Molecular phylogeny of onygenalean fungi based on small subunit ribosomal DNA (SSU rDNA) sequences

Mycoscience ◽  
1999 ◽  
Vol 40 (3) ◽  
pp. 251-258 ◽  
Author(s):  
Masato Sugiyama ◽  
Akiko Ohara ◽  
Takashi Mikawa
Keyword(s):  
Molecular Phylogeny ◽  
Ribosomal Dna ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Rdna Sequences ◽  
Small Subunit Ribosomal Dna

A phylogenetic study of the Micarea prasina group shows that Micarea micrococca includes three distinct lineages

2009 ◽  
Vol 42 (1) ◽  
pp. 7-21 ◽  
Author(s):  
Paweł CZARNOTA ◽  
Beata GUZOW-KRZEMIŃSKA
Keyword(s):  
Maximum Likelihood ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Maximum Parsimony ◽  
Small Subunit ◽  
Sister Species ◽  
Phylogenetic Study ◽  
Rdna Sequences ◽  
Small Subunit Ribosomal Dna

AbstractThe phylogeny of the Micarea prasina group was investigated using mitochondrial small subunit ribosomal DNA sequences from 14 taxa representing this group, four other members of the genus Micarea, and Psilolechia lucida as an outgroup. A total of 31 new mtSSU rDNA sequences were generated, including 10 from the M. micrococca complex. Bayesian, maximum parsimony (MP) and maximum likelihood (ML) methods were used to analyse the data. The results show that M. micrococca is not monophyletic and forms three strongly supported lineages: 1) M. micrococca s. str., 2) M. byssacea (Th. Fr.) Czarnota, Guzow-Krzemińska & Coppins comb. nov., and 3) a putative taxon that requires further studies. Micarea viridileprosa is a sister species to M. micrococca s. str. and the recently described M. nowakii is a sister species to M. prasina s. str. The placement of M. tomentosa within the M. prasina group is confirmed. Micarea hedlundii appears to be more closely related to the M. micrococca complex than M. prasina s. str. Descriptions, illustrations, taxonomic remarks, distribution and habitat data for M. micrococca s. str. and M. byssacea are provided. A lectotype for Biatora byssacea Hampe non Zwackh and a neotype for Catillaria prasina β [var.] byssacea are selected.

Molecular phylogeny of Laminariales (Phaeophyceae) inferred from small subunit ribosomal DNA sequences

1999 ◽  
Vol 47 (2) ◽  
pp. 109-114 ◽  
Author(s):  
Sung Min Boo ◽  
Wook Jae Lee ◽  
Hwan Su Yoon ◽  
Atsushi Kato ◽  
Hiroshi Kawai
Keyword(s):  
Molecular Phylogeny ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
Small Subunit ◽  
Small Subunit Ribosomal Dna

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.

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.

scholarly journals Small Subunit Ribosomal DNA-Based Phylogenetic Analysis of Foliar Nematodes (Aphelenchoides spp.) and Their Quantitative Detection in Complex DNA Backgrounds

2012 ◽  
Vol 102 (12) ◽  
pp. 1153-1160 ◽  
Author(s):  
Katarzyna Rybarczyk-Mydłowska ◽  
Paul Mooyman ◽  
Hanny van Megen ◽  
Sven van den Elsen ◽  
Mariëtte Vervoort ◽  
...  
Keyword(s):  
Ribosomal Dna ◽  
Developmental Stages ◽  
Nematode Species ◽  
Morphological Characters ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Rapid Screening ◽  
Quantitative Detection ◽  
Small Subunit Ribosomal Dna ◽  
Plant Parasitic

Foliar nematodes, plant-parasitic representatives of the genus Aphelenchoides, constitute a minority in a group dominated by fungivorous species. Distinction between (mostly harmless) fungal feeding Aphelenchoides species and high impact plant parasites such as A. besseyi, A. fragariae, A. ritzemabosi, and A. subtenuis is severely hampered by the scarcity of informative morphological characters, some of which are only observable in specific developmental stages. Poor description of a number of non-plant-parasitic Aphelenchoides species further complicates identification. Based on (nearly) full-length small subunit ribosomal DNA (SSU rDNA) sequences (≈1,700 bp), a phylogenetic tree was generated, and the four target species appeared as distinct, well-supported groups. Notably, this genus does not constitute a monophyletic group: A. besseyi and A. ritzemabosi cluster together and they are phylogenetically isolated from A. fragariae, A. subtenuis, and most other fungivorous species. A phylum-wide SSU rDNA framework was used to identify species-specific DNA motifs. For the molecular detection of four plant-parasitic Aphelenchoides species, polymerase chain reaction primers were developed with high, identical annealing temperatures (63°C). Within the molecular framework presented here, these primers can be used for the rapid screening of plant material and soil for the presence of one or multiple foliar nematode species.

scholarly journals Phylogenetic relationships, based on SSU rDNA sequences, among the didelphic genera of the family Trichodoridae from Portugal

Nematology ◽  
2010 ◽  
Vol 12 (2) ◽  
pp. 171-180 ◽  
Author(s):  
Isabel M. Duarte ◽  
Maria Teresa M. de Almeida ◽  
Derek J.F. Brown ◽  
Isabel Marques ◽  
Roy Neilson ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Small Subunit ◽  
Ssu Rdna ◽  
Indigenous Populations ◽  
Molecular Analyses ◽  
Rdna Sequences ◽  
The Family ◽  
Northern Regions ◽  
First Time ◽  
Small Subunit Ribosomal Dna

Abstract A survey of virus vector trichodorid nematodes was carried out in the central and northern regions of Portugal. Morphobiometric identification showed the presence of trichodorid species previously reported from Portugal, except for Paratrichodorus porosus, which is reported for the first time in Continental Europe. Small subunit ribosomal DNA (SSU rDNA) sequences of ten different species occurring in Portugal were obtained and a phylogenetic analysis based on their alignment was performed to infer relationships among the different Portuguese trichodorid species and three non-indigenous populations (Nanidorus minor, P. allius and P. teres). The resulting phylogenetic tree is in agreement with the currently accepted classification for Trichodoridae, except for Nanidorus, which clusters together with Trichodorus species, while the genera Paratrichodorus and Trichodorus appear as two distinct groups. A better understanding of the generic groupings in the family Trichodoridae was found. Based on the new molecular analyses we herein accept Nanidorus as a valid genus.

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