De novo assembly of the Pneumocystis jirovecii genome from a single bronchoalveolar lavage fluid specimen from a patient

mBio

Volumn 4, Issue 1, 2013, Pages

  Cissé, Ousmane H ^a,b   Pagni, Marco ^b   Hauser, Philippe M ^a  

^a LAUSANNE UNIVERSITY HOSPITAL   (Switzerland)

^b SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL RNA; GENOMIC DNA; RIBOSOME RNA; AMINO ACID; FUNGAL DNA; VIRULENCE FACTOR;

AMINO ACID METABOLISM; AMINO ACID SYNTHESIS; ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; FUNGAL GENOME; GENOME ANALYSIS; GENOME SIZE; HUMAN; LUNG LAVAGE; MICROBIOME; NONHUMAN; PHYLOGENETIC TREE; PNEUMOCYSTIS JIROVECI; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE ANALYSIS; BIOSYNTHESIS; CHEMISTRY; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; PHYLOGENY; PNEUMOCYSTIS PNEUMONIA;

AMINO ACIDS; BASE COMPOSITION; BIOSYNTHETIC PATHWAYS; BRONCHOALVEOLAR LAVAGE FLUID; DNA, FUNGAL; GENOME, FUNGAL; HUMANS; PHYLOGENY; PNEUMOCYSTIS JIROVECII; PNEUMONIA, PNEUMOCYSTIS; SEQUENCE ANALYSIS, DNA; VIRULENCE FACTORS;

EID: 84874633718     PISSN: 21612129     EISSN: 21507511     Source Type: Journal    
DOI: 10.1128/mBio.00428-12     Document Type: Article

References (16)

1. Thomas CF, Jr, limper AH. 2007. Current insights into the biology and pathogenesis of Pneumocystis pneumonia. Nat. Rev. Microbiol. 5:298-308.
2. Lu JJ, et al. 1994. Typing of Pneumocystis carinii strains that infect humans based on nucleotide sequence variations of internal transcribed spacers of rRNA genes. J. Clin. Microbiol. 32:2904-2912.
3. Cushion MT, et al. 2007. Transcriptome of Pneumocystis carinii during fulminate infection: carbohydrate metabolism and the concept of a compatible parasite. PLoS One 2:e423. http://dx.doi.org/10.1371/journal.pone.0000423.
4. Hauser PM, et al. 2010. Comparative genomics suggests that the fungal pathogen pneumocystis is an obligate parasite scavenging amino acids from its host's lungs. PLoS One 5:e15152. http://dx.doi.org/10.1371 /journal.pone.0015152.
5. Payne SH, Loomis WF. 2006. Retention and loss of amino acid biosynthetic pathways based on analysis of whole-genome sequences. Eukaryot. Cell 5:272-276.
6. Cushion MT, Stringer JR. 2010. Stealth and opportunism: alternative lifestyles of species in the fungal genus Pneumocystis. Annu. Rev. Microbiol. 64:431-452.
7. Merhej V, Royer-Carenzi M, Pontarotti P, Raoult D. 2009. Massive comparative genomic analysis reveals convergent evolution of specialized bacteria. Biol. Direct 4:13.
8. Lorenz MC, Fink GR. 2001. The glyoxylate cycle is required for fungal virulence. Nature 412:83-86.
9. Demanche C, et al. 2001. Phylogeny of Pneumocystis carinii from 18 primate species confirms host specificity and suggests coevolution. J. Clin. Microbiol. 39:2126-2133.
10. Wakefield AE, Stringer JR, Tamburrini E, Dei-Cas E. 1998. Genetics, metabolism and host specificity of Pneumocystis carinii. Med. Mycol. 36(Suppl 1):183-193.
11. Vargas SL, et al. 2001. Search for primary infection by Pneumocystis carinii in a cohort of normal, healthy infants. Clin. Infect. Dis. 32: 855-861.
12. Vargas SL, et al. 2010. Pneumocystis colonization in older adults and diagnostic yield of single versus paired noninvasive respiratory sampling. Clin. Infect. Dis. 50:e19-e21.
13. Vargas SL, et al. 2003. Pregnancy and asymptomatic carriage of Pneumocystis jiroveci. Emerg. Infect. Dis. 9:605-606.
14. Miller RF, Ambrose HE, Wakefield AE. 2001. Pneumocystis carinii f. sp. hominis DNA in immunocompetent health care workers in contact with patients with P. carinii pneumonia. J. Clin. Microbiol. 39:S89-S91.
15. Slaven BE, et al. 2006. Draft assembly and annotation of the Pneumocystis carinii genome. J. Eukaryot. Microbiol. 53(Suppl 1):S89-S91.
16. Sesterhenn TM, et al. 2010. Sequence and structure of the linear mitochondrial genome of Pneumocystis carinii. Mol. Genet. Genomics 283: 63-72.