scholarly journals Taxonomic relationships in the genus <i>Ammonia</i> (Foraminifera) based on ribosomal DNA sequences

2000 ◽  
Vol 19 (1) ◽  
pp. 85-95 ◽  
Author(s):  
Maria Holzmann ◽  
Jan Pawlowski
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Large Subunit ◽  
Morphological Variability ◽  
Small Subunit ◽  
Lsu Rdna ◽  
Taxonomic Relationships ◽  
Rdna Sequences ◽  
Ecological Features ◽  
Genotypic Group

Abstract. The genus Ammonia is a common benthic foraminifer which is widely distributed in nearshore marine environments. Its large morphological variability causes considerable difficulties in species identification. In the present study, we investigated taxonomic relationships in Ammonia by using a molecular approach based on ribosomal DNA sequences. We obtained 149 partial large subunit ribosomal DNA (LSU rDNA) sequences and 23 small subunit ribosomal DNA (SSU rDNA) sequences from 88 living Ammonia specimens which were collected from free-living populations in 14 localities. Sequence analysis revealed the presence of eight distinct genotypic groups (T1–T7, T9) and one distinct genotype that is represented by one specimen (T8). Examination of morphological characters shows that only one genotypic group can be clearly distinguished by its morphology. Biogeographical and ecological features are used for an additional characterization and it seems that the different groups live in relatively well defined environmental conditions and that only one genotypic group is cosmopolitan, while the others have a rather restricted geographical distribution. According to our study, three of the genotypic groups can be regarded as distinct species.

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.

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.

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.

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.

Discovery of a free-living nematode phylogenetically related to vertebrate parasites of the genus Strongyloides (Nematoda : Strongyloidoidea): morphological, anatomical and molecular characterisation

2016 ◽  
Vol 30 (4) ◽  
pp. 387
Author(s):  
Ren-E Huang ◽  
Runsheng Li ◽  
Zhongying Zhao
Keyword(s):  
Culture Media ◽  
Large Subunit ◽  
Molecular Genetic ◽  
Small Subunit ◽  
Land Snails ◽  
Rrna Genes ◽  
Lsu Rdna ◽  
Free Living ◽  
Rdna Sequences ◽  
Free Living Nematode

Nematodes are important, largely because they frequently act as parasites and threaten the health of plants, animals and even humans. Here, we describe an interesting free-living nematode from land snails on Luofu Mountain, Guangdong, China. Alloionema luofuensis, sp. nov. is phylogenetically related to slug-parasite A. appendiculatum and the well-known vertebrate parasites Strongyloides spp. based on small subunit (SSU) and the D2-D3 domain of large subunit (LSU) rDNA sequences. The new species possesses an extremely transparent body and is easily maintained using C. elegans culture media, suggesting a possible application prospect of this free-living nematode as a comparative model system for its related parasites. Morphology and anatomy of the gonochoristic A. luofuensis, sp. nov. adult were described and illustrated. The species is characterised by a filiform tail bisexually, ‘rhabditiform’ oesophagus and ‘rhabditid-like’ female anatomy, but its male caudal region is completely different from that of typical rhabditid nematodes, being absent from an enveloping bursa. It is the first marker taxon characterised morphologically as well as molecularly from the family Alloionematidae, a group of nematodes with hyperdiverse molecular genetic variations underlying highly conserved anatomy. Further molecular and genetic studies on A. luofuensis, sp. nov. populations hold promise to provide insight into evolution of the clade consisting of vertebrate parasites of the heterogonic nematode genus Strongyloides. This is because of its unusual high levels of heterozygosity maintained by the conserved rRNA genes of partial SSU and the D2-D3 domain of LSU for the type isolate of this species.

scholarly journals Isolation and Characterization of a Novel Facultative Anaerobic Filamentous Fungus from Japanese Rice Field Soil

2009 ◽  
Vol 2009 ◽  
pp. 1-9 ◽  
Author(s):  
Akio Tonouchi
Keyword(s):  
Filamentous Fungus ◽  
Rice Field ◽  
Large Subunit ◽  
Small Subunit ◽  
Lsu Rdna ◽  
Field Soil ◽  
Rice Field Soil ◽  
Rdna Sequences ◽  
Isolation And Characterization

A novel filamentous fungus strain designated RB-1 was isolated into pure culture from Japanese rice field soil through an anaerobic role tube technique. The strain is a mitosporic fungus that grows in both aerobic and strict anaerobic conditions using various mono-, di-, tri-, and polysaccharides with acetate and ethanol productions. The amount of acetate produced was higher than that of ethanol in both aerobic and anaerobic cultures. The characteristic verrucose or punctuate conidia of RB-1 closely resembled those of some strains of the genusThermomyces, a thermophilic or mesophilic anamorphic ascomycete. However, based on phylogenetic analysis with the small subunit (SSU) and large subunit (LSU) rDNA sequences, RB-1 was characterized as a member of the class Lecanoromycetes of the phylum Ascomycota. Currently, RB-1 is designated as an anamorphic ascomycete and is phylogenetically considered anincertae sediswithin the class Lecanoromycetes.

First taxonomic description of multivalvulidan myxosporean parasites from elasmobranchs: Kudoa hemiscylli n.sp. and Kudoa carcharhini n.sp. (Myxosporea: Multivalvulidae)

Parasitology ◽  
2010 ◽  
Vol 137 (13) ◽  
pp. 1885-1898 ◽  
Author(s):  
R. J. GLEESON ◽  
M. B. BENNETT ◽  
R. D. ADLARD
Keyword(s):  
Host Species ◽  
New Records ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Small Subunit ◽  
Lsu Rdna ◽  
Rdna Sequences ◽  
Taxonomic Description ◽  
Molecular Phylogenetic ◽  
Potential Impact

SUMMARYMyxosporean parasites are significant parasites of fishes not only for their apparent high diversity but also for their potential impact on fish health and/or marketability. Regardless, our knowledge of most myxosporeans, especially those found in elasmobranch hosts, is superficial. A study of multivalvulidan diversity in a range of elasmobranchs from Queensland, Western Australia and the Northern Territory (Australia) was conducted to address this knowledge gap. Specimens were collected from a total of 3 orders, 9 families and 31 species of elasmobranchs. Myxosporean infections referable to the genus Kudoa were discovered in host muscle and characterized morphologically and genetically. Both small subunit (SSU) and large subunit (LSU) rDNA sequences were used in molecular phylogenetic analyses. Kudoa spp. infected 27 of the 31 species of elasmobranchs examined, representing new records of this parasite genus in 26, of the 27, host species. Kudoids were observed in all 3 orders, and 7 out of the 9 families of elasmobranchs investigated. This paper reports the first 2 multivalvulidan species to be formally described from elasmobranchs, Kudoa hemiscylli n.sp. characterized from Hemiscyllium ocellatum (and 8 other host species) and Kudoa carcharhini n. sp. characterized from Carcharhinus cautus (and 2 other host species). Phylogenetic analyses revealed that kudoids from elasmobranchs form a separate lineage to those of teleosts, but are anchored within the overall kudoid clade.

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.

A Re-Examination of Generic Concepts of Baeomycetoid Lichens Based on Phylogenetic Analyses of Nuclear ssu and Lsu Ribosomal Dna

1999 ◽  
Vol 31 (5) ◽  
pp. 409-418 ◽  
Author(s):  
Jamie L. Platt ◽  
Joseph W. Spatafora
Keyword(s):  
Ribosomal Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Small Subunit ◽  
Lsu Rdna ◽  
Character State ◽  
Nucleotide Sequence Data ◽  
Lichen Symbiosis ◽  
Data Support

AbstractThe lichen symbiosis has evolved several times within the fungal kingdom, although the total number of lichenization events leading to extant taxa is still unclear. Two lichenized families, the Icmadophilaceae and Baeomycetaceae have been classified in the Helotiales. Because the Helotiales are predominantly nonlichenized, this suggests that these families represent independent evolutionary episodes of lichenization from the Lecanorales. As a first step towards understanding the evolution of the lichen symbiosis within this order, we tested recent hypotheses concerning the segregation of lichen genera between the two lichen families. Specifically, we used phylogenetic analyses of nucleotide sequence data from nuclear small-subunit and large-subunit ribosomal DNA to test the morphology-based hypotheses that Dibaeis is a distinct genus from Baeomyces and that Dibaeis is a member of the Icmadophilaceae rather than the Baeomycetaceae. Phylogenetic analyses of nuclear SSU rDNA and combined SSU and LSU rDNA data support the hypothesis that Dibaeis is more closely related to IcmadophUa than it is to Baeomyces. Therefore, these data support the resurrection of Dibaeis from its previous synonymy with Baeomyces based on the characters of ascocarp colour and ascus morphology. The recognition of two distinct genera is also consistent with character state distribution of unique lichen acids.

Sign in / Sign up

Export Citation Format

Share Document