DNA barcoding of lichenized fungi demonstrates high identification success in a floristic context

• Published in: The New phytologist Vol. 191; no. 1; pp. 288 - 300
• Main Authors: Kelly, Laura J., Hollingsworth, Peter M., Coppins, Brian J., Ellis, Christopher J., Harrold, Paul, Tosh, James, Yahr, Rebecca
• Format: Journal Article
• Language: English
• Published: Oxford, UK John Wiley & Sons 01.07.2011; Blackwell Publishing Ltd; Wiley Subscription Services, Inc
• Subjects: Bar codes; Biological taxonomies; Context; Datasets; Deoxyribonucleic acid; DNA; DNA barcoding; DNA Barcoding, Taxonomic; DNA, Fungal - chemistry; DNA, Ribosomal Spacer - chemistry; Fungi; Gene sequencing; Genera; internal transcribed spacer; Internal transcribed spacers; lichen; lichenized fungi; Lichens; Lichens - classification; Lichens - genetics; Mycology; Nucleic Acid Amplification Techniques; Phylogeny; Polymerase chain reaction; Ribosomal DNA; Sequence Analysis, DNA; Species; Species diversity; species identification; Species Specificity; Specimens; Taxonomy; Usnea; Usnea - classification; Usnea - genetics
• ISSN: 0028-646X; 1469-8137
• DOI: 10.1111/j.1469-8137.2011.03677.x

Efforts are currently underway to establish a standard DNA barcode region for fungi; we tested the utility of the internal transcribed spacer (ITS) of nuclear ribosomal DNA for DNA barcoding in lichen-forming fungi by sampling diverse species across eight orders. Amplification of the ITS region (ITS1—5.8S—ITS2) was conducted for 351 samples, encompassing 107, 55 and 28 species, genera and families, respectively, of lichenized fungi. We assessed the ability of the entire ITS vs the ITS2 alone to discriminate between species in a taxonomic dataset (members of the genus Usnea) and a floristic dataset. In the floristic dataset, 96.3% of sequenced samples could be assigned to the correct species using ITS or ITS2; a barcode gap for ITS is present in 92.1% of species. Although fewer species have a barcode gap in the taxonomic dataset (73.3% with ITS and 68.8% with ITS2), up to 94.1% of samples were assigned to the correct species using BLAST. While discrimination between the most closely related species will remain challenging, our results demonstrate the potential to identify a high percentage of specimens to the correct species, and the remainder to the correct genus, when using DNA barcoding in a floristic context.