Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi
Внутренний транскрибируемый спейсерный (ITS) регион ядерной рибосомной ДНК как универсальный маркер ДНК-штрихкодирования грибов
2012-03-27
SCID: 54.1/ttw3pbpg
Discuss with AI
barcode gapfungal DNA barcodinginternal transcribed spacer (ITS)nuclear ribosomal RNA cistronspecies identification
Figures from the paper
Abstract (AI)
Six DNA regions were evaluated as potential DNA barcodes for Fungi, the second largest kingdom of eukaryotic life, by a multinational, multilaboratory consortium. The region of the mitochondrial cytochrome c oxidase subunit 1 used as the animal barcode was excluded as a potential marker, because it is difficult to amplify in fungi, often includes large introns, and can be insufficiently variable. Three subunits from the nuclear ribosomal RNA cistron were compared together with regions of three representative protein-coding genes (largest subunit of RNA polymerase II, second largest subunit of RNA polymerase II, and minichromosome maintenance protein). Although the protein-coding gene regions often had a higher percent of correct identification compared with ribosomal markers, low PCR amplification and sequencing success eliminated them as candidates for a universal fungal barcode. Among the regions of the ribosomal cistron, the internal transcribed spacer (ITS) region has the highest probability of successful identification for the broadest range of fungi, with the most clearly defined barcode gap between inter- and intraspecific variation. The nuclear ribosomal large subunit, a popular phylogenetic marker in certain groups, had superior species resolution in some taxonomic groups, such as the early diverging lineages and the ascomycete yeasts, but was otherwise slightly inferior to the ITS. The nuclear ribosomal small subunit has poor species-level resolution in fungi. ITS will be formally proposed for adoption as the primary fungal barcode marker to the Consortium for the Barcode of Life, with the possibility that supplementary barcodes may be developed for particular narrowly circumscribed taxonomic groups.
Key Findings
1
A multinational, multilaboratory consortium evaluated six DNA regions as potential universal barcode markers across the fungal kingdom.
2
Compared with ITS, the large subunit provided superior resolution in some groups, while the small subunit showed poor species-level resolution; ITS was recommended as the primary fungal barcode.
3
Mitochondrial cytochrome c oxidase subunit 1 was excluded because fungal amplification is difficult, introns are common, and variability can be insufficient.
4
Protein-coding markers sometimes achieved higher identification accuracy than ribosomal regions, but poor PCR amplification and sequencing success prevented universal use.
5
Supplementary barcodes may be needed for narrowly circumscribed fungal taxonomic groups.
6
The nuclear ribosomal ITS region showed the highest overall identification success and the clearest barcode gap between interspecific and intraspecific variation.
Research Object
Fungi and candidate DNA barcode regions, particularly the nuclear ribosomal internal transcribed spacer (ITS) region
Research Subject
The comparative identification performance, amplification and sequencing success, species resolution, and barcode-gap characteristics of candidate regions for universal fungal DNA barcoding
Publication Details
Publication Date
2012-03-27
Journal
Publisher
ISSN
Open access PDF
Access Type
Author Information
Download PDF
Subscribe to digest