Fungal DNA barcoding
DNA barcoding projects at Kew include harvesting sequences from fungarium specimens to populate publicly accessible sequence databases, identification of mycorrhizal fungi on plant roots, and diversity surveys of tropical macrofungi.
Diversity of mushrooms collected at a cloud forest reserve on the western slopes of the Andes in northwest Ecuador (above) and a snapshot of a DNA sequence chromatogram from a DNA sequencer (below). (Photo: Bryn Dentinger)
DNA barcoding is a systematic way to link DNA data with reference specimens to facilitate identification. There is a lack of DNA sequence data associated with the record number of specimens in Kew's fungal collection; currently only about 400 out of its ~1.25 million specimens are represented in GenBank. This neglect masks the true value of Kew's fungarium, which, being the largest and one of the most extensive collections of fungi from around the world, offers a tremendous opportunity for generating voucher-based DNA barcodes. Barcoding of Kew's fungarium will provide invaluable service to the scientific community as well as improve public access to the information contained within this extensive repository of preserved fungi.
The objectives of this project are to develop a high specimen throughput facility for DNA barcoding one of the world's premier fungal collections, to investigate options for enhancement of the fungal identification services carried out at Kew, to investigate inter- and intra-specific genetic diversity and species delimitation, and thus to enhance the utility and value of the collections held in Kew's fungarium.
Kew Mycology has been involved in fundamental work to establish an official barcode marker for fungi. A recent study compared the utility of the "universal barcode" marker, a portion of the mitochondrial cytochrome oxidase I gene (a.k.a. COI or COX1), with the most widely used genetic region for identification of fungi (nuclear ribosomal internal transcribed spacers; ITS) for DNA barcoding in mushrooms and allies (Dentinger et al. 2011). It was demonstrated that the COI gene in mushrooms and allies can be interrupted by multiple large introns at variable locations, introducing an insurmountable technical hindrance to high-throughput data generation with this locus. Moreover, COI sequences compared directly with ITS were less variable and, ultimately, unable to distinguish among closely related species of Boletus that were resolved using ITS. This work has contributed to a recently submitted, formal proposal to designate ITS as the official DNA barcode marker for Fungi (Schoch et al., submitted).
Another study into the use of the fungal collections at Kew in order to enhance the taxonomic coverage in GenBank has been carried out (Brock et al. 2009). DNA sequences of the ITS region were generated from a diverse set of 279 specimens, and bioinformatic analyses showed that c. 70% of the fungarium taxonomic diversity was not yet represented in GenBank and that a further c. 10% of the sequences matched solely to "environmental samples'" or fungi otherwise unidentified. It is concluded that the not-yet-sampled diversity residing in fungaria can substantially enlarge the coverage of GenBank's fully identified sequence pool to ameliorate the problem of environmental unknowns and to aid in the detection of truly novel fungi by molecular data.
Several additional current but independent research projects at Kew are using DNA barcoding methods. For example, DNA barcoding is being applied to understanding species diversity of British waxcaps (genus Hygrocybe) and earthtongues (family Geoglossaceae), the ecology of mycorrhizae, and coevolution of mushrooms, insects, and orchids in a tripartite mimicry system.
Key publications 2006-2011:
- Dentinger, B.T.M., Didukh, M.Y. Moncalvo, J.-M. (2011). Comparing COI and ITS as DNA barcode markers for mushrooms and allies (Agaricomycotina). PLoS ONE 6(9): e25081. doi:10.1371/journal.pone.0025081
- Bidartondo, M.I., Brock, P.M. & Doring, H. (2009). How to know unknown fungi: the role of a herbarium. New Phytol. 181: 719-724.
- Bidartondo, M.I., Ameri, G. & Doring, H. (2009). Closing the mycorrhizal DNA sequence gap. Mycological Research 113: 1025-1026.