scholarly journals An updated view of kinetoplastid phylogeny using environmental sequences and a closer outgroup: proposal for a new classification of the class Kinetoplastea

2004 ◽  
Vol 54 (5) ◽  
pp. 1861-1875 ◽  
Author(s):  
David Moreira ◽  
Purificación López-García ◽  
Keith Vickerman
Keyword(s):  
18S Rrna ◽  
Phylogenetic Analyses ◽  
Pcr Amplification ◽  
Rrna Genes ◽  
Close Relative ◽  
New Classification ◽  
Direct Pcr ◽  
Scientific Attention ◽  
18S Rrna Genes

Given their ecological and medical importance, the classification of the kinetoplastid protists (class Kinetoplastea) has attracted much scientific attention for a long time. Morphology-based taxonomic schemes distinguished two major kinetoplastid groups: the strictly parasitic, uniflagellate trypanosomatids and the biflagellate bodonids. Molecular phylogenetic analyses based on 18S rRNA sequence comparison suggested that the trypanosomatids emerged from within the bodonids. However, these analyses revealed a huge evolutionary distance between the kinetoplastids and their closest relatives (euglenids and diplonemids) that makes very difficult the correct inference of the phylogenetic relationships between the different kinetoplastid groups. Using direct PCR amplification of 18S rRNA genes from hydrothermal vent samples, several new kinetoplastid-like sequences have been reported recently. Three of them emerge robustly at the base of the kinetoplastids, breaking the long branch leading to the euglenids and diplonemids. One of these sequences belongs to a close relative of Ichthyobodo necator (a fish parasite) and of the ‘Perkinsiella amoebae’-like endosymbiont of Neoparamoeba spp. amoebae. The authors have studied the reliability of their basal position and used all these slow-evolving basal-emerging sequences as a close outgroup to analyse the phylogeny of the apical kinetoplastids. They thus find a much more stable and resolved kinetoplastid phylogeny, which supports the monophyly of groups that very often emerged as polyphyletic in the trees rooted using the traditional, distant outgroup sequences. A new classification of the class Kinetoplastea is proposed based on the results of the phylogenetic analysis presented. This class is now subdivided into two new subclasses, Prokinetoplastina (accommodating the basal species I. necator and ‘Perkinsiella amoebae’) and Metakinetoplastina (containing the Trypanosomatida together with three additional new orders: Eubodonida, Parabodonida and Neobodonida). The classification of the species formerly included in the genus Bodo is also revised, with the amendment of this genus and the genus Parabodo and the creation of a new genus, Neobodo.

Phylogeny of hymenolepidids (Cestoda: Cyclophyllidea) from mammals: sequences of 18S rRNA and COI genes confirm major clades revealed by the 28S rRNA analyses

2021 ◽  
Vol 95 ◽  
Author(s):  
B. Neov ◽  
G.P. Vasileva ◽  
G. Radoslavov ◽  
P. Hristov ◽  
D.T.J. Littlewood ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
18S Rrna ◽  
Phylogenetic Analyses ◽  
The Other ◽  
Rrna Genes ◽  
Host Switching ◽  
28S Rrna ◽  
Mitochondrial Cytochrome ◽  
Rapid Radiation ◽  
18S Rrna Genes

Abstract The aim of the study is to test a hypothesis for the phylogenetic relationships among mammalian hymenolepidid tapeworms, based on partial (D1–D3) nuclear 28S ribosomal RNA (rRNA) genes, by estimating new molecular phylogenies for the group based on partial mitochondrial cytochrome c oxidase I (COI) and nuclear 18S rRNA genes, as well as a combined analysis using all three genes. New sequences of COI and 18S rRNA genes were obtained for Coronacanthus integrus, C. magnihamatus, C. omissus, C. vassilevi, Ditestolepis diaphana, Lineolepis scutigera, Spasskylepis ovaluteri, Staphylocystis tiara, S. furcata, S. uncinata, Vaucherilepis trichophorus and Neoskrjabinolepis sp. The phylogenetic analyses confirmed the major clades identified by Haukisalmi et al. (Zoologica Scripta 39: 631–641, 2010): Ditestolepis clade, Hymenolepis clade, Rodentolepis clade and Arostrilepis clade. While the Ditestolepis clade is associated with soricids, the structure of the other three clades suggests multiple evolutionary events of host switching between shrews and rodents. Two of the present analyses (18S rRNA and COI genes) show that the basal relationships of the four mammalian clades are branching at the same polytomy with several hymenolepidids from birds (both terrestrial and aquatic). This may indicate a rapid radiation of the group, with multiple events of colonizations of mammalian hosts by avian parasites.

scholarly journals Genetic diversity in the Alpine flatworm <i>Crenobia alpina</i>

Web Ecology ◽  
2017 ◽  
Vol 17 (2) ◽  
pp. 29-35 ◽  
Author(s):  
Martin Brändle ◽  
Jan Sauer ◽  
Lars Opgenoorth ◽  
Roland Brandl
Keyword(s):  
18S Rrna ◽  
Phylogenetic Analyses ◽  
Rrna Genes ◽  
Dispersal Ability ◽  
European Alps ◽  
Habitat Specificity ◽  
Limited Dispersal ◽  
The Alps ◽  
18S Rrna Genes ◽  
Species Speciation

Abstract. The freshwater flatworm Crenobia alpina (Platyhelminthes, Tricladida, Planariidae) lives almost exclusively in cold springs and crenal streams and possesses only limited dispersal ability. In this study fragments of the COI and 18S rRNA genes were used to estimate genetic divergences among 37 C. alpina populations from the European Alps. Phylogenetic analyses revealed five geographically and genetically distinct groups and at least 10 distinct lineages of C. alpina across the European Alps. Our study suggests that C. alpina represents a complex of numerous cryptic species. Speciation (allopatric and/or sympatric) may have been facilitated by the orogenetic activity of the Alps and the high habitat specificity.

Description of Rotylenchus arasbaranensis n. sp. from Iran with discussion on the taxonomic status of Plesiorotylenchus Vovlas, Castillo & Lamberti, 1993 (Nematoda: Hoplolaimidae)

Nematology ◽  
2014 ◽  
Vol 16 (9) ◽  
pp. 1019-1045 ◽  
Author(s):  
Mohammad Reza Atighi ◽  
Ebrahim Pourjam ◽  
Razieh Ghaemi ◽  
Majid Pedram ◽  
Gracia Liébanas ◽  
...  
Keyword(s):  
18S Rrna ◽  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Original Description ◽  
Molecular Data ◽  
Rrna Genes ◽  
Molecular Studies ◽  
18S Rrna Genes ◽  
First Time ◽  
Partial 18S

Rotylenchus arasbaranensis n. sp., a new monosexual species is described and illustrated based on morphological, morphometric and molecular studies. The new species is characterised by having an offset and hemispherical lip region with 5-6 annuli, 32-36 μm long stylet, vulva located at 43.9-59.2% with a single epiptygma and rounded tail, rarely bilobed, with 6-8 annuli. The species R. striaticeps and the male of R. buxophilus are reported for the first time from Iran and R. fragaricus is reported and studied for the second time after its original description. The results of the phylogenetic analyses based on the sequences of the D2-D3 expansion region of the 28S, ITS1-rRNA and the partial 18S rRNA genes were provided for the studied species, confirming their differences from each other and determining the position of them and their relationships with closely related taxa. Also, the validity of Plesiorotylenchus is discussed on the basis of molecular data and its synonymisation (with only one sequence) with Rotylenchus is accepted.

A morphological and molecular reinvestigation of Janickina pigmentifera (Grassi, 1881) Chatton 1953 – an amoebozoan parasite of arrow-worms (Chaetognatha)

2021 ◽  
Vol 71 (11) ◽  
Author(s):  
Ekaterina Volkova ◽  
Alexander Kudryavtsev
Keyword(s):  
18S Rrna ◽  
Phylogenetic Analyses ◽  
18S Rrna Gene ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Intracellular Symbiont ◽  
Microscopic Features ◽  
Parasitic Lifestyle ◽  
18S Rrna Genes ◽  
Arrow Worms

Amoebozoan parasites of arrow-worms (Chaetognatha) were isolated from their hosts living in plankton of the Bay of Villefranche (Mediterranean Sea). Based on the light microscopic characters, the amoebae were identified as Janickina pigmentifera (Grassi, 1881) by their limax locomotive form and due to the presence of the intracellular symbiont, Perkinsela amoebae, surrounded by a layer of pigment granules. Sequences of the 18S rRNA gene of both J. pigmentifera and its symbiont were obtained for the first time. The molecular phylogenetic analyses of 18S rRNA gene placed J. pigmentifera within the genus Neoparamoeba, a taxon also characterized by the presence of a symbiont, known as Perkinsela amoebae-like organism (PLO). The 18S rRNA gene sequence of P. amoebae from J. pigmentifera grouped with the sequences of 18S rRNA genes of PLOs from Neoparamoeba branchiphila and Neoparamoeba invadens. The first photo documentation of the light microscopic features of J. pigmentifera, such as locomotive form, the morphology of the nucleus and P. amoebae have been provided. The new results support the affinity of J. pigmentifera with the family Paramoebidae suggested previously based on the presence of PLO. In contrast to Janickina, typical members of Paramoebidae (Neoparamoeba and Paramoeba) have a flattened, dactylopodial locomotive form. This discrepancy in morphology can be explained by the obligate parasitic lifestyle of Janickina.

The use of large and small subunits of ribosomal DNA in evaluating phylogenetic relationships between species ofCornudiscoidesKulkarni, 1969 (Monogenoidea: Dactylogyridae) from India

2016 ◽  
Vol 91 (2) ◽  
pp. 206-214 ◽  
Author(s):  
J. Verma ◽  
N. Agrawal ◽  
A.K. Verma
Keyword(s):  
Ribosomal Dna ◽  
18S Rrna ◽  
Phylogenetic Analyses ◽  
Rrna Genes ◽  
28S Rrna ◽  
Ganges River ◽  
Mystus Vittatus ◽  
Ribosomal Subunits ◽  
18S Rrna Genes ◽  
High Degree

AbstractTwo partial regions of ribosomal DNA (28S and 18S) were used to evaluate genetic variations among the species ofCornudiscoides,viz.C. proximus, C. geminusandC. agarwali, all parasites ofMystus vittatus(Bagridae) from River Gomati, Ganges River basin, India. Our findings demonstrated that both the large and small ribosomal subunits are useful for species identification and genetic characterization of parasites, leading to resolution of inter/intra-relationships at generic and specific levels. The secondary structures of all three species for 28S and 18S rRNA genes contained exact pattern matches (EMPs) displaying the high degree of similarity among them. The phylogenetic analyses within the members of Dactylogyridae demonstrated that species ofCornudiscoidescluster together for 28S rRNA and 18S rRNA genes.

scholarly journals Eucaryotic Diversity in a Hypersaline Microbial Mat

2007 ◽  
Vol 74 (1) ◽  
pp. 329-332 ◽  
Author(s):  
Leah M. Feazel ◽  
John R. Spear ◽  
Alicia B. Berger ◽  
J. Kirk Harris ◽  
Daniel N. Frank ◽  
...  
Keyword(s):  
18S Rrna ◽  
Microbial Mat ◽  
Rrna Genes ◽  
Clone Libraries ◽  
18S Rrna Genes

ABSTRACT To determine the eucaryotic diversity of the hypersaline Guerrero Negro microbial mat, we amplified 18S rRNA genes from DNA extracted from this mat and constructed and analyzed clone libraries. The extent of eucaryotic diversity detected was remarkably low, only 15 species among 890 clones analyzed. Six eucaryotic kingdoms were represented, as well as a novel cluster of sequences. Nematode sequences dominated the clone libraries.

scholarly journals Crenosoma striatum in lungs of European hedgehogs (Erinaceus europeus) from Portugal

2020 ◽  
Vol 57 (2) ◽  
pp. 179-184
Author(s):  
P. F. Barradas ◽  
A. R. Flores ◽  
T. L. Mateus ◽  
F. Carvalho ◽  
F. Gärtner ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
18S Rrna ◽  
Population Sample ◽  
Genetic Data ◽  
Rrna Genes ◽  
12S Rrna ◽  
Rrna Gene ◽  
Mitochondrial 12S Rrna ◽  
18S Rrna Genes

SummaryCrenosoma striatum is a host-specifi c metastrongiloid nematode causing respiratory tract disease in hedgehogs (Erinaceus europaeus). Since few studies have reported C. striatum in hedgehogs and little genetic data is available concerning this lungworm, this study aimed to determine the occurrence of C. striatum in a population sample of hedgehogs from Portugal, additionally providing morphological, histological and molecular data. From 2017 to 2018 a survey of infection was carried out in 11 necropsied hedgehogs. Worms were extracted from fresh lung tissues and microscopically evaluated. Molecular characterization of partial mitochondrial (12S rRNA) and nuclear (18S rRNA) genes was performed. The presence of lungworms in pulmonary tissues of five hedgehogs (45.5%) was detected. Morphological and histopathological analyses evidenced adult forms of nematodes consistent with C. striatum. Molecular characterization of 18S rRNA genes confirmed the classifi cation as C. striatum. Also, novel genetic data characterizing the mitochondrial (12S rRNA) gene of C. striatum is presented.This is the first report of C. striatum infection in hedgehogs of Portugal. The findings here reported provide new insights regarding the geographic distribution and the molecular identification of this lungworm species.

scholarly journals Molecular identification and phylogenetic analysis of suaeda maritima from parangipettai coastal areas, southeast coast of india

2020 ◽  
Vol 7 (1) ◽  
pp. 28-34
Author(s):  
Anbarasi G ◽  
Vishnupriya B
Keyword(s):  
18S Rrna ◽  
Spinacia Oleracea ◽  
Genetic Material ◽  
Rrna Genes ◽  
Atriplex Canescens ◽  
Salt Marsh Plant ◽  
Suaeda Maritima ◽  
Atriplex Torreyi ◽  
18S Rrna Genes ◽  
Study Species

Conventional taxonomy is limited with delineating species and controversies arise with DNA barcoding based identifications. Hence, an alternative supporting approach is very much needed to identify species and differentiate them within the species based on the genetic material. 18S rRNA genes have been particularly helpful in analyzing phylogeny at the species level. In addition, bioinformatics which represents a new, growing area of science uses computational approaches to answer biological questions. Salt tolerant costal salt marsh plant of Suaeda maritima was selected for 18s rRNA sequencing to solve the ambiguity in itsspecies level identification. Similarity search of study species shared 99% similarity with 5 species of Atriplex canescens clone s128, Atriplex torreyi var. griffithsii clone p508, Spinacia oleracea, Oenothera laciniata clone,Beta vulgaris. Phylogenetic tree infer that S.maritima is closely related to Spinacia oleracea and Oenothera laciniata. Atriplex canescens (fourwing saltbush), Atriplex torreyi and Phaulothamnus spinescens, Celosia argentea found to be closely related and are in one group. Hence, this study result clearly shows thus study species evaluated from angiosperm and provides key step in understanding the evolution of salt tolerance in angiosperm.

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