (12).
The draft genome sequence of P. aeruginosa AH16 consists of 6,765,326 bases with a G+C content of 66.13%. The assembled genome has approximately 17.7-fold coverage, with an N50 contig size of 93,892 bp. There are 6,332 putative coding sequences (CDS), 58 tRNA genes, 4 rRNA operons, and 15 ISs in strain AH16. Interestingly, no CRISPRs were found in the genome of strain AH16, indicating the possible reason for the formation of the larger accessory genome. In comparison with other genome sequences of P. aeruginosa strains, strain AH16 shares a conserved core genome (nearly 90%) and a divergent accessory genome consisting of several pathogenicity islands, antibiotic resistance islands, and prophages, including homologues of pathogenicity island PAPI-1 and three virulence-related islands in strain LESB58. Eleven antibiotic resistance genes, which are associated with the resistance to β-lactam, aminoglycoside, chloramphenicol, and fluoroquinolone, were identified by the ARDB database (7).
More detailed analysis of the announced genome and a comparative analysis with the genomes of other P. aeruginosa strains remain to be done in a future study.
Nucleotide sequence accession numbers.
This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under accession no. ALJH00000000. The version described in this paper is the first version, ALJH01000000.
ACKNOWLEDGMENTS
We are grateful to Huajun Zheng and colleagues for genome sequencing performed at the Chinese National Human Genome Center at Shanghai.
This work was funded by the National Natural Science Foundation of China (no. 81173629).
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