Morphological and genomic characterization of Filobasidiella depauperata: a homothallic sibling species of the pathogenic cryptococcus species complex.

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The fungal species Cryptococcus neoformans and Cryptococcus gattii cause respiratory and neurological disease in animals and humans following inhalation of basidiospores or desiccated yeast cells from the environment. Sexual reproduction in C. neoformans and C. gattii is controlled by a bipolar system in which a single mating type locus (MAT) specifies compatibility. These two species are dimorphic, growing as yeast in the asexual stage, and producing hyphae, basidia, and basidiospores during the sexual stage. In contrast, Filobasidiella depauperata, one of the closest related species, grows exclusively as hyphae and it is found in association with decaying insects. Examination of two available strains of F. depauperata showed that the life cycle of this fungal species shares features associated with the unisexual or same-sex mating cycle in C. neoformans. Therefore, F. depauperata may represent a homothallic and possibly an obligately sexual fungal species. RAPD genotyping of 39 randomly isolated progeny from isolate CBS7855 revealed a new genotype pattern in one of the isolated basidiospores progeny, therefore suggesting that the homothallic cycle in F. depauperata could lead to the emergence of new genotypes. Phylogenetic analyses of genes linked to MAT in C. neoformans indicated that two of these genes in F. depauperata, MYO2 and STE20, appear to form a monophyletic clade with the MATa alleles of C. neoformans and C. gattii, and thus these genes may have been recruited to the MAT locus before F. depauperata diverged. Furthermore, the ancestral MATa locus may have undergone accelerated evolution prior to the divergence of the pathogenic Cryptococcus species since several of the genes linked to the MATa locus appear to have a higher number of changes and substitutions than their MATalpha counterparts. Synteny analyses between C. neoformans and F. depauperata showed that genomic regions on other chromosomes displayed conserved gene order. In contrast, the genes linked to the MAT locus of C. neoformans showed a higher number of chromosomal translocations in the genome of F. depauperata. We therefore propose that chromosomal rearrangements appear to be a major force driving speciation and sexual divergence in these closely related pathogenic and saprobic species.





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Rodriguez-Carres, Marianela, Keisha Findley, Sheng Sun, Fred S Dietrich and Joseph Heitman (2010). Morphological and genomic characterization of Filobasidiella depauperata: a homothallic sibling species of the pathogenic cryptococcus species complex. PLoS One, 5(3). p. e9620. 10.1371/journal.pone.0009620 Retrieved from

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Fred Samuel Dietrich

Associate Professor of Molecular Genetics and Microbiology

My laboratory is interested in fungal genomics.

In particular we use genomic sequencing of fungal strains and species in comparative analysis. Starting with the sequencing of Saccharomyces cerevisiae strain S288C, I have been involved in the genome sequencing and annotation of Ashbya gossypiiCryptococcus neoformans var. grubii and ~100 additional S. cerevisiae strains. We currently use Illumina paired end and mate paired sequencing, as this is at presently the most cost effective widely used technology capable of generating high accuracy, zero gap whole genome sequences. The 100-genomes S. cerevisiae data as well as the fully updated fully annotated A. gossypii sequence (Genbank numbers AE016814-AE016820), which spans all seven chromosomes from telomere to telomere, were generated using Illumina data. In my laboratory we strive to utilize comparative genomics data to understand aspects of basic fungal biology. Some of our specific areas of interest are filamentous growth, mapping of complex traits, horizontal gene transfer, and identification of RNA coding genes. This work involves a combination of experimental work and bioinformatics analysis. Research in S. cerevisiae has greatly benefitted from an accurate, annotated S. cerevisiae reference genome, and that research into the tremendous diversity in this organism will similarly benefit from the availability of a large number of accurate, fully annotated genome sequences. The use of genomic information to better understand the biology of these organisms, and this is what students in my laboratory generally work on.

What is the set of genes found in a pathogenic fungus such as Cryptococcus?

Our interest in this human pathogen is to expand beyond looking at one isolate and to investigate the diversity in the population. Are there genes found in some Cryptococcus neoformans isolates but not in others? Are there regions of the genome or individual genes which are highly diverged between Cryptococcus isolates? Efforts are now underway at Stanford University to sequence the genome of the JEC21 strain of Cryptococcus. This is a strain that has been agreed upon by the community of Cryptococcus researchers as a reference strain. Obtaining the DNA sequence of this strain is only the start however. From that sequence identifying the complete set of genes will be a considerable challenge requiring both bioinformatic as well as experimental tools. While this work on gene identification is going on we plan on addressing the question of how much do other Cryptococcus isolates differ from JEC21.

What is the set of genes in humans?

The complete DNA sequence of human and mouse will become available soon. This does not mean that we will know the complete set of human or mouse genes. Our current state of knowledge does not allow us to accurately predict human genes directly from DNA sequence. We are interested in applying to the human genome some of the experimental and bioinformatic tools we are developing and utilizing in fungal systems.

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