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

Kelly, Laura J.; Hollingsworth, Peter M.; Coppins, B. J.; Ellis, Christopher J.; Harrold, Paul; Tosh, James; Yahr, Rebecca

doi:10.1111/j.1469-8137.2011.03677.x

Cited by 121 publications

(133 citation statements)

References 78 publications

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“…In Aspergillus, ITS sequences are identical in several complexes of critical mycotoxigenic, industrial, and medically important species, and additional markers are necessary (52). Although the ITS region is a potentially effective DNA barcode in several lichenized lineages (53), genetic drift may prevent lineage sorting of ancestral polymorphisms in some slowly evolving groups.…”

Section: Discussionmentioning

confidence: 99%

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Schoch

Seifert

Huhndorf

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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2,910

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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 proteincoding 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.DNA barcoding | fungal biodiversity T he absence of a universally accepted DNA barcode for Fungi, the second most speciose eukaryotic kingdom (1, 2), is a serious limitation for multitaxon ecological and biodiversity studies. DNA barcoding uses standardized 500-to 800-bp sequences to identify species of all eukaryotic kingdoms using primers that are applicable for the broadest possible taxonomic group. Reference barcodes must be derived from expertly identified vouchers deposited in biological collections with online metadata and validated by available online sequence chromatograms. Interspecific variation should exceed intraspecific variation (the barcode gap), and barcoding is optimal when a sequence is constant and unique to one species (3, 4). Ideally, the barcode locus would be the same for all kingdoms. A region of the mitochondrial gene encoding the cytochrome c oxidase subunit 1 (CO1) is the barcode for animals (3, 4) and the default marker adopted by the Consortium for the Barcode of Life for all groups of organisms, including fungi (5). In Oomycota, part of the kingdom Stramenopila historically studied by mycologists, the de facto barcode internal transcribed spacer (ITS) region is suitable for identification, but the default CO1 marker is more reliable in a few clades of closely related species (6)...

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Section: Discussionmentioning

confidence: 99%

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Schoch

Seifert

Huhndorf

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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4,265

2,910

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“…Although in some cases the ITS region has been shown to be effective for molecular identification using DNA barcoding (Kelly et al 2011;Schoch et al 2012), including species within the Rhizoplaca melanophthalma species-complex, the reliance on a single locus for inferring relationships and circumscribing species is problematic because the history of a single gene might not be representative of the organismal history. Within the R. melanophthalma species-complex relationships among species-level lineages are largely unsupported in the ITS topology ( Fig.…”

Section: Discussionmentioning

confidence: 99%

“…the sample coverage of the group (Roe et al 2010;Kelly et al 2011;Kiss 2012;Orock et al 2012;Schoch et al 2012).…”

mentioning

confidence: 99%

DNA barcode identification of lichen-forming fungal species in the Rhizoplaca melanophthalma species-complex (Lecanorales, Lecanoraceae), including five new species

Leavitt¹,

Fernández-Mendoza²,

Pérez‐Ortega³

et al. 2013

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Citation: Leavitt SD, Fernández-Mendoza F, Pérez-Ortega S, Sohrabi M, Divakar PK, Lumbsch TH, St. Clair LLS (2013) DNA barcode identification of lichen-forming fungal species in the Rhizoplaca melanophthalma species-complex (Lecanorales, Lecanoraceae), including five new species. MycoKeys 7: 1-22. doi: 10.3897/mycokeys.7.4508 Abstract Recent studies using sequence data from multiple loci and coalescent-based species delimitation have revealed several species-level lineages within the phenotypically circumscribed taxon Rhizoplaca melanophthalma sensu lato. Here, we formally describe five new species within this group, R. occulta, R. parilis, R. polymorpha, R. porterii, and R. shushanii, using support from the coalescent-based species delimitation method implemented in the program Bayesian Phylogenetics and Phylogeography (BPP) as the diagnostic feature distinguishing new species. We provide a reference DNA sequence database using the ITS marker as a DNA barcode for identifying species within this complex. We also assessed intraspecific genetic distances within the six R. melanophthalma sensu lato species. While intraspecific genetic distances within the five new species were less than or equal to the lowest interspecific pairwise comparison values, an overlap in genetic distances within the R. melanophthalma sensu stricto clade suggests the potential for additional Leavitt et al. / MycoKeys 7: 1-22 (2013) 2 phenotypically cryptic lineages within this broadly distributed lineage. Overall, our results demonstrate the potential for accurately identifying species within the R. melanophthalma group by using molecularbased identification methods.

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“…Schoch et al, (2012) found the ITS region to be among the markers with highest probability of correct identifications for a very broad group of sampled fungi. Additional fungal studies have provided support for the ITS region as a suitable fungal barcode (Seena et al, 2010;Dentinger et al, 2011;Kelly et al, 2011). Moreover, most environmental surveys (metagenomic studies) of fungi are using the ITS region in their studies (e.g.…”

Section: Colonization Rates and Spore Populationmentioning

confidence: 99%

Arbuscular Mycorrhizal Fungi Diversity in Two Different Regions in Saudi Arabia

Albaqami¹,

Sohaibani²,

Murugan³

2018

Int.J.Curr.Microbiol.App.Sci

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

Cited by 121 publications

References 78 publications

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

DNA barcode identification of lichen-forming fungal species in the Rhizoplaca melanophthalma species-complex (Lecanorales, Lecanoraceae), including five new species

Arbuscular Mycorrhizal Fungi Diversity in Two Different Regions in Saudi Arabia

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