A critique of DNA sequence analysis in the taxonomy of filamentous Ascomycetes and ascomycetous anamorphs

1995 ◽  
Vol 73 (S1) ◽  
pp. 760-767 ◽  
Author(s):  
Keith A. Seifert ◽  
Brenda D. Wingfield ◽  
Michael J. Wingfield
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Scientific Method ◽  
Species Concept ◽  
Emotional Reactions ◽  
Species Concepts ◽  
Sexual State ◽  
Taxonomic Studies ◽  
Holomorphic Classification ◽  
Phylogenetic Scheme

The validity of reclassifying filamentous, ascomycetous anamorphs solely on the basis of ribosomal DNA sequences is examined. We suggest that emotional reactions to the debate are a consequence of often unacknowledged philosophical biases. From the perspective of the scientific method, neither morphological nor sequence-based taxonomic studies are inherently superior. A review of published information on the internal transcribed spacer of filamentous Ascomycetes and ascomycetous anamorphs demonstrates that uniform species concepts based on DNA sequences alone are presently infeasible. Because a phylogenetic scheme should classify species, the concept that fungi can be typified or classified solely by DNA sequences is challenged. Similarly, because no adequate nonmorphological species concept exists for anamorphic fungi that lack a sexual state, integration of the Deuteromycetes into the holomorphic classification on the basis of DNA sequences alone is also presently impractical. Key words: DNA sequencing, fungal taxonomy, internal transcribed spacer, species concepts.

A new species of Chlorociboria (Helotiales, Ascomycota) on herbaceous stems from China

Phytotaxa ◽  
2017 ◽  
Vol 312 (1) ◽  
pp. 111
Author(s):  
HUAN-DI ZHENG ◽  
WEN-YING ZHUANG
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Central China ◽  
Nuclear Ribosomal Dna ◽  
Light Blue ◽  
Ectal Excipulum ◽  
A New Species

A new species, namely Chlorociboria herbicola, is discovered on herbaceous stems in central China. Morphologically, the new fungus is distinctive by the combination of light blue-green apothecia, rectangular cells in ectal excipulum, and elongate-ellipsoidal ascospores with rounded ends. Phylogenetic analyses of the internal transcribed spacer and large subunit of nuclear ribosomal DNA sequences confirm its ascription in Chlorociboria and distinction from the known species of the genus.

scholarly journals First Report of Musk Thistle Rust (Puccinia carduorum) in California and Nevada

Plant Disease ◽  
2002 ◽  
Vol 86 (7) ◽  
pp. 814-814 ◽  
Author(s):  
D. M. Woods ◽  
M. J. Pitcairn ◽  
D. G. Luster ◽  
W. L. Bruckart
Keyword(s):  
Ribosomal Rna ◽  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
East Coast ◽  
Rust Fungus ◽  
The United States ◽  
Rust Disease ◽  
Carduus Nutans ◽  
Its1 And Its2 ◽  
Spacer Dna

Musk thistle, Carduus nutans L., is an introduced weed of pastures, rangelands, and natural areas in much of North America. Puccinia carduorum Jacky, an autoecious rust fungus from Turkey, has been evaluated for biological control of musk thistle since 1978, including a field study near Blacksburg, VA, from 1987 to 1990. After release of the fungus in Virginia, rusted musk thistle was found in eight eastern states by 1992, in Missouri by 1994 (1), and in Oklahoma by 1997 (2). A rust disease was discovered on musk thistle near Mt. Shasta, CA, on 22 September 1998, and near Mogul, NV, on 12 August 1999. The pathogen was identified as P. carduorum on the basis of pathogenicity on musk thistle and urediniospore morphology (ovate spores, 21 μm diameter, three germ pores equatorial in location, and echinulations over the upper two-thirds to three-quarters of urediniospores). Ribosomal RNA internal transcribed spacer DNA sequences (ITS1 and ITS2) were identical to those from the isolate obtained after the field release in Virginia, verifying that the California isolate is P. carduorum. The initial California infestation was observed on a few plants late in the season, and by September 2000, nearly 100% of plants were infected. The occurrence of P. carduorum in California is apparently the result of natural, unaided spread of the fungus on musk thistle from the East Coast of the United States. References: (1) A. B. A. M. Baudoin and W. L. Bruckart. Plant Dis. 80:1193, 1996. (2) L. J. Littlefield et al. Plant Dis. 82:832, 1998.

scholarly journals A phylogenetic framework for reassessing generic concepts and species delimitation in the lichenized family Trypetheliaceae (Ascomycota: Dothideomycetes)

2016 ◽  
Vol 48 (6) ◽  
pp. 739-762 ◽  
Author(s):  
Robert LÜCKING ◽  
Matthew P. NELSEN ◽  
André APTROOT ◽  
Roselvira BARILLAS DE KLEE ◽  
Paulina A. BAWINGAN ◽  
...  
Keyword(s):  
Species Delimitation ◽  
Type Species ◽  
Species Concept ◽  
Species Concepts ◽  
Additional Species ◽  
Secondary Chemistry ◽  
The Family ◽  
Phylogenetic Framework ◽  
Phenotypic Features

AbstractWe provide an expanded and updated, 2-locus phylogeny (mtSSU, nuLSU) of the lichenized fungal family Trypetheliaceae, with a total of 196 ingroup OTUs, in order to further refine generic delimitations and species concepts in this family. As a result, the following 15 clades are recognized as separate genera, including five newly established genera: Aptrootia, Architrypethelium, Astrothelium (including the bulk of corticate species with astrothelioid ascospores; synonyms: Campylothelium, Cryptothelium, Laurera), Bathelium s. str. (excluding B. degenerans and relatives which fall into Astrothelium), the reinstated Bogoriella (for tropical, lichenized species previously placed in Mycomicrothelia), Constrictolumina gen. nov. (for tropical, lichenized species of Arthopyrenia), Dictyomeridium gen. nov. (for a subgroup of species with muriform ascospores previously placed in Polymeridium), Julella (provisionally, as the type species remains unsequenced), Marcelaria (Laurera purpurina complex), Nigrovothelium gen. nov. (for the Trypethelium tropicum group), Novomicrothelia gen. nov. (for an additional species previously placed in Mycomicrothelia), Polymeridium s. str., Pseudopyrenula, Trypethelium s. str. (T. eluteriae group), and Viridothelium gen. nov. (for the Trypethelium virens group). All recognized genera are phenotypically characterized and a discussion on the evolution of phenotypic features in the family is given. Based on the obtained phylogeny, species delimitations are revised and the importance of characters such as thallus morphology, hymenial inspersion, and secondary chemistry for taxonomic purposes is discussed, resulting in a refined species concept.

Pseudohydnum brunneiceps (Auriculariales, Basidiomycota), a new species from Central China

Phytotaxa ◽  
2020 ◽  
Vol 441 (1) ◽  
pp. 87-94
Author(s):  
YAN-LIU CHEN ◽  
MING-SHENG SU ◽  
LIN-PING ZHANG ◽  
QIN ZOU ◽  
FEI WU ◽  
...  
Keyword(s):  
New Species ◽  
Molecular Phylogeny ◽  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Phylogenetic Analyses ◽  
Central China ◽  
Jiangxi Province ◽  
Line Drawings ◽  
A New Species ◽  
Representative Samples

Pseudohydnum brunneiceps is described as a new species from Jiangxi Province, central China. Morphologically, it is characterized by a gelatinous basidiocarps, pilei pale yellowish brown, dark reddish brown to blackish velutinate, spines conical and white, and basidiospores globose to broadly ellipsoidal. Phylogenetic analyses of DNA sequences from partial 28S region and internal transcribed spacer (ITS) also confirm that P. brunneiceps forms an independent lineage within Pseudohydnum. A description, photographs of the fresh basidiomata and line-drawings of the microstructures are provided. In addition, the previous records of P. gelatinosum in China should be re-evaluated by more representative samples by molecular phylogeny.

A molecular phylogeographic study based on DNA sequences from individual metacercariae ofParagonimus mexicanusfrom Guatemala and Ecuador

2003 ◽  
Vol 77 (1) ◽  
pp. 33-38 ◽  
Author(s):  
M. Iwagami ◽  
C. Monroy ◽  
M.A. Rosas ◽  
M.R. Pinto ◽  
A.G. Guevara ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
Distinct Species ◽  
Genetic Distances ◽  
Ribosomal Gene ◽  
Chain Reaction ◽  
Geographic Origins ◽  
Polymerase Chain ◽  
Second Internal Transcribed Spacer ◽  
Phylogeographic Study

AbstractA molecular phylogeographic study ofParagonimus mexicanuscollected from Guatemala and Ecuador was performed. Genomic DNA was extracted from individual metacercariae, and two gene regions (partial mitochondrial cytochromecoxidase subunit 1 (CO1) and the second internal transcribed spacer of the nuclear ribosomal gene repeat (ITS2)) were amplified by the polymerase chain reaction (PCR). Sequences segregated in a phylogenetic tree according to their geographic origins. ITS2 sequences from Ecuador and Guatemala differed at only one site. Pairwise distances among CO1 sequences within a country were always lower than between countries. Nevertheless, genetic distances between countries were less than between geographical forms ofP. westermanithat have been suggested to be distinct species. This result suggests that populations from Guatemala and Ecuador are genetically differentiated perhaps at the level of subspecies.

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