Abstract
We present the scaffolded genome assembly of Pseudomonas aeruginosa Boston 41501, now publicly available in GenBank (JOVK00000000) in 10 contigs placed into a single scaffold. The 6.82-Mbp genome contains 66.1% G+C content and 6,295 coding sequences, including type 4 pilus and type 3 secretion system production genes.
GENOME ANNOUNCEMENT
Pseudomonas aeruginosa is a Gram-negative member of the Gammaproteobacteria found in a wide variety of environments (soil water, animals, humans, and hospitals). P. aeruginosa Boston 41501 (ATCC 27853) is a quality control strain often used in opportunistic pathogen research and originally isolated from a blood culture. Most human infections are hospital acquired and/or limited to immunocompromised persons. Recently the U.S. Centers for Disease Control and Prevention elevated the risk of antibiotic-resistant P. aeruginosa infection to “serious” due to estimates of 6,700 cases and 400 deaths annually (1).
High-quality genomic DNA was extracted from a stationary-phase purified isolate using a Qiagen Genomic-tip 500 at the USARMIID Diagnostic Systems Division (DSD) per the manufacturer’s recommendations. Draft sequence data included a 100-bp Illumina library (128-fold genome coverage) and a separate long-insert paired-end library (8,792- ± 2,198-bp insert, 35-fold genome coverage) (Roche 454 Titanium platform). The two data sets were assembled together in Newbler (Roche) and the consensus sequences computationally shredded into 2-kbp overlapping fake reads (shreds). The raw reads were also assembled in Velvet and those consensus sequences computationally shredded into 1.5-kbp overlapping shreds (2). Draft data from all platforms were then assembled together with Allpaths and the consensus sequences computationally shredded into 10-kbp overlapping shreds (3). We then integrated the Newbler consensus shreds, Velvet consensus shreds, Allpaths consensus shreds, and a subset of the long-insert read pairs using parallel Phrap (High Performance Software, LLC). Possible misassemblies were corrected, and some gap closure was accomplished with manual editing in Consed (4–6).
Automatic annotation of the P. aeruginosa Boston 41501 genome utilized an Ergatis-based workflow at LANL with minor manual curation. The final annotated assembly (6,295 coding sequences, 31 rRNAs, and 66 tRNAs in the 6,819,384-bp genome sequence) is available in GenBank (accession number JOVK00000000), and raw data can be provided upon request. Preliminary review of the annotations finds at least 28% of the virulence genes noted by Feinbaum et al. (7) and both type 4 pilus and type 3 secretion systems (8).
Nucleotide sequence accession number.
This genome sequence is available in GenBank under the accession number JOVK00000000.
ACKNOWLEDGMENTS
Funding for this effort was provided by the Defense Threat Reduction Agency’s Joint Science and Technology Office (DTRA J9-CB/JSTO).
This article is approved by LANL for unlimited release (LA-UR-14-25642).
Footnotes
Citation Minogue TD, Daligault HE, Davenport KW, Broomall SM, Bruce DC, Chain PS, Coyne SR, Gibbons HS, Jaissle J, Chertkov O, Freitas T, Rosenzweig CN, Xu Y, Johnson SL. 2014. Draft genome assembly of Pseudomonas aeruginosa quality control reference strain Boston 41501. Genome Announc. 2(5):e00960-14. 10.1128/genomeA.00960-14.
REFERENCES
- 1. Centers for Disease Control and Prevention (CDC) 2013. Antibiotic resistance threats in the United States. U.S. Centers for Disease Control and Prevention, Atlanta, GA. http://www.cdc.gov/drugresistance/threat-report-2013/pdf/ar-threats-2013-508.pdf [Google Scholar]
- 2. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18:821–829. 10.1101/gr.074492.107 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3. Butler J, MacCallum I, Kleber M, Shlyakhter IA, Belmonte MK, Lander ES, Nusbaum C, Jaffe DB. 2008. ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res. 18:810–820. 10.1101/gr.7337908 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4. Ewing B, Hillier L, Wendl MC, Green P. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175–185. 10.1101/gr.8.3.175 [DOI] [PubMed] [Google Scholar]
- 5. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186–194 [PubMed] [Google Scholar]
- 6. Gordon D, Abajian C, Green P. 1998. Consed: a graphical tool for sequence finishing. Genome Res. 8:195–202. 10.1101/gr.8.3.195 [DOI] [PubMed] [Google Scholar]
- 7. Feinbaum RL, Urbach JM, Liberati NT, Djonovic S, Adonizio A, Carvunis AR, Ausubel FM. 2012. Genome-wide identification of Pseudomonas aeruginosa virulence-related genes using a Caenorhabditis elegans infection model. PLOS Pathog. 8 e1002813. 10.1371/journal.ppat.1002813 [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8. Gellatly SL, Hancock RE. 2013. Pseudomonas aeruginosa: new insights into pathogenesis and host defenses. Pathog. Dis. 67:159–173. 10.1111/2049-632X.12033 [DOI] [PubMed] [Google Scholar]