Philippe M. Hauser and Marco Pagni (Vital-IT group, Swiss Institute of Bioinformatics) are leaders of the Pneumocystis jirovecii genome sequence project supported by the Swiss National Science Foundation. P. jirovecii is a fungus which causes severe pneumonia in immunocompromised humans. The lack of a culture method in vitro has hampered progress in the understanding of its biology. Sequencing P. jirovecii genome is complicated by the fact that its DNA can be isolated only from bronchoalveolar lavage specimens or lungs of patients with Pneumocystis pneumonia. This implies small amounts of sample DNA and contamination with other DNAs, including from the host. Random DNA amplification followed by high throughput sequencing allow now to sequence P. jirovecii genome. In order to perform comparative genomics, we are also sequencing the genome of Taphrina deformans, a close relative infecting plants (P. jirovecii: http://www.ncbi.nlm.nih.gov/bioproject/68827 ; T. deformans: http://www.ncbi.nlm.nih.gov/bioproject/74523).
The P. jirovecii genome sequence is now published, and has been commented by the American Society for Microbiology.