Project description:Research into secondary metabolism (SM) production by fungi has resulted in the discovery of diverse, biologically active compounds with significant medicinal applications. The fungi rich in SM production are taxonomically concentrated in the subkingdom Dikarya, which comprises the phyla Ascomycota and Basidiomycota. Here, we explore the potential for SM production in Mucoromycota and Zoopagomycota, two phyla of nonflagellated fungi that are not members of Dikarya, by predicting and identifying core genes and gene clusters involved in SM. The majority of non-Dikarya have few genes and gene clusters involved in SM production except for the amphibian gut symbionts in the genus Basidiobolus Basidiobolus genomes exhibit an enrichment of SM genes involved in siderophore, surfactin-like, and terpene cyclase production, all these with evidence of constitutive gene expression. Gene expression and chemical assays also confirm that Basidiobolus has significant siderophore activity. The expansion of SMs in Basidiobolus are partially due to horizontal gene transfer from bacteria, likely as a consequence of its ecology as an amphibian gut endosymbiont.
Project description:Fungal genomes range in size from 2.3 Mb for the microsporidian Encephalitozoon intestinalis up to 8000 Mb for Entomophaga aulicae, with a mean genome size of 37 Mb. Basidiobolus, a common inhabitant of vertebrate guts, is distantly related to all other fungi, and is unique in possessing both EF-1? and EFL genes. Using DNA sequencing and a quantitative PCR approach, we estimated a haploid genome size for Basidiobolus at 350 Mb. However, based on allelic variation, the nuclear genome is at least diploid, leading us to believe that the final genome size is at least 700 Mb. We also found that EFL was in three times the copy number of its putatively functionally overlapping paralog EF-1?. This suggests that gene or genome duplication may be an important feature of B. ranarum evolution, and also suggests that B. ranarum may have mechanisms in place that favor the preservation of functionally overlapping genes.
Project description:Some cases of fungal infection remained undiagnosed, especially when the pathogens are uncommon, require specific conditions for in vitro growth, or when several microbial species are present in the specimen. Ultra-Deep Sequencing (UDS) could be considered as a precise tool in the identification of involved pathogens in order to upgrade patient treatment. In this study, we report the implementation of UDS technology in medical laboratory during the follow-up of an atypical fungal infection case. Thanks to UDS technology, we document the first case of gastro-intestinal basidiobolomycosis (GIB) due to Basidiobolus meristosporus. The diagnosis was suspected after histopathological examination but conventional microbiological methods failed to supply proof. The final diagnosis was made by means of an original approach based on UDS. DNA was extracted from the embedded colon biopsy obtained after hemicolectomy, and a fragment encompassing the internal transcribed spacer (ITS) rDNA region was PCR-amplified. An Amplicon library was then prepared using Genome Sequencer Junior Titanium Kits (Roche/454 Life Sciences) and the library was pyrosequenced on a GS Junior (Roche/454 Life Sciences). Using this method, 2,247 sequences with more than 100 bases were generated and used for UDS analysis. B. meristosporus represented 80% of the sequences, with an average homology of 98.8%. A phylogenetic tree with Basidiobolus reference sequences confirmed the presence of B. meristosporus (bootstrap value of 99%). Conclusion : UDS-based diagnostic approaches are ready to integrate conventional diagnostic testing to improve documentation of infectious disease and the therapeutic management of patients.
