Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous
TL;DR: The results suggest that the ancestral ITS2 types may have arisen following an ancient interspecific hybridization or gene duplication which occurred prior to the evolutionary radiation of the Gibberella fujikuroi complex and related species of Fusarium.
About: This article is published in Molecular Phylogenetics and Evolution.The article was published on 1997-02-01. It has received 1764 citations till now. The article focuses on the topics: Lineage (evolution) & Phylogenetic tree.
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Conrad L. Schoch1, Keith A. Seifert, Sabine M. Huhndorf2, Vincent Robert3 +157 more•Institutions (59)
TL;DR: 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.
Abstract: 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.
4,116 citations
Cites background from "Two divergent intragenomic rDNA ITS..."
...Specialized identification databases use several markers [e.g., translation elongation factor 1-α for Fusarium (30) and β-tubulin for Penicillium (31)], but there is little standardization....
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...ITS sequences shared among different species have already been documented in species-rich Pezizomycotina genera with shorter amplicons, such as the economically important genera Cladosporium (49), Penicillium (50), and Fusarium (51)....
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...O’Donnell K, Cigelnik E (1997) Two divergent intragenomic rDNA ITS2 types within a monophyletic lineage of the fungus Fusarium are nonorthologous....
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...Intragenomic variation, such as the existence of multiple paralogous or nonorthologous copies within single fruiting bodies of basidiomycetes (54, 55) and ascomycetes (56) or within axenic cultures (51), may lead to higher estimates of infraspecific variability (57, 58) or generation of barcodes that act only as representative sequences of multiple variable repeats (59, 60)....
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...Gilmore SR, Gräfenhan T, Louis-Seize G, Seifert KA (2009) Multiple copies of cytochrome oxidase 1 in species of the fungal genus Fusarium....
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TL;DR: Despite the near-universal usage of ITS sequence data in plant phylogenetic studies, its complex and unpredictable evolutionary behavior reduce its utility for phylogenetic analysis, and it is suggested that more robust insights are likely to emerge from the use of single-copy or low-copy nuclear genes.
1,718 citations
Cites background from "Two divergent intragenomic rDNA ITS..."
...…a suite of orthologous and paralogous loci exist (e.g., Buckler et al., 1997; Hartmann et al., 2001; Ko and Jung, 2002; Mayol and Rossell o, 2001; O Donnell and Cigelnik, 1997; among others), which may or may not be sampled by a single PCR experiment and which often are not fully homogenized via…...
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TL;DR: Testing whether lineages of the Panama disease pathogen have a monophyletic origin by comparing DNA sequences of nuclear and mitochondrial genes indicates Panama disease of banana is caused by fungi with independent evolutionary origins.
Abstract: Panama disease of banana, caused by the fungus Fusarium oxysporum f. sp. cubense, is a serious constraint both to the commercial production of banana and cultivation for subsistence agriculture. Previous work has indicated that F. oxysporum f. sp. cubense consists of several clonal lineages that may be genetically distant. In this study we tested whether lineages of the Panama disease pathogen have a monophyletic origin by comparing DNA sequences of nuclear and mitochondrial genes. DNA sequences were obtained for translation elongation factor 1α and the mitochondrial small subunit ribosomal RNA genes for F. oxysporum strains from banana, pathogenic strains from other hosts and putatively nonpathogenic isolates of F. oxysporum. Cladograms for the two genes were highly concordant and a partition-homogeneity test indicated the two datasets could be combined. The tree inferred from the combined dataset resolved five lineages corresponding to “F. oxysporum f. sp. cubense” with a large dichotomy between two taxa represented by strains most commonly isolated from bananas with Panama disease. The results also demonstrate that the latter two taxa have significantly different chromosome numbers. F. oxysporum isolates collected as nonpathogenic or pathogenic to other hosts that have very similar or identical elongation factor 1α and mitochondrial small subunit genotypes as banana pathogens were shown to cause little or no disease on banana. Taken together, these results indicate Panama disease of banana is caused by fungi with independent evolutionary origins.
1,639 citations
TL;DR: Phylogenetic relationships of the phyto-pathogenic Gibberella fujikuroi species complex were investigated by maximum parsimony analysis of DNA sequences from multiple loci.
Abstract: Phylogenetic relationships of the phyto-pathogenic Gibberella fujikuroi species complex were investigated by maximum parsimony analysis of DNA sequences from multiple loci. Gene trees inferred from...
947 citations
TL;DR: FUSARIUM-ID v. 1.0, a publicly available database of partial translation elongation factor 1-alpha (TEF) DNA sequences, presently representing a selected sample of the diversity of the genus diversity, with excellent representation of Type-B trichothecene toxin producers, and the Gibberella fujikuroi, Fusarium oxysporum and F. solani species complexes.
Abstract: One of the greatest impediments to the study of Fusarium has been the incorrect and confused application of species names to toxigenic and pathogenic isolates, owing in large part to intrinsic limitations of morphological species recognition and its application. To address this problem, we have created FUSARIUM-ID v. 1.0, a publicly available database of partial translation elongation factor 1-alpha (TEF) DNA sequences, presently representing a selected sample of the diversity of the genus diversity, with excellent representation of Type-B trichothecene toxin producers, and the Gibberella fujikuroi, Fusarium oxysporum and F. solani species complexes. Users can generate sequences using primers that are conserved across the genus, and use the sequence as a query to BLAST the database, which can be accessed at http://fusarium.cbio.psu.edu, or in a phylogenetic analysis. Correct identification of a known species in these groups often can be performed using this gene region alone. This growing database will contain only vouchered sequences attached to publicly available cultures. In the future, FUSARIUM-ID will be expanded to include additional sequences, including multiple sequences from the same species, sequences from new and revised species, and information from additional genes.
938 citations
Cites background from "Two divergent intragenomic rDNA ITS..."
...Moreover, many fusaria within the Gibberella clade possess non-orthologous copies of the ITS2, which can lead to incorrect phylogenetic inferences (O’Donnell and Cigelnik, 1997; O’Donnell et al., 1998a)....
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References
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01 Jan 1990
26,241 citations
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01 Jan 2002
TL;DR: PAUP* 4.0 Beta is a major upgrade of the bestselling software for the inference of evolutionary trees, for use in Macintosh or Windows/DOS-based formats.
Abstract: PAUP* 4.0 Beta is a major upgrade of the bestselling software for the inference of evolutionary trees, for use in Macintosh or Windows/DOS-based formats. This version is for use in Macintosh. Please note it is currently only available as a Beta version. For more information (and the Linux/UNIX version), visit www.sinauer.com/detail.php?id=8060
4,329 citations
TL;DR: This work uses computer simulations and a laboratory-generated phylogeny to test bootstrapping results of parsimony analyses, and indicates that any given bootstrap proportion provides an unbiased but highly imprecise measure of repeatability, unless the actual probability of replicating the relevant result is nearly one.
Abstract: Bootstrapping is a common method for assessing confidence in phylogenetic anal? yses. Although bootstrapping was first applied in phylogenetics to assess the repeatability of a given result, bootstrap results are commonly interpreted as a measure of the probability that a phylogenetic estimate represents the true phylogeny. Here we use computer simulations and a laboratory-generated phylogeny to test bootstrapping results of parsimony analyses, both as measures of repeatability (i.e., the probability of repeating a result given a new sample of characters) and accuracy (i.e., the probability that a result represents the true phylogeny). Our results indicate that any given bootstrap proportion provides an unbiased but highly imprecise measure of repeatability, unless the actual probability of replicating the relevant result is nearly one. The imprecision of the estimate is great enough to render the estimate virtually useless as a measure of repeatability. Under conditions thought to be typical of most phylogenetic analyses, however, bootstrap proportions in majority-rule consensus trees provide biased but highly con? servative estimates of the probability of correctly inferring the corresponding clades. Specifically, under conditions of equal rates of change, symmetric phylogenies, and internodal change of 70% usually correspond to a probability of >95% that the corresponding dade is real. However, under conditions of very high rates of internodal change (approaching randomization of the characters among taxa) or highly unequal rates of change among taxa, bootstrap proportions >50% are overestimates of accuracy. (Boot? strapping; accuracy; repeatability; phylogeny; parsimony; precision; statistical analyses; simu? lations.)
4,057 citations
"Two divergent intragenomic rDNA ITS..." refers background or methods in this paper
...fujikuroi complex (Leslie, 1995); however, only members of MP-C are namedG. fujikuroi sensu stricto.Teleomorph binomials have not been proposed for all MPs.F. udum is the only other species within theG. fujikuroi complex for which a teleomorph is known (Rai andUpadhyay, 1982); teleomorphs are unknown for theF. oxysporum complex. Gerlach andNirenberg (1982) recognize two species and one variety not included in the present study:F....
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...Support for the phylogenetic groupings was obtained with bootstrap analyses (Hillis and Bull, 1993) using 200–1000 replications with random addition input orders of sequences during each heuristic search, and decay indices (Donoghue et al....
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