On the phylogeny of Ophiostoma, Ceratocystis s.s., and Microascus, and relationships within Ophiostoma based on partial ribosomal DNA sequences

1993 ◽  
Vol 71 (9) ◽  
pp. 1249-1265 ◽  
Author(s):  
G. Hausner ◽  
J. Reid ◽  
G. R. Klassen
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Large Subunit ◽  
Small Subunit ◽  
Data Set ◽  
Rdna Sequences ◽  
Morphological Criteria ◽  
Small Subunit Rdna ◽  
Rdna Sequence Data ◽  
Large Subunit Rdna

Phylogenetic analysis of partial rDNA sequences suggests that Ophiostoma should remain the sole genus of the Ophiostomataceae, and this should be the sole family within the Ophiostomatales, whereas Ceratocystis s.s. would be best disposed within the Microascales. Although morphological criteria suggest that the genus Ophiostoma is heterogeneous, analysis of partial small subunit rDNA sequence data shows that Ophiostoma (excluding O. roraimense) represents a monophyletic taxon. Analysis of a partial large subunit rDNA data set, which included sequences from 55 species assignable to Ophiostoma, failed to support the strict subdivision of the genus based on either ascospore characters or the nature of the anamorph. Key words: Ceratocystis, Microascus, Ophiostoma, partial rDNA sequences, phylogeny.

scholarly journals Morphology, genetic characterization and molecular phylogeny of pinworm Skrjabinema longicaudatum n. sp. (Oxyurida: Oxyuridae) from the endangered Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae)

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Yi-Fan Cao ◽  
Hui-Xia Chen ◽  
Yang Li ◽  
Dang-Wei Zhou ◽  
Shi-Long Chen ◽  
...  
Keyword(s):  
New Species ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Small Subunit ◽  
Sister Relationship ◽  
Tibetan Antelope ◽  
A New Species

Abstract Background The Tibetan antelope Pantholops hodgsonii (Abel) (Artiodactyla: Bovidae) is an endangered species of mammal endemic to the Qinghai-Tibetan Plateau. Parasites and parasitic diseases are considered to be important threats in the conservation of the Tibetan antelope. However, our present knowledge of the composition of the parasites of the Tibetan antelope remains limited. Methods Large numbers of nematode parasites were collected from a dead Tibetan antelope. The morphology of these nematode specimens was observed using light and scanning electron microscopy. The nuclear and mitochondrial DNA sequences, i.e. small subunit ribosomal DNA (18S), large subunit ribosomal DNA (28S), internal transcribed spacer (ITS) and cytochrome c oxidase subunit 1 (cox1), were amplified and sequenced for molecular identification. Moreover, phylogenetic analyses were performed using maximum likelihood (ML) inference based on 28S and 18S + 28S + cox1 sequence data, respectively, in order to clarify the systematic status of these nematodes. Results Integrated morphological and genetic evidence reveals these nematode specimens to be a new species of pinworm Skrjabinema longicaudatum (Oxyurida: Oxyuridae). There was no intraspecific nucleotide variation between different individuals of S. longicaudatum n. sp. in the partial 18S, 28S, ITS and cox1 sequences. However, a high level of nucleotide divergence was revealed between the new species and its congeners in 28S (8.36%) and ITS (20.3–23.7%) regions, respectively. Molecular phylogenetic results suggest that the genus Skrjabinema should belong to the subfamily Oxyurinae (Oxyuroidea: Oxyuridae), instead of the subfamily Syphaciidae or Skrjabinemiinae in the traditional classification, as it formed a sister relationship to the genus Oxyuris. Conclusions A new species of pinworm Skrjabinema longicaudatum n. sp. (Oxyurida: Oxyuridae) is described. Skrjabinema longicaudatum n. sp. represents the first species of Oxyurida (pinworm) and the fourth nematode species reported from the Tibetan antelope. Our results contribute to the knowledge of the species diversity of parasites from the Tibetan antelope, and clarify the systematic position of the genus Skrjabinema.

Molecular Phylogenetics of Ramaria and Related Genera: Evidence from Nuclear Large Subunit and Mitochondrial Small Subunit rDNA Sequences

Mycologia ◽  
2001 ◽  
Vol 93 (3) ◽  
pp. 465 ◽  
Author(s):  
Andrea J. Humpert ◽  
Eric L. Muench ◽  
Admir J. Giachini ◽  
Michael A. Castellano ◽  
Joseph W. Spatafora
Keyword(s):  
Molecular Phylogenetics ◽  
Large Subunit ◽  
Small Subunit ◽  
Rdna Sequences ◽  
Small Subunit Rdna

scholarly journals Blastobotrys americana sp. nov., Blastobotrys illinoisensis sp. nov., Blastobotrys malaysiensis sp. nov., Blastobotrys muscicola sp. nov., Blastobotrys peoriensis sp. nov. and Blastobotrys raffinosifermentans sp. nov., novel anamorphic yeast species

2007 ◽  
Vol 57 (5) ◽  
pp. 1154-1162 ◽  
Author(s):  
Cletus P. Kurtzman
Keyword(s):  
Type Strain ◽  
Yeast Species ◽  
Novel Species ◽  
Large Subunit ◽  
Small Subunit ◽  
Its2 Rdna ◽  
Small Subunit Rdna ◽  
Anamorphic Yeast ◽  
Large Subunit Rdna ◽  
Cytochrome Oxidase Ii

The genus Blastobotrys, which now includes species previously assigned to the synonymous genera Arxula and Sympodiomyces, represents the anamorph of the ascosporogenous genus Trichomonascus. Six novel species are proposed for assignment to Blastobotrys. They were detected from their unique nucleotide sequences in large-subunit rDNA, ITS1–5.8S–ITS2 rDNA, mitochondrial small-subunit rDNA and the cytochrome oxidase II gene. The proposed novel species are Blastobotrys americana sp. nov. (type strain NRRL Y-6844T=CBS 10337T; substrate unknown; Kansas, USA), Blastobotrys illinoisensis sp. nov. (type strain NRRL YB-1343T=CBS 10339T; from forest debris; Illinois, USA), Blastobotrys malaysiensis sp. nov. (type strain NRRL Y-6417T=CBS 10336T; from soil; Malaysia), Blastobotrys muscicola sp. nov. (type strain NRRL Y-7993T=CBS 10338T; from moss; Louisiana, USA), Blastobotrys peoriensis sp. nov. (type strain NRRL YB-2290T=CBS 10340T; from a fungus; Peoria, IL, USA) and Blastobotrys raffinosifermentans sp. nov. (type strain NRRL Y-27150T=CBS 6800T; substrate unknown).

A new Agonimia from Europe with a flabelliform thallus

2011 ◽  
Vol 44 (1) ◽  
pp. 55-66 ◽  
Author(s):  
Beata GUZOW-KRZEMIŃSKA ◽  
Josef P. HALDA ◽  
Paweł CZARNOTA
Keyword(s):  
Czech Republic ◽  
New Species ◽  
Great Britain ◽  
Dna Sequences ◽  
Sequence Data ◽  
Small Subunit ◽  
The Czech Republic ◽  
Rdna Sequence Data ◽  
Small Subunit Ribosomal Dna ◽  
A New Species

AbstractAgonimia flabelliformis sp. nov. (Verrucariaceae, Ascomycota) is described as a new species from the Czech Republic, Germany and Great Britain. Except for the distinctive, flabelliform to minutely coralloid thallus the species mostly resembles A. allobata. It differs from other related species of Agonimia in the absence of cortical papillae and in ascospore size. The distinctness of the new species and its placement within the genus Agonimia is supported by analyses of mitochondrial small subunit ribosomal DNA sequences from several samples of the taxon, and from many other representatives of Verrucariales including newly sequenced A. repleta and A. vouauxii. Additionally, ITS rDNA sequence data supports the distinction of A. flabelliformis from A. allobata. However, A. allobata was found to be highly variable and relationships, as well as the monophyly of taxa within Agonimia, are still unresolved and need further investigation.

Revisiting the phylogeny of Ocellularieae, the second largest tribe within Graphidaceae (lichenized Ascomycota: Ostropales)

Phytotaxa ◽  
2014 ◽  
Vol 189 (1) ◽  
pp. 52 ◽  
Author(s):  
Ekaphan Kraichak ◽  
Sittiporn Parnmen ◽  
Robert Lücking ◽  
EIMY RIVAS PLATA ◽  
André Aptroot ◽  
...  
Keyword(s):  
Molecular Phylogeny ◽  
Rna Polymerase ◽  
Rna Polymerase Ii ◽  
Large Subunit ◽  
Small Subunit ◽  
New Combinations ◽  
New Name ◽  
Small Subunit Rdna ◽  
Large Subunit Rdna ◽  
First Time

We present an updated 3-locus molecular phylogeny of tribe Ocellularieae, the second largest tribe within subfamily Graphidoideae in the Graphidaceae. Adding 165 newly generated sequences from the mitochondrial small subunit rDNA (mtSSU), the nuclear large subunit rDNA (nuLSU), and the second largest subunit of the DNA-directed RNA polymerase II (RPB2), we currently distinguish 218 species among the sequenced material, including the outgroup. This corresponds to almost half the species at this point recognized within this tribe. The newly generated sequences include 23 newly described species and one newly described genus published elsewhere in this volume. For the first time, Sarcographina cyclospora Müll. Arg., in spite of its distinctly lirellate ascomata, is shown to belong in tribe Ocellularieae, as strongly supported sister to Ocellularia inturgescens (Müll. Arg.) Mangold. The following six new combinations are proposed: Melanotrema lynceodes (Nyl.) Rivas Plata, Lücking & Lumbsch, Ocellularia curranii (Vain.) Kraichak, Lücking & Lumbsch, O. khasiana (Patw. & Nagarkar) Kraichak, Lücking & Lumbsch, O. cinerea (Müll. Arg.) Kraichak, Lücking & Lumbsch, O. erodens (R. C. Harris) Kraichak, Lücking & Lumbsch, and O. laeviuscula (Nyl) Kraichak, Lücking & Lumbsch. Further, the new name Ocellularia hernandeziana Kraichak, Lücking & Lumbsch is introduced for Myriotrema ecorticatum. The nomenclatural status of the name Ocellularia microstoma is clarified.

Small-subunit rDNA sequences from representatives of selected families of the Gigartinales and Rhodymeniales (Rhodophyta). 3. Delineating the Gigartinales sensu stricto

2004 ◽  
Vol 82 (1) ◽  
pp. 43-74 ◽  
Author(s):  
Gary W Saunders ◽  
Anthony Chiovitti ◽  
Gerald T Kraft
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Family Relationships ◽  
Small Subunit ◽  
Sensu Stricto ◽  
Rdna Sequences ◽  
Small Subunit Rdna ◽  
First Time ◽  
Small Subunit Ribosomal Dna ◽  
Ordinal Level

Nuclear small-subunit ribosomal DNA sequences were determined for 65 members of the Gigartinales and related orders. With representatives of 15 families of the Gigartinales sensu Kraft and Robins included for the first time, our alignment now includes members of all but two of the ca. 40 families. Our data continue to support ordinal status for the Plocamiales, to which we provisionally transfer the Pseudoanemoniaceae and Sarcodiaceae. The Halymeniales is retained at the ordinal level and consists of the Halymeniaceae (including the Corynomorphaceae), Sebdeniaceae, and Tsengiaceae. In the Halymeniaceae, Grateloupia intestinalis is only distantly related to the type species, Grateloupia filicina, but is closely affiliated with the genus Polyopes. The Nemastomatales is composed of the Nemastomataceae and Schizymeniaceae. The Acrosymphytaceae (now including Schimmelmannia, formerly of the Gloiosiphoniaceae) and the Calosipho niaceae (represented by Schmitzia) have unresolved affinities and are considered as incertae sedis among lineage 4 orders. We consider the Gigartinales sensu stricto to include 29 families, although many contain only one or a few genera and mergers will probably result following further investigation. Although the small-subunit ribosomal DNA was generally too conservative to resolve family relationships within the Gigartinales sensu stricto, a few key conclusions are supported. The Hypneaceae, questionably distinct from the Cystocloniaceae on anatomical grounds, is now subsumed into the latter family. As recently suggested, the Wurdemanniaceae should be incorporated into the Solieriaceae, but the latter should not be merged with the Areschougiaceae. The Corynocystaceae Kraft, fam. nov., is described and added to the Gigartinales sensu stricto.Key words: Corynocystaceae, Cryptonemiales, Florideophyceae, Gigartinales, Rhodymeniales, systematics.

Phylogeny of the rust fungi: an approach using nuclear large subunit ribosomal DNA sequences

2003 ◽  
Vol 81 (1) ◽  
pp. 12-23 ◽  
Author(s):  
Wolfgang Maier ◽  
Dominik Begerow ◽  
Michael Weiß ◽  
Franz Oberwinkler
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Large Subunit ◽  
Rust Fungi ◽  
Monophyletic Group ◽  
Neighbor Joining ◽  
Natural Group ◽  
Outgroup Species ◽  
Large Subunit Rdna

Sequence data from nuclear large subunit ribosomal DNA was used to infer phylogenetic relationships of selected genera of the Uredinales. We investigated 52 rust fungi representing nine families and three outgroup species. Neighbor joining analysis and a Bayesian method of phylogenetic inference using Monte Carlo Markov chains confirm the rust fungi as a natural group and indicate that Puccinia, Uromyces, Endophyllum, and Cumminsiella have a common origin. The autoecious Rosaceae-rusts Phragmidium, Kuehneola, Triphragmium, and Trachyspora are a monophyletic group. The gasteroid genus Ochropsora is closely related to Tranzschelia. While the Pucciniastreae sensu Dietel (1938) is recognized as a monophyletic group in neighbor joining analysis, the Pucciniaceae s.l. (Dietel 1928) is supported by Bayesian analysis. The following genera appear to be monophyletic: Chrysomyxa, Coleosporium, Cronartium, Gymnosporangium, Melampsora, Phragmidium, and Tranzschelia, whereas the genera Puccinia, Pucciniastrum, Thekopsora, and Uromyces are not.Key words: molecular phylogeny, systematics, nuclear large subunit rDNA, Basidiomycota, Urediniomycetes, Uredinales.

scholarly journals Sequences of psychrophilic fungi amplified from glacier-preserved ascolichens

2000 ◽  
Vol 78 (11) ◽  
pp. 1450-1459 ◽  
Author(s):  
Paula T DePriest ◽  
Natalia V Ivanova ◽  
Dianne Fahselt ◽  
Vagn Alstrup ◽  
Andrea Gargas
Keyword(s):  
Phylogenetic Analysis ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Large Subunit ◽  
Ice Core ◽  
Small Subunit ◽  
Rdna Sequences ◽  
Three Samples ◽  
Tyrolean Iceman ◽  
Small Subunit Ribosomal Dna

Ribosomal DNA sequences were amplified from subfossils of the ascolichen Umbilicaria cylindrica (L.) Delise ex Duby collected at the ablating edges of Greenland glaciers. Surprisingly, phylogenetic analysis indicated that the amplified rDNA sequences were not closely related to those of the lichen-forming fungus but rather represented two groups of psychrophilic basidiomycetes (orders Cystofilobasidiales and Sporidiales) and one group of ascomycetes (order Leotiales). Two of these groups, the Sporidiales and the Leotiales, include other fungi previously detected in DNA extracted from the grass clothing of the Tyrolean Iceman desiccated and frozen for over 3000 years and also in 2000- and 4000-year-old ice core samples from northern Greenland. Large subunit ribosomal DNA sequences representing the group Cystofilobasidiales were nearly identical to those of the basidioyeast saprobe Mrakia frigida. The adjacent internal transcribed spacer sequence was more than 98% similar to those from three samples of U. cylindrica from different sites that had been subjected to ice burial for various lengths of time, suggesting they also were Mrakia sequences. Although ancient contamination of multiple U. cylindrica specimens with fungi such as Mrakia cannot be ruled out, it is more probable that saprobic colonization of the subfossil tissues by psychrophilic fungi proceeded during recent ice melt.Key words: ancient DNA, small subunit ribosomal DNA, 18S ribosomal DNA, phylogenetic analysis, psychrophilic fungi, lichen-forming fungi.

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