Fungal Molecular Systematics
01 Jan 1991-Annual Review of Ecology, Evolution, and Systematics (Annual Reviews 4139 El Camino Way, P.O. Box 10139, Palo Alto, CA 94303-0139, USA)-Vol. 22, Iss: 1, pp 525-564
TL;DR: The fungi, as thus defined, are of great importance for the following reasons: (a) They are the primary decomposers in all terrestrial ecosystems; (b) they are important symbiotic associates of vascular plants both in mutualistic and parasitic relationships.
Abstract: The fungi comprise both members of the kingdom Fungi as we now recognize it (Ascomycota, Basidiomycota, Zygomycota, and Chytridiomycota) and fungal-like protists such as the Oomycota and the cellular and acellular slime molds (Myxomycota and Acrasiomycota). Treating this admittedly polyphyletic assemblage as a group is useful because these organisms often fill rather similar roles within ecosystems, and they have traditionally been studied almost exclusively by mycologists and plant pathologists. Throughout this review, Fungi will refer to the Kingdom, fungi to the organisms studied by mycologists. The fungi, as thus defined, are of great importance for the following reasons: (a) They are the primary decomposers in all terrestrial ecosystems; (b) they are important symbiotic associates of vascular plants both in mutualistic and parasitic relationships; (c) they constitute the overwhelming majority of plant pathogens and as such have a tremendous eco-
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TL;DR: Nine sets of oligonucleotide primers constructed on the basis of the results of DNA hybridization of cloned genes from Neurospora crassa and Aspergillus nidulans may provide useful tools for phylogenetic studies and genome analyses in filamentous ascomycetes and deuteromycete affiliations, as well as for the rapid differentiation of fungal species by PCR.
Abstract: We constructed nine sets of oligonucleotide primers on the basis of the results of DNA hybridization of cloned genes from Neurospora crassa and Aspergillus nidulans to the genomes of select filamentous ascomycetes and deuteromycetes (with filamentous ascomycete affiliations). Nine sets of primers were designed to amplify segments of DNA that span one or more introns in conserved genes. PCR DNA amplification with the nine primer sets with genomic DNA from ascomycetes, deuteromycetes, basidiomycetes, and plants revealed that five of the primer sets amplified a product only from DNA of the filamentous ascomycetes and deuteromycetes. The five primer sets were constructed from the N. crassa genes for histone 3, histone 4, beta-tubulin, and the plasma membrane ATPase. With these five primer sets, polymorphisms were observed in both the size of and restriction enzyme sites in the amplified products from the filamentous ascomycetes. The primer sets described here may provide useful tools for phylogenetic studies and genome analyses in filamentous ascomycetes and deuteromycetes (with ascomycete affiliations), as well as for the rapid differentiation of fungal species by PCR.
3,179 citations
TL;DR: Divergence in the variable D1/D2 domain of large subunit (26S) ribosomal DNA is generally sufficient to resolve individual species, resulting in the prediction that 55 currently recognized taxa are synonyms of earlier described species.
Abstract: Approximately 500 species of ascomycetous yeasts, including members of Candida and other anamorphic genera, were analyzed for extent of divergence in the variable D1/D2 domain of large subunit (26S) ribosomal DNA. Divergence in this domain is generally sufficient to resolve individual species, resulting in the prediction that 55 currently recognized taxa are synonyms of earlier described species. Phylogenetic relationships among the ascomycetous yeasts were analyzed from D1/D2 sequence divergence. For comparison, the phylogeny of selected members of the Saccharomyces clade was determined from 18S rDNA sequences. Species relationships were highly concordant between the D1/D2 and 18S trees when branches were statistically well supported.
2,174 citations
Cites background from "Fungal Molecular Systematics"
...comycetes (Order Saccharomycetales), which include budding yeasts and yeastlike taxa such as Ascoidea andCephaloascus ; asci of this group are not formed in or on fruiting bodies, (2) the Euascomycetes, a sister group to the Hemiascomycetes, represent the ‘filamentous’ species, some of which are dimorphic; asci of nearly all species form within or upon fruiting bodies, and (3) the ‘Archiascomycetes’, a phylogenetically broad assemblage of yeastlike taxa basal to the preceding two groups and comprised of the genera Schizosaccharomyces, Saitoella, Protomyces, Taphrina andPneumocystis(Barns et al., 1991; Bruns et al., 1991; Eriksson et al., 1993; Hausner et al., 1992; Hendriks et al., 1992; Kurtzman 1993a,b; Kurtzman & Robnett, 1991, 1994a, 1995, 1997; Liu & Kurtzman, 1991; Nishida & Sugiyama, 1993; Walker, 1985; Wilmotte et al., 1993)....
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...As a result, interest has turned to other molecular comparisons that include sequencing, restriction fragment length polymorphisms (Bruns et al., 1991) and random amplified polymorphic DNA (Hadrys et al....
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...As a result, interest has turned to other molecular comparisons that include sequencing, restriction fragment length polymorphisms (Bruns et al., 1991) and random amplified polymorphic DNA (Hadrys et al., 1992). Of these, sequencing appears the most robust because strain comparisons are easily made and, with the selection of appropriate genes, both close and distant relationships can be resolved. For example, Peterson & Kurtzman (1991) sequenced the variable D2 domain (ca....
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...As a result, interest has turned to other molecular comparisons that include sequencing, restriction fragment length polymorphisms (Bruns et al., 1991) and random amplified polymorphic DNA (Hadrys et al., 1992)....
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...…basal to the preceding two groups and comprised of the genera Schizosaccharomyces, Saitoella, Protomyces, Taphrina andPneumocystis(Barns et al., 1991; Bruns et al., 1991; Eriksson et al., 1993; Hausner et al., 1992; Hendriks et al., 1992; Kurtzman 1993a,b; Kurtzman & Robnett, 1991, 1994a, 1995,…...
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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.
1,764 citations
Cites background from "Fungal Molecular Systematics"
...fujikuroi complex only 55% (Bruns et al., 1991), compared with 96% and 100%, respectively, reported here....
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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: Progresses ranging from the identification of novel genes and pathogens to the quantitation of characterized nucleotide sequences and some recent developments in instrumentation, methodology, and applications of the PCR are presented.
Abstract: The polymerase chain reaction (PCR) has dramatically altered how molecular studies are conducted as well as what questions can be asked. In addition to simplifying molecular tasks typically carried out with the use of recombinant DNA technology, PCR has allowed a spectrum of advances ranging from the identification of novel genes and pathogens to the quantitation of characterized nucleotide sequences. PCR can provide insights into the intricacies of single cells as well as the evolution of species. Some recent developments in instrumentation, methodology, and applications of the PCR are presented in this review.
1,178 citations
References
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TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Abstract: A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
57,055 citations
TL;DR: The recently‐developed statistical method known as the “bootstrap” can be used to place confidence intervals on phylogenies and shows significant evidence for a group if it is defined by three or more characters.
Abstract: The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data. In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
40,349 citations
01 Jan 1990
26,241 citations
TL;DR: A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction, which significantly improves the specificity, yield, sensitivity, and length of products that can be amplified.
Abstract: A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction. The enzyme, isolated from Thermus aquaticus, greatly simplifies the procedure and, by enabling the amplification reaction to be performed at higher temperatures, significantly improves the specificity, yield, sensitivity, and length of products that can be amplified. Single-copy genomic sequences were amplified by a factor of more than 10 million with very high specificity, and DNA segments up to 2000 base pairs were readily amplified. In addition, the method was used to amplify and detect a target DNA molecule present only once in a sample of 10(5) cells.
17,663 citations