Skip to Main Content
Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungiAuthor(s): Daniel L. Lindner; Tor Carlsen; Henrik Nilsson; Marie Davey; Trond Schumacher; Havard Kauserud
Source: Ecology and Evolution. 3(6): 1751-1764.
Publication Series: Scientific Journal (JRNL)
Station: Northern Research Station
Download Publication (1.61 MB)
DescriptionThe rDNA internal transcribed spacer (ITS) region has been accepted as a DNA barcoding marker for fungi and is widely used in phylogenetic studies; however, intragenomic ITS variability has been observed in a broad range of taxa, including prokaryotes, plants, animals, and fungi, and this variability has the potential to inflate species richness estimates in molecular investigations of environmental samples. In this study 454 amplicon pyrosequencing of the ITS1 region was applied to 99 phylogenetically diverse axenic single-spore cultures of fungi (Dikarya: Ascomycota and Basidiomycota) to investigate levels of intragenomic variation. Three species (one Basidiomycota and two Ascomycota), in addition to a positive control species known to contain ITS paralogs, displayed levels of molecular variation indicative of intragenomic variation; taxon inflation due to presumed intragenomic variation was ≈9%. Intragenomic variability in the ITS region appears to be widespread but relatively rare in fungi (≈3-5% of species investigated in this study), suggesting this problem may have minor impacts on species richness estimates relative to PCR and/or pyrosequencing errors. Our results indicate that 454 amplicon pyrosequencing represents a powerful tool for investigating levels of ITS intragenomic variability across taxa, which may be valuable for better understanding the fundamental mechanisms underlying concerted evolution of repetitive DNA regions.
- Check the Northern Research Station web site to request a printed copy of this publication.
- Our on-line publications are scanned and captured using Adobe Acrobat.
- During the capture process some typographical errors may occur.
- Please contact Sharon Hobrla, email@example.com if you notice any errors which make this publication unusable.
- We recommend that you also print this page and attach it to the printout of the article, to retain the full citation information.
- This article was written and prepared by U.S. Government employees on official time, and is therefore in the public domain.
CitationLindner, Daniel L.; Carlsen, Tor; Nilsson, Henrik; Davey, Marie; Schumacher, Trond; Kauserud, Havard. 2013. Employing 454 amplicon pyrosequencing to reveal intragenomic divergence in the internal transcribed spacer rDNA region in fungi. Ecology and Evolution. 3(6): 1751-1764.
KeywordsEnvironmental sequencing, operational taxonomic units, pyrosequencing, species richness
- Improving ITS sequence data for identification of plant pathogenic fungi
- Conservation and management of forest fungi in the Pacific Northwestern United States: an integrated ecosystem approach.
- Revision of leccinoid fungi, with emphasis on North American taxa, based on molecular and morphological data
XML: View XML