scholarly journals Molecular systematics of the Phyllachorales (ascomycota, fungi) based on 18S ribosomal DNA sequences

2003 ◽  
Vol 46 (3) ◽  
pp. 315-322 ◽  
Author(s):  
Denise Wanderlei-Silva ◽  
Eduardo Ramalho Neto ◽  
Richard Hanlin
Keyword(s):  
Molecular Systematics ◽  
Ribosomal Dna ◽  
Dna Sequences ◽  
18S Rdna ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
The Other ◽  
Maximum Parsimony Analysis ◽  
Rrna Gene ◽  
Parsimony Analysis

In order to evaluate the monophyly of the Phyllachorales from a molecular standpoint and elucidate its phylogenetic relationships with other orders, a segment of the 18S rRNA gene from several representatives of the Phyllachorales, including species of Glomerella, Phyllachora, Coccodiella (=Coccostroma), Sphaerodothis, Ophiodothella, as well as Magnaporthe was sequenced. Maximum Parsimony analysis revealed that the Phyllachorales was a polyphyletic assemblage of taxa. None of the other members of the Phyllachorales, which produced either a clypeus or stroma, clustered with Glomerella. Of the taxa examined, was Coccodiella the closest relative of Phyllachora. Magnaporthe was closely related to the Diaporthales. Our 18S rDNA data highly supported Glomerella being accommodated in a separate family.

scholarly journals Confirmatory Evidence from 18S rRNA Gene Analysis for In Vivo Development of Propamidine Resistance in a Temporal Series ofAcanthamoeba Ocular Isolates from a Patient

1998 ◽  
Vol 42 (8) ◽  
pp. 2144-2145 ◽  
Author(s):  
Dolena R. Ledee ◽  
David V. Seal ◽  
Thomas J. Byers
Keyword(s):  
Mixed Infection ◽  
Dna Sequences ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Gene Analysis ◽  
Rrna Gene ◽  
Temporal Series ◽  
Before And After

ABSTRACT DNA sequences of three 18S rRNA gene alleles present in trophozoites obtained before and after therapy forAcanthamoeba keratitis substantiate a previous report that the infection was due to a single Acanthamoeba strain. Thus, the possibility that propamidine resistance which developed during therapy was due to a mixed infection was ruled out.

scholarly journals Comparison of potential diatom ‘barcode’ genes (the 18S rRNA gene and ITS, COI, rbcL) and their effectiveness in discriminating and determining species taxonomy in the Bacillariophyta

2015 ◽  
Vol 65 (Pt_4) ◽  
pp. 1369-1380 ◽  
Author(s):  
Liliang Guo ◽  
Zhenghong Sui ◽  
Shu Zhang ◽  
Yuanyuan Ren ◽  
Yuan Liu
Keyword(s):  
Phylogenetic Trees ◽  
18S Rrna ◽  
Mitochondrial Gene ◽  
Large Subunit ◽  
18S Rrna Gene ◽  
Marine Ecology ◽  
The Other ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Potential Marker

Diatoms form an enormous group of photoautotrophic micro-eukaryotes and play a crucial role in marine ecology. In this study, we evaluated typical genes to determine whether they were effective at different levels of diatom clustering analysis to assess the potential of these regions for barcoding taxa. Our test genes included nuclear rRNA genes (the nuclear small-subunit rRNA gene and the 5.8S rRNA gene+ITS-2), a mitochondrial gene (cytochrome c-oxidase subunit 1, COI), a chloroplast gene [ribulose-1,5-biphosphate carboxylase/oxygenase large subunit (rbcL)] and the universal plastid amplicon (UPA). Calculated genetic divergence was highest for the internal transcribed spacer (ITS; 5.8S+ITS-2) (p-distance of 1.569, 85.84 % parsimony-informative sites) and COI (6.084, 82.14 %), followed by the 18S rRNA gene (0.139, 57.69 %), rbcL (0.120, 42.01 %) and UPA (0.050, 14.97 %), which indicated that ITS and COI were highly divergent compared with the other tested genes, and that their nucleotide compositions were variable within the whole group of diatoms. Bayesian inference (BI) analysis showed that the phylogenetic trees generated from each gene clustered diatoms at different phylogenetic levels. The 18S rRNA gene was better than the other genes in clustering higher diatom taxa, and both the 18S rRNA gene and rbcL performed well in clustering some lower taxa. The COI region was able to barcode species of some genera within the Bacillariophyceae. ITS was a potential marker for DNA based-taxonomy and DNA barcoding of Thalassiosirales, while species of Cyclotella, Skeletonema and Stephanodiscus gathered in separate clades, and were paraphyletic with those of Thalassiosira. Finally, UPA was too conserved to serve as a diatom barcode.

scholarly journals On the identity of Aleochara (Coprochara) pauxilla (Mulsant & Rey, 1874) (Coleoptera: Staphylinidae).

2001 ◽  
Vol 51 (1) ◽  
pp. 223-229
Author(s):  
Christian Maus
Keyword(s):  
Molecular Systematics ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene

Identität und taxonomischer Status von Aleochara pauxilla (Mulsant & Rey, 1874) werden aufgrund der morphologischen Merkmalen und DNA-Sequenzdaten (COI/II- und 18S rRNA-Gene) untersucht. A. pauxilla (Mulsant & Rey, 1874) ist ein Synonym von A. verna, A. pauxilla auct. nec Mulsant & Rey ist konspezifisch mit A. binotata. Ein Lectotypus für A. pauxilla wird designiert.StichwörterColeoptera, Staphylinidae, Aleocharinae, Aleochara, Coprochara, taxonomy, molecular systematics, COI/II, 18S rRNA.Nomenklatorische Handlungenpauxilla Mulsant & Rey, 1874 (Baryodma), Lectotype; syn. n. of Aleochara verna Sharp, 1836

scholarly journals Soil-dwelling polychaetes: enigmatic as ever? Some hints on their phylogenetic relationships as suggested by a maximum parsimony analysis of 18S rRNA gene sequences

2001 ◽  
Vol 70 (3) ◽  
pp. 127-138 ◽  
Author(s):  
Emilia Rota ◽  
Patrick Martin ◽  
Christer Erséus
Keyword(s):  
Phylogenetic Relationships ◽  
Maximum Parsimony ◽  
Systematic Position ◽  
18S Rrna Gene ◽  
Maximum Parsimony Analysis ◽  
Rrna Gene ◽  
Parsimony Analysis ◽  
Data Set ◽  
Independent Evidence ◽  
Rdna Sequences

To re-evaluate the various hypotheses on the systematic position of Parergodrilus heideri Reisinger, 1925 and Hrabeiella periglandulata Pizl & Chalupský, 1984, the sole truly terrestrial non-clitellate annelids known to date, their phylogenetic relationships were investigated using a data set of new 18S rDNA sequences of these and other five relevant annelid taxa, including an unknown species of Ctenodrilidae, as well as homologous sequences already available for 18 polychaetes, one aphanoneuran, 11 clitellates, two pogonophorans, one echiuran, one sipunculan, three molluscs and two arthropods. Two different alignments were constructed, according to an algorithmic method (Clustal W) and on the basis of a secondary structure model (DCSE), A maximum parsimony analysis was performed with arthropods as an unambiguous outgroup. With both alignments, the resulting topology confirms the validity of grouping P. heideri and Stygocapitella subterranean Knöllner, 1934 into the family Parergodrilidae. Hrabeiella periglandulata never clusters with them and its position relative to this and other polychaete families is still obscure, but a close relationship with aphanoneurans is suggested by the most parsimonious trees. All these taxa appear to be far from the Clitellata. Most relationships among polychaetes are not supported by significant bootstrap and Bremer values. These polytomies are corroborated by independent evidence and are interpreted as resulting from an ancient emergence and a rapid radiation of Polychaeta.

scholarly journals Ecological and evolutionary patterns in the enigmatic protist genus Percolomonas (Heterolobosea; Discoba) from diverse habitats

2019 ◽  
Author(s):  
Denis V. Tikhonenkov ◽  
Soo Hwan Jhin ◽  
Yana Eglit ◽  
Kai Miller ◽  
Andrey Plotnikov ◽  
...  
Keyword(s):  
18S Rdna ◽  
Phylogenetic Trees ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Heterotrophic Flagellate ◽  
Evolutionary Patterns ◽  
The Usa ◽  
Saline Habitats ◽  
Morphological Differences

AbstractThe heterotrophic flagellate Percolomonas cosmopolitus (Heterolobosea) is often observed in saline habitats worldwide that range from coastal waters to saturated brines. However, only two cultures assigned to this morphospecies have been examined using molecular methods, and their 18S rRNA gene sequences are extremely different. Further the salinity tolerances of individual strains are unknown. Thus, our knowledge on the autecology and diversity in this morphospecies is deficient. Here, we report 18S rRNA gene data on seven strains similar to P. cosmopolitus from seven geographically remote locations (New Zealand, Kenya, Korea, Poland, Russia, Spain, and the USA) with sample salinities ranging from 4‰ to 280‰, and compare morphology and salinity tolerance of the nine available strains. Percolomonas cosmopolitus-like strains show few-to-no consistent morphological differences, and form six clades separated by often extremely large 18S rDNA divergences (up to 42.4%). Some strains grew best at salinities from 75 to 125‰ and represent halophiles. All but one of these belonged to two geographically heterogeneous clusters that formed a robust monophyletic group in phylogenetic trees; this likely represents an ecologically specialized subclade of halophiles. Our results suggest that P. cosmopolitus is a cluster of several cryptic species (at least), which are unlikely to be distinguished by geography. Interestingly, the 9 Percolomonas strains formed a clade in 18S rDNA phylogenies, unlike most previous analyses based on two sequences.

scholarly journals An analysis on the divergence of Chironomid spp. based on the study of 18S rRNA and polytene chromosome organization in the species revealing the role of environment on speciation

2021 ◽  
Vol 82 (1) ◽  
Author(s):  
Sanjay Kumar Dey ◽  
Swapna Bhaduri ◽  
Trilochan Midya
Keyword(s):  
Polytene Chromosome ◽  
Dna Sequences ◽  
18S Rrna ◽  
Molecular Classification ◽  
18S Rrna Gene ◽  
Chromosome Band ◽  
Chromosome Organization ◽  
Rrna Gene ◽  
Molecular Architecture ◽  
Chironomid Species

Abstract Background Nine species of Chironomus evolved throughout the world were measured for their divergence with regard to their DNA sequences concerning 18S rRNA since it is conserved for a specific species. With the advancement of the field of molecular evolution, cytogenetics requires further correlation between molecular architecture and morphological features of a species to compare amongst others to decipher their role in speciation. Therefore, divergence of DNA sequences of the Chironomus were compared with differences in the polytene chromosome features of most of the species under this investigation to evaluate underlying correlation among them, if any, to finally establish a novel method of molecular classification broadly applicable in cytogenetics studies. Results When Chironomus javanus Kieffer was considered as a reference organism, an in silico pair-wise alignment of sequences for the 18S rRNA gene regions of the other eight different species of the same genus exhibited nucleotide sequence homology ranging from 67 to 98%. This divergence of the species under consideration might be due to environmental impact causing alteration of nitrogenous bases probably due to mismatch pairing in DNA replication. This may be suggested as a cause of evolution of species in nature. A concomitant study on the polytene chromosome band patterns of majority of these species belonging to this series also indicated a divergence ranging from 10% to 30%. Conclusions Sequence analysis based on 18S rRNA of nine species of Chironomus under this investigation shows a similarity in the polytene chromosome organization in most of the Chironomid species of the series. Hence, molecular divergence in the species is consistent with cytological difference among Chironomid species. Therefore, molecular data based on 18S rRNA and cytological characters based on the polytene chromosome features of the Chironomid species may be useful for their taxonomical recognition. Moreover, variations concerning two aspects of this study may be correlated to their environmental distinctions.

scholarly journals Analytical validation of a real-time hydrolysis probe PCR assay for quantifying Plasmodium falciparum parasites in experimentally infected human adults

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Claire Y. T. Wang ◽  
Emma L. Ballard ◽  
Zuleima Pava ◽  
Louise Marquart ◽  
Jane Gaydon ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Plasmodium Falciparum ◽  
18S Rrna ◽  
Drug Efficacy ◽  
18S Rrna Gene ◽  
Molecular Techniques ◽  
Qpcr Assay ◽  
Rrna Gene ◽  
Analytical Sensitivity ◽  
Blood Samples

Abstract Background Volunteer infection studies have become a standard model for evaluating drug efficacy against Plasmodium infections. Molecular techniques such as qPCR are used in these studies due to their ability to provide robust and accurate estimates of parasitaemia at increased sensitivity compared to microscopy. The validity and reliability of assays need to be ensured when used to evaluate the efficacy of candidate drugs in clinical trials. Methods A previously described 18S rRNA gene qPCR assay for quantifying Plasmodium falciparum in blood samples was evaluated. Assay performance characteristics including analytical sensitivity, reportable range, precision, accuracy and specificity were assessed using experimental data and data compiled from phase 1 volunteer infection studies conducted between 2013 and 2019. Guidelines for validation of laboratory-developed molecular assays were followed. Results The reportable range was 1.50 to 6.50 log10 parasites/mL with a limit of detection of 2.045 log10 parasites/mL of whole blood based on a parasite diluted standard series over this range. The assay was highly reproducible with minimal intra-assay (SD = 0.456 quantification cycle (Cq) units [0.137 log10 parasites/mL] over 21 replicates) and inter-assay (SD = 0.604 Cq units [0.182 log10 parasites/mL] over 786 qPCR runs) variability. Through an external quality assurance program, the QIMR assay was shown to generate accurate results (quantitative bias + 0.019 log10 parasites/mL against nominal values). Specificity was 100% after assessing 164 parasite-free human blood samples. Conclusions The 18S rRNA gene qPCR assay is specific and highly reproducible and can provide reliable and accurate parasite quantification. The assay is considered fit for use in evaluating drug efficacy in malaria clinical trials.

scholarly journals 16S rRNA gene and 18S rRNA gene diversity in microbial mat communities in meltwater ponds on the McMurdo Ice Shelf, Antarctica

Polar Biology ◽  
2021 ◽  
Author(s):  
Eleanor E. Jackson ◽  
Ian Hawes ◽  
Anne D. Jungblut
Keyword(s):  
16S Rrna ◽  
18S Rrna ◽  
High Throughput Sequencing ◽  
Microbial Mats ◽  
Gene Diversity ◽  
Salinity Gradient ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Ice Shelf ◽  
The Impact

AbstractThe undulating ice of the McMurdo Ice Shelf, Southern Victoria Land, supports one of the largest networks of ice-based, multiyear meltwater pond habitats in Antarctica, where microbial mats are abundant and contribute most of the biomass and biodiversity. We used 16S rRNA and 18S rRNA gene high-throughput sequencing to compare variance of the community structure in microbial mats within and between ponds with different salinities and pH. Proteobacteria and Cyanobacteria were the most abundant phyla, and composition at OTU level was highly specific for the meltwater ponds with strong community sorting along the salinity gradient. Our study provides the first detailed evaluation of eukaryote communities for the McMurdo Ice Shelf using the 18S rRNA gene. They were dominated by Ochrophyta, Chlorophyta and Ciliophora, consistent with previous microscopic analyses, but many OTUs belonging to less well-described heterotrophic protists from Antarctic ice shelves were also identified including Amoebozoa, Rhizaria and Labyrinthulea. Comparison of 16S and 18S rRNA gene communities showed that the Eukaryotes had lower richness and greater similarity between ponds in comparison with Bacteria and Archaea communities on the McMurdo Ice shelf. While there was a weak correlation between community dissimilarity and geographic distance, the congruity of microbial assemblages within ponds, especially for Bacteria and Archaea, implies strong habitat filtering in ice shelf meltwater pond ecosystems, especially due to salinity. These findings help to understand processes that are important in sustaining biodiversity and the impact of climate change on ice-based aquatic habitats in Antarctica.

scholarly journals 18S rRNA gene sequences of leptocephalus gut contents, particulate organic matter, and biological oceanographic conditions in the western North Pacific

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tsuyoshi Watanabe ◽  
Satoshi Nagai ◽  
Yoko Kawakami ◽  
Taiga Asakura ◽  
Jun Kikuchi ◽  
...  
Keyword(s):  
Organic Matter ◽  
Particulate Organic Matter ◽  
North Pacific ◽  
Western North Pacific ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Gut Contents ◽  
Rrna Gene ◽  
Marine Snow ◽  
Chlorophyll Maximum

AbstractEel larvae apparently feed on marine snow, but many aspects of their feeding ecology remain unknown. The eukaryotic 18S rRNA gene sequence compositions in the gut contents of four taxa of anguilliform eel larvae were compared with the sequence compositions of vertically sampled seawater particulate organic matter (POM) in the oligotrophic western North Pacific Ocean. Both gut contents and POM were mainly composed of dinoflagellates as well as other phytoplankton (cryptophytes and diatoms) and zooplankton (ciliophoran and copepod) sequences. Gut contents also contained cryptophyte and ciliophoran genera and a few other taxa. Dinoflagellates (family Gymnodiniaceae) may be an important food source and these phytoplankton were predominant in gut contents and POM as evidenced by DNA analysis and phytoplankton cell counting. The compositions of the gut contents were not specific to the species of eel larvae or the different sampling areas, and they were most similar to POM at the chlorophyll maximum in the upper part of the thermocline (mean depth: 112 m). Our results are consistent with eel larvae feeding on marine snow at a low trophic level, and feeding may frequently occur in the chlorophyll maximum in the western North Pacific.

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