Molecular phylogeny of Amanita based on large-subunit ribosomal DNA sequences: implications for taxonomy and character evolution

Mycologia ◽  
1999 ◽  
Vol 91 (4) ◽  
pp. 610-618 ◽  
Author(s):  
Dennis Drehmel ◽  
Jean-Marc Moncalvo ◽  
Rytas Vilgalys
Keyword(s):  
Molecular Phylogeny ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Large Subunit ◽  
Character Evolution

Phylogenetic studies on nuclear large subunit ribosomal DNA sequences of smut fungi and related taxa

1997 ◽  
Vol 75 (12) ◽  
pp. 2045-2056 ◽  
Author(s):  
Dominik Begerow ◽  
Robert Bauer ◽  
Franz Oberwinkler
Keyword(s):  
Molecular Phylogeny ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Large Subunit ◽  
The Other ◽  
Lsu Rdna ◽  
Smut Fungi ◽  
Neighbor Joining ◽  
Phylogenetic Studies ◽  
Key Words Basidiomycete

To show phylogenetic relationships among the smut fungi and their relatives, we sequenced a part of the nuclear LSU rDNA from 43 different species of smut fungi and related taxa. Our data were combined with the existing sequences of seven further smut fungi and 17 other basidiomycetes. Two sets of sequences were analyzed. The first set with a representative number of simple septate basidiomycetes, complex septate basidiomycetes, and smut fungi was analyzed with the neighbor-joining method to estimate the general topology of the basidiomycetes phylogeny and the positions of the smut fungi. The tripartite subclassification of the basidiomycetes into the Urediniomycetes, Ustilaginomycetes, and Hymenomycetes was confirmed and two groups of smut fungi appeared. The smut genera Aurantiosporium, Microbotryum, Fulvisporium, and Ustilentyloma are members of the Urediniomycetes, whereas the other smut species tested are members of the Ustilaginomycetes with Entorrhiza as a basal taxon. The second set of 46 Ustilaginomycetes was analyzed using the neighbor-joining and the maximum parsimony methods to show the inner topology of the Ustilaginomycetes. The results indicated three major lineages among Ustilaginomycetes corresponding to the Entorrhizomycetidae, Exobasidiomycetidae, and Ustilaginomycetidae. The Entorrhizomycetidae are represented by Entorrhiza species. The Ustilaginomycetidae contain at least two groups, the Urocystales and Ustilaginales. The Exobasidiomycetidae include five orders, i.e., Doassansiales, Entylomatales, Exobasidiales, Georgefischeriales, and Tilletiales, and Graphiola phoenicis and Microstroma juglandis. Our results support a classification mainly based on ultrastructure. The description of the Glomosporiaceae is emended. The Doassansiopsaceae, Melanotaeniaceae, and Urocystaceae are proposed as new taxa. Key words: basidiomycete systematics, LSU rDNA, Microbotryales, molecular phylogeny, smut fungi, Ustilaginomycetes.

On the subdivision of Ceratocystis s.l., based on partial ribosomal DNA sequences

1993 ◽  
Vol 71 (1) ◽  
pp. 52-63 ◽  
Author(s):  
G. Hausner ◽  
J. Reid ◽  
G. R. Klassen
Keyword(s):  
Key Words ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Cell Walls ◽  
Large Subunit ◽  
Rdna Sequences

Analyses of partial rDNA sequences from both the small and large subunit genes of species of Ceratocystis s.l. support the contention that species that lack Chalara anamorphs, are resistant to cycloheximide, and have rhamnose in their cell walls should be assigned to Ophiostoma, whereas only species with Chalara anamorphs should be accommodated in Ceratocystis s.s. The data also show that Ceratocystiopsis is polyphyletic, and Sphaeronaemella fimicola appears to have little relation to either Ceratocystis or Ophiostoma. Key words: Ceratocystis, Ophiostoma, phylogeny, partial rDNA sequences.

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.

scholarly journals Phylogenetic Relationships of Agaric Fungi Based on Nuclear Large Subunit Ribosomal DNA Sequences

2000 ◽  
Vol 49 (2) ◽  
pp. 278-305 ◽  
Author(s):  
Jean-Marc Moncalvo ◽  
François M. Lutzoni ◽  
Stephen A. Rehner ◽  
Jacqui Johnson ◽  
Rytas Vilgalys
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Large Subunit

scholarly journals Phylogeny of the Labeoninae (Teleostei, Cypriniformes) based on nuclear DNA sequences and implications on character evolution and biogeography

2012 ◽  
Vol 58 (6) ◽  
pp. 837-850 ◽  
Author(s):  
Lanping Zheng ◽  
Junxing Yang ◽  
Xiaoyong Chen
Keyword(s):  
Molecular Phylogeny ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Morphological Characters ◽  
Character Evolution ◽  
Lower Lip ◽  
Molecular Phylogenetic Tree ◽  
Systematic Exploration ◽  
Molecular Phylogenetic ◽  
History Of

Abstract The Labeoninae is a subfamily of the family Cyprinidae, Order Cypriniformes. Oromandibular morphology within the Labeoninae is the greatest among cyprinid fishes. Although several phylogenetic studies about labeonines have been undertaken the results have been inconsistent and a comprehensive phylogeny is needed. Further, an incongruence between morphological and molecular phylogeny requires a systematic exploration of the significance of morphological characters on the basis of the molecular phylogeny. In this study, a total of 292 nucleotide sequences from 73 individuals (representing 24 genera and 73 species) of Labeoninae were analyzed. The results of the phylogenetic analysis indicate that there are four major clades within Labeoninae and three monophyletic lineages within the fourth clade. Results of the character evolution show that all oroman-dibular morphological characters are homoplastically distributed on the molecular phylogenetic tree and suggests that these characters evolved several times during the history of labeonines. In particular, the labeonine , a specific disc on the lower lip, has been acquired three times and reversed twice. These morphological characters do not have systematic significance but can be useful for taxonomy. The results of biogeography suggest that the Labeoninae originated from Southeast Asia and separately dispersed to Africa, East Asia and South Asia.

A preliminary overview of the Diaporthales based on large subunit nuclear ribosomal DNA sequences

Mycologia ◽  
2002 ◽  
Vol 94 (6) ◽  
pp. 1017-1031 ◽  
Author(s):  
Lisa A. Castlebury ◽  
Amy Y. Rossman ◽  
Walter J. Jaklitsch ◽  
Larissa N. Vasilyeva
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Large Subunit ◽  
Nuclear Ribosomal Dna

scholarly journals Cryphonectriaceae on Myrtales in China: phylogeny, host range, and pathogenicity

2020 ◽  
Vol 45 (1) ◽  
pp. 101-131 ◽  
Author(s):  
W. Wang ◽  
G.Q. Li ◽  
Q.L. Liu ◽  
S.F. Chen
Keyword(s):  
New Species ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Fungal Pathogens ◽  
Southern China ◽  
Large Subunit ◽  
Morphological Characteristics ◽  
Psidium Guajava ◽  
Fungal Species ◽  
Canker Disease

Plantation-grown Eucalyptus (Myrtaceae) and other trees residing in the Myrtales have been widely planted in southern China. These fungal pathogens include species of Cryphonectriaceae that are well-known to cause stem and branch canker disease on Myrtales trees. During recent disease surveys in southern China, sporocarps with typical characteristics of Cryphonectriaceae were observed on the surfaces of cankers on the stems and branches of Myrtales trees. In this study, a total of 164 Cryphonectriaceae isolates were identified based on comparisons of DNA sequences of the partial conserved nuclear large subunit (LSU) ribosomal DNA, internal transcribed spacer (ITS) regions including the 5.8S gene of the ribosomal DNA operon, two regions of the β-tubulin (tub2/tub1) gene, and the translation elongation factor1-alpha (tef1) gene region, as well as their morphological characteristics. The results showed that eight species reside in four genera of Cryphonectriaceae occurring on the genera Eucalyptus, Melastoma (Melastomataceae), Psidium (Myrtaceae), Syzygium (Myrtaceae), and Terminalia (Combretaceae) in Myrtales. These fungal species include Chrysoporthe deuterocubensis, Celoporthe syzygii, Cel. eucalypti, Cel. guang-dongensis, Cel. cerciana, a new genus and two new species, as well as one new species of Aurifilum. These new taxa are hereby described as Parvosmorbus gen. nov., Par. eucalypti sp. nov., Par. guangdongensis sp. nov., and Aurifilum terminali sp. nov. Pathogenicity tests showed that the eight species of Cryphonectriaceae are pathogenic to two Eucalyptus hybrid seedlings, Melastoma sanguineum branches, and Psidium guajava and Syzygium jambos seedlings. Theoveralldatashowedthat Chr. deuterocubensis is the most aggressive, followed by Par. eucalypti. Significant differences in tolerance were observed between the two tested Eucalyptus hybrid genotypes, suggesting that disease-tolerant genotypes can be selected for disease management in the Eucalyptus industry.

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