E SCHMID-SIEGERT ¹, S RICHARD ², M PAGNI¹, PM HAUSER<sup>2

1</sup>Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland , ²Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland

Pneumocystis jirovecii is an obligate parasite that causes severe pneumonia in immuno-compromised individuals. The lack of culture in vitro for this fungal pathogen complicates its study. Using high throughput sequencing and a dedicated bioinformatics strategy, we recently succeeded in assembling the P. jirovecii genome from a single bronchoalveolar lavage fluid specimen from a patient. However, telomeres could not be assembled because of the repetitive nature of both their sequences and the subtelomeric gene families encoding varying surface antigens. In the present work, we used single molecule real-time sequencing and dedicated bioinformatics to assemble the P. jirovecii telomeres from a patient infected with a single strain. Three different families of genes encoding isoforms of the major surface glycoprotein were identified: (i) classic, (ii) without the 5’ conserved sequence, and (iii) pseudogenic. A single classic gene would be expressed in each cell thanks to its localization downstream of a subtelomeric expression site which is present at a single copy in the genome. The localization of the classic genes within the proximal regions of the subtelomeres suggests that exchange of telomeres’ ends through recombination at the 5’ conserved sequence might be responsible for changes of the expressed isoform. The absence of the 5’ conserved sequence in the second family, and the localization of this family in distal regions of the subtelomeres suggest that these genes are not expressed but might be involved in recombination events creating mosaic classic genes. The studied population of P. jirovecii cells appeared to share a core of telomeres which provided the isoform present at the expression site that we identified by PCR in several subpopulations. Other families of genes encoding other surface proteins were also present in the subtelomeres. The expression of the latter genes remains to be characterized.