Lower level relationships in the mushroom genus Cortinarius (Basidiomycota, Agaricales): A comparison of RPB1, RPB2, and ITS phylogenies

Frøslev, Tobias Guldberg; Matheny, P. Brandon; Hibbett, David S.

doi:10.1016/j.ympev.2005.06.016

Cited by 144 publications

(99 citation statements)

References 47 publications

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“…RPB2 gene ranks the next (16/19, 84.2%, Table 2). This result conforms to the previous studies in certain other fungal groups [38,[52][53][54]. The other two genes, β-tubulin and ITS, had undesirable intra-and inter-variations and exhibited relatively poor species resolution capacity (Table 2), which indicated that the partial β-tubulin gene and ITS gene are inadequate to identify closely related species.…”

Section: Discussionsupporting

confidence: 90%

DNA barcoding of the fungal genus Neonectria and the discovery of two new species

Zhao

Luo

Zhuang

et al. 2011

Sci. China Life Sci.

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To determine a suitable DNA barcode for the genus Neonectria, the internal transcribed spacer rDNA, β-tubulin, EF-1α, and RPB2 genes were selected as candidate markers. A total of 205 sequences from 19 species of the genus were analyzed. Intraand inter-specific divergences and the ease of nucleotide sequence acquisition were treated as criteria to evaluate the feasibility of a DNA barcode. Our results indicated that any single gene among the candidate markers failed to serve as a successful barcode, while the combination of the partial EF-1α and RPB2 genes recognized all species tested. We tentatively propose the combined partial EF-1α and RPB2 genes as a DNA barcode for the genus. During this study, two cryptic species were discovered, based on the combined data of morphology and DNA barcode information. We described and named these two new species N. ditissimopsis and N. microconidia. intra-specific variation, inter-specific variation, morphology, DNA barcode, sequence analysis Citation:Zhao P, Luo J, Zhuang W Y, et al. DNA barcoding of the fungal genus Neonectria and the discovery of two new species . Sci China Life Sci, 2011, 54: 664 -674,

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Section: Discussionsupporting

confidence: 90%

DNA barcoding of the fungal genus Neonectria and the discovery of two new species

Zhao

Luo

Zhuang

et al. 2011

Sci. China Life Sci.

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“…Prior to the present study, published phylogenies that spanned the breath of the genus were based exclusively on analyses of domains D1ϩD2 of the nuclear large subunit (LSU) ribosomal DNA (rDNA) (17,39), primarily because this region is conserved enough such that a genus-wide alignment reflects positional homology and secondarily because of the ready availability of diverse fusarial LSU rDNA sequences from GenBank. However, because the LSU molecule is so highly conserved and the region (19,23), several studies have demonstrated the utility of RPB2 nucleotide variation at the species level in diverse fungi (10,16). The present study highlighted two attractive features of RPB2 nucleotide sequence data for phylogeny reconstruction within Fusarium: the region sequenced (1.8 kb) was easily aligned across the entire genus, and the wealth of phylogenetic signal contained within this locus provided strong bootstrap support for many clades for the first time.…”

Section: Discussionmentioning

confidence: 99%

Phylogenetic Diversity and Microsphere Array-Based Genotyping of Human Pathogenic Fusaria, Including Isolates from the Multistate Contact Lens-Associated U.S. Keratitis Outbreaks of 2005 and 2006

et al. 2007

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To characterize the full spectrum of the causal agents involved and their potential sources, partial DNA sequences from three loci (RPB2, EF-1␣, and nuclear ribosomal rRNA) totaling 3.48 kb were obtained from 91 corneal and 100 isolates from the patient's environment (e.g., contact lens and lens cases). We also sequenced a 1.8-kb region encoding the RNA polymerase II second largest subunit (RPB2) from 126 additional pathogenic isolates to better understand how the keratitis outbreak isolates fit within the full phylogenetic spectrum of clinically important fusaria. These analyses resulted in the most robust phylogenetic framework for Fusarium to date. In addition, RPB2 nucleotide variation within a 72-isolate panel was used to design 34 allele-specific probes to identify representatives of all medically important species complexes and 10 of the most important human pathogenic Fusarium in a single-well diagnostic assay, using flow cytometry and fluorescent microsphere technology. The multilocus data revealed that one haplotype from each of the three most common species comprised 55% of CDC's corneal and environmental isolates and that the corneal isolates comprised 29 haplotypes distributed among 16 species. The high degree of phylogenetic diversity represented among the corneal isolates is consistent with multiple sources of contamination.

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“…Portions of the translation elongation factor (EF-1␣) and DNA-directed RNA polymerase second largest subunit (RPB2) were selected based on their demonstrated utility in previous studies (54,56,57,85). DNA-directed RNA polymerase subunit 1 (RPB1) was chosen based on published species-level studies from the Assembling the Fungal Tree of Life (AFTOL) project (18,42). PCR and sequencing primers used for these three loci are provided in Table 2.…”

Section: Methodsmentioning

confidence: 99%

Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections

O’Donnell¹,

et al. 2010

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Because less than one-third of clinically relevant fusaria can be accurately identified to species level using phenotypic data (i.e., morphological species recognition), we constructed a three-locus DNA sequence database to facilitate molecular identification of the 69 Fusarium species associated with human or animal mycoses encountered in clinical microbiology laboratories. The database comprises partial sequences from three nuclear genes: translation elongation factor 1␣ (EF-1␣), the largest subunit of RNA polymerase (RPB1), and the second largest subunit of RNA polymerase (RPB2). These three gene fragments can be amplified by PCR and sequenced using primers that are conserved across the phylogenetic breadth of Fusarium. Phylogenetic analyses of the combined data set reveal that, with the exception of two monotypic lineages, all clinically relevant fusaria are nested in one of eight variously sized and strongly supported species complexes. The monophyletic lineages have been named informally to facilitate communication of an isolate's clade membership and genetic diversity. To identify isolates to the species included within the database, partial DNA sequence data from one or more of the three genes can be used as a BLAST query against the database which is Web accessible at FUSARIUM-ID (http://isolate.fusariumdb.org) and the Centraalbureau voor Schimmelcultures (CBS-KNAW) Fungal Biodiversity Center (http://www.cbs.knaw.nl/fusarium). Alternatively, isolates can be identified via phylogenetic analysis by adding sequences of unknowns to the DNA sequence alignment, which can be downloaded from the two aforementioned websites. The utility of this database should increase significantly as members of the clinical microbiology community deposit in internationally accessible culture collections (e.g., CBS-KNAW or the Fusarium Research Center) cultures of novel mycosis-associated fusaria, along with associated, corrected sequence chromatograms and data, so that the sequence results can be verified and isolates are made available for future study.

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Lower level relationships in the mushroom genus Cortinarius (Basidiomycota, Agaricales): A comparison of RPB1, RPB2, and ITS phylogenies

Cited by 144 publications

References 47 publications

DNA barcoding of the fungal genus Neonectria and the discovery of two new species

DNA barcoding of the fungal genus Neonectria and the discovery of two new species

Phylogenetic Diversity and Microsphere Array-Based Genotyping of Human Pathogenic Fusaria, Including Isolates from the Multistate Contact Lens-Associated U.S. Keratitis Outbreaks of 2005 and 2006

Internet-Accessible DNA Sequence Database for Identifying Fusaria from Human and Animal Infections

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