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PMID: 21434928 Published · ppublish English Evaluation Study Journal Article Research Support, Non-U.S. Gov't

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

The New phytologist ·Vol. 191 ·No. 1 ·2011-07-00 ·Pages 288-300

Kelly LJ, Hollingsworth PM, Coppins BJ, Ellis CJ, Harrold P, Tosh J, Yahr R

Abstract

• 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.

MeSH Terms
DNA Barcoding, Taxonomic DNA, Fungal/chemistry DNA, Ribosomal Spacer/chemistry Lichens/classification,genetics Nucleic Acid Amplification Techniques Phylogeny Sequence Analysis, DNA Species Specificity Usnea/classification,genetics
Chemicals
DNA, Fungal DNA, Ribosomal Spacer
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Kelly Laura J
Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK. | Present address: Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3DS, UK.
Hollingsworth Peter M
Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK.
Coppins Brian J
Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK.
Ellis Christopher J
Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK.
Harrold Paul
Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK.
Tosh James
Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK.
Yahr Rebecca
Science Division, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK.
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Article Info
Journal
The New phytologist
Abbr.
New Phytol
ISSN
1469-8137
DOI
10.1111/j.1469-8137.2011.03677.x
Published
2011-07-00
Epub
2011-00-22
Pages
288-300
Language
English
Region
England
NLM ID
9882884
Subset
IM
Grants
Medical Research Council · MR/K001744/1 · United Kingdom
External Links
PubMed source DOI: 10.1111/j.1469-8137.2011.03677.x View journal details
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