Draft Genome Sequence of Penicillium marneffei Strain PM1

GENOME ANNOUNCEMENT

Penicillium marneffei is the most important thermal dimorphic, pathogenic fungus causing respiratory, skin, and systemic mycosis in China and Southeast Asia. The appearance of the HIV pandemic saw the emergence of opportunistic infections caused by P. marneffei in HIV-positive patients. About 8% of AIDS patients in Hong Kong are infected with P. marneffei (6). In Thailand, penicilliosis is the third most common indicator disease of AIDS, following tuberculosis and cryptococcosis (7). Aiming at improving our understanding of its mechanisms of pathogenesis and thermal dimorphism, the genome sequencing project of P. marneffei, in collaboration with the Beijing Genome Institute, was commenced in 2002.

The genome sequence of P. marneffei PM1 was determined with the whole-genome shotgun method, similarly to our previous sequencing of the Laribacter hongkongensis genome (10). PM1 was isolated from an HIV-negative patient suffering from culture-documented penicilliosis in Hong Kong. A genomic DNA library was made in pUC18 carrying inserts of 3.0 to 5.0 kb prepared by physical shearing using the sonication method. Single ends of 315,580 clones, representing a 6-fold coverage of the P. marneffei genome, were sequenced. The Phred/Phrap/Consed software package was used for base calling and sequence assembly (1–5). Protein-coding genes and introns were predicted using FGENESH (Softberry).

The draft genome of PM1 consists of 2,780 sequence contigs with a total length of 28,887,485 bp and a G+C content of 47%. Contigs were ordered into 273 supercontigs with a total length of 28.42 Mb. The number of protein-coding genes predicted was 10,060, with 9,257 (92%) longer than 100 amino acids. The average gene density is one gene per 2.8 kb. The protein-coding sequence occupies 62.1% (51.2% excluding introns) of the sequenced portion of the genome. An estimated total of 28,180 introns, varying from 15 to 1,617 nucleotides long with a mean length of 111 nucleotides, are distributed among 91% of P. marneffei genes. The telomere tandem repeat identified is TTAGGG.

With the availability of the draft genome sequence, the complete mitochondrial genome sequence of P. marneffei, a circular DNA molecule of 35,438 bp with a G+C content of 25%, was determined; the sequence was more closely related to those of molds than to those of yeasts (12). All meiotic genes (except HOP1) and genes encoding putative pheromone processing enzymes, pheromone receptors, and pheromone response pathway proteins in Aspergillus fumigatus and Aspergillus nidulans and a putative MAT-1α box mating-type gene were present, suggesting that P. marneffei can potentially be a heterothallic fungus that does not switch mating type (8). Genes encoding Mp1p homologues were identified and used for construction of a highly discriminative multilocus sequence typing scheme for P. marneffei (9). Twenty-three putative polyketide synthase (PKS) genes and two putative PKS-nonribosomal peptide synthase hybrid genes were identified, a diversity much higher than those of other pathogenic thermal dimorphic fungi, such as Histoplasma capsulatum (one PKS gene) and Coccidioides immitis (10 PKS genes) (11). Further in-depth analysis would uncover additional clues that explain the virulent and thermal dimorphic behaviors of this unique Penicillium species.