Barcoding of fungal herbarium collections by next-generation sequencing technology


Since the publication of Nova Plantarum Genera by Pier Antonio Micheli in 1737, marking the start of modern mycology, researchers have described approximately 148,000 species of fungi. However, this only represents about 2.5–6.7% of the estimated diversity in the Kingdom Fungi. DNA barcoding is one of the modern tools to detect species diversity—and thus to discover undescribed species—faster and more accurately. Researchers identified the internal transcribed spacer (ITS) region of the ribosomal DNA as the universal barcode of fungi. This region consists of two spacer regions that surround the 5.8S component, which participates in the function of ribosomes and thus is very conservative. For the majority of fungi, the interspecific variation exceeds the intraspecific variation.


The ITS region is hard to amplify for species in some higher taxonomic groups. Both the ITS1 and ITS2 spacer regions are highly variable, and we do not know the extent of this variability in taxa for which no ITS sequence data exist. An important result of this variability is primer mismatches when we use standard universal or fungal primers. Second, PCR amplification success is low when herbarium collections are sequenced. An important reason for this is that the DNA of preserved material undergoes degradation.


The goal of this project is to test the usefulness of a next-generation sequencing technology in generating ITS barcodes of herbarium collections between 1 and 64 years old. The technology makes use of ribosomal regions that are more conservative and surround the entire ITS region. These are the small subunit (SSU) and large subunit (LSU) ribosomal RNA gene regions. The sequenced regions is between 4,000 and 6,000 base pairs in size. During this project, the student will become familiar with fungal nomenclature and taxonomy and with the challenges of molecular-based research. The results of this master’s project will be part of a multi-institutional publication.


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