Comparative Genomics Suggests Primary Homothallism of Pneumocystis Species

ABSTRACT Pneumocystis species are fungal parasites of mammal lungs showing host specificity. Pneumocystis jirovecii colo-nizes humans and causes severe pneumonia in immunosuppressed individuals. In the absence of in vitro cultures, the life cycle of these fungi remains poorly known. Sexual reproduction probably occurs, but the system of this process and the mating type (MAT) genes involved are not characterized. In the present study, we used comparative genomics to investigate the issue in P. ji-rovecii and Pneumocystis carinii, the species infecting rats, as well as in their relative Taphrina deformans. We searched sex-related genes using 103 sequences from the relative Schizosaccharomyces pombe as queries. Genes homologous to several sex-related role categories were identified in all species investigated, further supporting sexuality in these organisms. Extensive in silico searches identified only three putativeMAT genes in each species investigated (matMc,matMi, andmatPi). In P. jirovecii, these genes clustered on the same contig, proving their contiguity in the genome. This organization seems compatible neither with heterothallism, because two differentMAT loci on separate DNAmolecules would have been detected, nor with secondary homothallism, because the latter involves generally moreMAT genes. Consistently, we did not detect cis-acting sequences for mating type switching in secondary homothallism, and PCR revealed identicalMAT genes in P. jirovecii isolates from six pa-tients. A strong synteny of the genomic region surrounding the putativeMAT genes exists between the two Pneumocystis species. Our results suggest the hypothesis that primary homothallism is the system of reproduction of Pneumocystis species and T. de-formans