Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life

Buchheim, Mark A.; Keller, Alexander; Koetschan, Christian; Förster, Frank; Merget, Benjamin; Wolf, Matthias

doi:10.1371/journal.pone.0016931

Cited by 90 publications

(78 citation statements)

References 107 publications

(164 reference statements)

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“…Its use has already been shown in Chlorophyta and plants (66,67) as well as in Oomycota (6). The possibility of multikingdom analyses of complex ecosystems like soil using the species-informative, stable, high copy number ITS mirrors the original vision of DNA barcoding, and it already seems feasible, for example, to amplify Fungi and other eukaryotes from soil (23).…”

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.

4,258

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.

4,258

2,910

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“…The argument as to whether ITS or ITS2 should be a universal or a local plant barcode has been profound (24,25) and continual since it was first proposed as a candidate barcode. The limitations of ITS have been well-documented in general terms.…”

Section: Discussionmentioning

confidence: 99%

“…2). Considering the tradeoffs between universality, sequence quality, discrimination, rate of throughput, and cost efficiency, we propose that ITS/ITS2 should be incorporated into the core barcode for land plants, as suggested by earlier (9,19) and more recent (13,25) studies. If a three-marker combination is adopted, ITS/ ITS2 should be added to the proposed core barcode (i.e., rbcL + matK + ITS/ITS2).…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants

D¹,

Gao²,

Li³

et al. 2011

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

709

436

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A two-marker combination of plastid rbcL and matK has previously been recommended as the core plant barcode, to be supplemented with additional markers such as plastid trnH-psbA and nuclear ribosomal internal transcribed spacer (ITS). To assess the effectiveness and universality of these barcode markers in seed plants, we sampled 6,286 individuals representing 1,757 species in 141 genera of 75 families (42 orders) by using four different methods of data analysis. These analyses indicate that (i) the three plastid markers showed high levels of universality (87.1-92.7%), whereas ITS performed relatively well (79%) in angiosperms but not so well in gymnosperms; (ii) in taxonomic groups for which direct sequencing of the marker is possible, ITS showed the highest discriminatory power of the four markers, and a combination of ITS and any plastid DNA marker was able to discriminate 69.9-79.1% of species, compared with only 49.7% with rbcL + matK; and (iii) where multiple individuals of a single species were tested, ascriptions based on ITS and plastid DNA barcodes were incongruent in some samples for 45.2% of the sampled genera (for genera with more than one species sampled). This finding highlights the importance of both sampling multiple individuals and using markers with different modes of inheritance. In cases where it is difficult to amplify and directly sequence ITS in its entirety, just using ITS2 is a useful backup because it is easier to amplify and sequence this subset of the marker. We therefore propose that ITS/ITS2 should be incorporated into the core barcode for seed plants.land plants | species identification | nuclear ribosomal (nr) DNA T he seed plants account for some 90% of land plant diversity, dominating terrestrial ecosystems and providing food, timber, drugs, fibers, fuels, and ornamentals for human use (1). Identification is an essential step for humans in using and conserving plants. Since the time of Linnaeus, botanists have used a range of character sources as taxonomic evidence for documenting plant biodiversity (2), including gross morphology, anatomy, embryology, palynology, pollination biology, chromosomes, proteins, secondary metabolites, and ad hoc use of DNA sequence data (3). However, it can still be difficult to rapidly and accurately identify plant species. In part, this is because of the huge diversity of plant species and the fact that identifications are often attempted from suboptimal material that lacks the key diagnostic characters. It is especially difficult in the case of closely related species where recent radiation, frequent hybridization, and high intraspecific variation can compound identification problems (4, 5).DNA barcoding, an approach to identify species based on sequences from a short, standardized DNA region, opens up a unique avenue for the identification of organisms (6, 7). Although CO1, a mitochondrial marker, is known to work relatively consistently in animal barcoding, this region has not been adopted for plants because of low substitution rates in the pla...

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“…However, DNA barcoding opened the new alternative and confined ways to identify algal species regardless of life stage. Many DNA markers were evaluated including chloroplast (rbcL, tufA and 23S), mitochondrial (COI) and nuclear genes (18S rDNA, nuITS1 and nuITS2) (15)(16)(17)(18). The protist working group of the CBOL recommended two step barcoding in which a universal barcode marker should be used first, followed by the use of a group-specific second barcode (19).…”

Section: Dna Barcoding Of Algaementioning

confidence: 99%

DNA barcoding of plants: Selection of core markers for taxonomic groups

Saddhe

Kumar²

2017

Plant Sci. Today

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Plant identification is a crucial and routine taxonomic procedure in order to understand and conserve the biodiversity. Anthropogenic activity, pollution, deforestation, and exploitation of natural resources have been threatening to the plant biodiversity. Unfortunately, the major concern of traditional identification of plants is the gradual declined number of taxonomic expertise and lack of tools which accurately discriminate plant seeds, plant parts and seedling, and herbal adulterant. Presently, it is of utmost importance that plant biodiversity to be preserved. To overcome this issues the advent of molecular marker based technique which utilized short fragment of DNA and correctly assign plant taxa to their taxonomic group, called as DNA barcoding. First time, single marker based taxon identification successfully implemented to an animal taxa using mitochondrial cytochrome I (COI) gene fragment. However, Plant DNA barcoding is more complex and it often requires more than one set of DNA markers. In the present review, we have compiled the recent progress of plant DNA barcoding in various taxonomic groups and utility of plastids and nuclear DNA based markers for plant identification.

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Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life

Cited by 90 publications

References 107 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

Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants

DNA barcoding of plants: Selection of core markers for taxonomic groups

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