12 research outputs found
Comparing COI and ITS as DNA Barcode Markers for Mushrooms and Allies (Agaricomycotina)
DNA barcoding is an approach to rapidly identify species using short, standard genetic markers. The mitochondrial cytochrome oxidase I gene (COI) has been proposed as the universal barcode locus, but its utility for barcoding in mushrooms (ca. 20,000 species) has not been established. We succeeded in generating 167 partial COI sequences (âŒ450 bp) representing âŒ100 morphospecies from âŒ650 collections of Agaricomycotina using several sets of new primers. Large introns (âŒ1500 bp) at variable locations were detected in âŒ5% of the sequences we obtained. We suspect that widespread presence of large introns is responsible for our low PCR success (âŒ30%) with this locus. We also sequenced the nuclear internal transcribed spacer rDNA regions (ITS) to compare with COI. Among the small proportion of taxa for which COI could be sequenced, COI and ITS perform similarly as a barcode. However, in a densely sampled set of closely related taxa, COI was less divergent than ITS and failed to distinguish all terminal clades. Given our results and the wealth of ITS data already available in public databases, we recommend that COI be abandoned in favor of ITS as the primary DNA barcode locus in mushrooms
Evolution of group I introns in Porifera: new evidence for intron mobility and implications for DNA barcoding
erformance of the COX1 gene as a marker for the study of metabolically active Pezizomycotina and Agaricomycetes fungal communities from the analysis of soil RNA
International audienceIn temperate forest soils, filamentous ectomycorrhizal and saprotrophic fungi affiliated to the Agaricomycetes and Pezizomycotina contribute to key biological processes. The diversity of soil fungal communities is usually estimated by studying molecular markers such as nuclear ribosomal gene regions amplified from soil-extracted DNA. However, this approach only reveals the presence of the corresponding genomic DNA in the soil sample and may not reflect the diversity of the metabolically active species. To circumvent this problem, we investigated the performance of the mitochondrial cytochrome c oxidase 1 (COX1)-encoding gene as a fungal molecular marker for environmental RNA-based studies. We designed PCR primers to specifically amplify Agaricomycetes and Pezizomycotina COX1 partial sequences and amplified them from both soil DNA and reverse-transcribed soil RNA. As a control, we also amplified the nuclear internal transcribed spacer ribosomal region from soil DNA. Fungal COX1 sequences were readily amplified from soil-extracted nucleic acids and were not significantly contaminated by nontarget sequences. We show that the relative abundance of fungal taxonomic groups differed between the different sequence data sets, with for example ascomycete COX1 sequences being more abundant among sequences amplified from soil DNA than from soil cDNAs
Development of a real-time PCR targeting the yidC gene for the detection of Mycoplasma hominis and comparison with quantitative culture
Mitochondrial Genome of Phlebia radiata Is the Second Largest (156 kbp) among Fungi and Features Signs of Genome Flexibility and Recent Recombination Events
Identification and Subtyping of Clinically Relevant Human and Ruminant Mycoplasmas by Use of Matrix-Assisted Laser Desorption IonizationâTime of Flight Mass Spectrometry
Phylogenetics of Mycoplasma hominis clinical strains associated with gynecological infections or infertility as disclosed by an expanded multilocus sequence typing scheme
The intraspecific variability of mitochondrial genes of Agaricus bisporus reveals an extensive group I intron mobility combined with low nucleotide substitution rates
Agaricus subrufescens : A review
International audienceMedicinal mushrooms have currently become a hot issue due to their various therapeutic properties. Of these, Agaricus subrufescens, also known as the "almond mushroom", has long been valued by many societies (i.e., Brazil, China, France, and USA). Since its discovery in 1893, this mushroom has been cultivated throughout the world, especially in Brazil where several strains of A. subrufescens have been developed and used as health food and alternative medicine. This article presents up-to-date information on this mushroom including its taxonomy and health promoting benefits. Medicinal properties of A. subrufescens are emphasized in several studies which are reviewed here. In addition, safety issues concerning the use of this fungus will be discussed