Evaluation of mitochondrial genes as DNA barcode for Basidiomycota

Vialle, Agathe; Feau, Nicolas; Allaire, Mathieu; Didukh, Maryna; Martin, Francis; Moncalvo, Jean‐Marc; Hamelin, Richard

doi:10.1111/j.1755-0998.2009.02637.x

Cited by 100 publications

(73 citation statements)

References 87 publications

(189 reference statements)

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“…They discussed the difficulty of PCR amplification of older herbarium specimens, and that DNA repair was successful in some cases. Vialle et al (2009) compared mitochondrial genes to rDNA markers in two genera of rusts, Chrysomyxa and Melampsora. They found rDNA had better species resolution than mitochondrial genes.…”

Section: Molecular Phylogenymentioning

confidence: 99%

One stop shop: backbones trees for important phytopathogenic genera: I (2014)

et al. 2014

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Many fungi are pathogenic on plants and cause significant damage in agriculture and forestry. They are also part of the natural ecosystem and may play a role in regulating plant numbers/density. Morphological identification and analysis of plant pathogenic fungi, while important, is often hampered by the scarcity of discriminatory taxonomic characters and the endophytic or inconspicuous nature of these fungi. Molecular (DNA sequence) data for plant pathogenic fungi have emerged as key information for diagnostic and classification studies, although hampered in part by non-standard laboratory practices and analytical methods. To facilitate current and future research, this study provides phylogenetic synopses for 25 groups of plant pathogenic fungi in the Ascomycota, Basidiomycota, Mucormycotina (Fungi), and Oomycota, using recent molecular data, up-to-date names, and the latest taxonomic insights. Lineagespecific laboratory protocols together with advice on their application, as well as general observations, are also provided. We hope to maintain updated backbone trees of these fungal lineages over time and to publish them jointly as new data emerge. Researchers of plant pathogenic fungi not covered by the present study are invited to join this future effort. Bipolaris, Botryosphaeriaceae,

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Section: Molecular Phylogenymentioning

confidence: 99%

One stop shop: backbones trees for important phytopathogenic genera: I (2014)

et al. 2014

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“…The degenerate primers applicable to many Ascomycota (11) are difficult to assess, because amplification failures may not reflect priming mismatches. Extreme length variation occurs because of multiple introns (9,(12)(13)(14), which are not consistently present in a species. Multiple copies of different lengths and variable sequences occur, with identical sequences sometimes shared by several species (11).…”

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confidence: 99%

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

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Seifert

Huhndorf

et al. 2012

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

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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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“…For animals, COI was retained. For fungi (generally kingdom Fungi and assorted other mycota) two main markers are under consideration: ITS and the adjacent region, the ribosomal 25S long subunit (LSU) (Seifert 2009 ), both of which have worked well for fungi (although they are not without their problems (Vialle et al 2009 )). Algae comprise an artifi cial group of phylogenetically unrelated autotrophic organisms.…”

Section: Genetic Identification Above and Below The Species Levelmentioning

confidence: 99%