A Molecular Phylogenetic Framework for the Phylum Ctenophora Using 18S rRNA Genes

2001 ◽  
Vol 21 (2) ◽  
pp. 218-230 ◽  
Author(s):  
Mircea Podar ◽  
Steven H.D. Haddock ◽  
Mitchell L. Sogin ◽  
G.Richard Harbison
Keyword(s):  
18S Rrna ◽  
Rrna Genes ◽  
Molecular Phylogenetic ◽  
Phylogenetic Framework ◽  
18S Rrna Genes

Phylogenetic analysis using rDNA reveals polyphyly of Oplophoridae (Decapoda:Caridea)

2010 ◽  
Vol 24 (2) ◽  
pp. 172 ◽  
Author(s):  
Tin-Yam Chan ◽  
Ho Chee Lei ◽  
Chi Pang Li ◽  
Ka Hou Chu
Keyword(s):  
Phylogenetic Analysis ◽  
18S Rrna ◽  
Morphological Characters ◽  
The Other ◽  
Rrna Genes ◽  
Deep Channel ◽  
The Family ◽  
Molecular Phylogenetic ◽  
18S Rrna Genes ◽  
Molar Process

Molecular phylogenetic analysis on nine of the ten genera in the caridean family Oplophoridae Dana, 1852, as well as 14 other caridean families using mitochondrial 16S and nuclear 18S rRNA genes, does not support the monophyletic status of Oplophoridae. Two disparate groups of oplophorids are revealed, with different morphological characters and ecology. It is proposed that the family Oplophoridae is restricted to the three genera Oplophorus, Systellaspis and Janicella. These three genera tend to be distributed in shallower water than the other oplophorid genera, and can also be distinguished from them by certain morphological characters. They have a thicker integument, superficial cuticular photophores and larger eyes, and the molar process of their mandibles is greatly reduced or bears a deep channel. The family Acanthephyridae Bate, 1888 is resurrected for the other seven genera, which are generally distributed in deeper water and are characterised by red soft integument, no cuticular photophores, smaller eyes and well-developed molar process of the mandibles without a deep channel. The relationships between these two families and other caridean families could not be clearly resolved in this study.

Phylogenetic relationships of Scelimeninae genera (Orthoptera: Tetrigoidea) based on COI, 16S rRNA and 18S rRNA gene sequences

Zootaxa ◽  
2018 ◽  
Vol 4482 (2) ◽  
pp. 392
Author(s):  
YA-ZHEN CHEN ◽  
WEI-AN DENG ◽  
JIA-MIN WANG ◽  
LI-LIANG LIN ◽  
SHAN-YI ZHOU
Keyword(s):  
16S Rrna ◽  
Genetic Distance ◽  
Phylogenetic Relationships ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Average Genetic Distance ◽  
Molecular Phylogenetic ◽  
18S Rrna Genes

Scelimeninae is an important subfamily of Tetrigoidea; however, the phylogenetic relationships within Scelimeninae are poorly understood, and its generic classification has remained unstable. In this study, the COI, 16S rRNA and 18S rRNA genes from 24 species in 9 genera within Scelimeninae were amplified and sequenced, the base composition and inter-species genetic distance of the combined sequence of COI, 16S rRNA and 18S rRNA genes were analyzed, and the molecular phylogenetic relationships were reconstructed using Maximum Likelihood (ML) and Bayesian inference (BI) methods. The results of sequence analysis showed that the total length of the combined COI, 16S rRNA and 18S rRNA gene sequence was 3507 bp, including 2345 conservative sites, 1144 variable sites and 901 parsimony-informative sites. The average A+T content was 63.5% and 78.1% in the COI, 16S rRNA sequences, respectively, indicating A+T bias. The average genetic distance between all species was 0.134, and the average genetic distance in the inner group (Scelimeninae) was 0.126. A phylogenetic tree based on the combined sequences of the COI, 16S rRNA and 18S rRNA genes showed that the phylogenetic relationships among 9 Scelimeninae genera were as follows: Criotettix + (((Zhengitettix + Hebarditettix) + (Falconius + (Scelimena + Paragavialidium))) + ((Eucriotettix + Thoradonta) + Loxilobus)). The molecular phylogenetic results generally support the morphological taxonomy; at the genus level, Criotettix, Scelimena, Paragavialidium, Thoradonta and Eucriotettix are monophyletic groups, Scelimena and Paragavialidium form sister groups, and Thoradonta and Eucriotettix also form sister groups, but the relationship between Hebarditettix and Zhengitettix needs further study. At the species level, synonyms may exist between Thoradonta spiculoba and Thoradonta transpicula and Thoradonta nodulosa and Thoradonta obtusilobata, but more studies are required to confirm this inference. 

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 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.

scholarly journals Investigating Microbial Eukaryotic Diversity from a Global Census: Insights from a Comparison of Pyrotag and Full-Length Sequences of 18S rRNA Genes

2014 ◽  
Vol 80 (14) ◽  
pp. 4363-4373 ◽  
Author(s):  
Alle A. Y. Lie ◽  
Zhenfeng Liu ◽  
Sarah K. Hu ◽  
Adriane C. Jones ◽  
Diane Y. Kim ◽  
...  
Keyword(s):  
Species Richness ◽  
Sanger Sequencing ◽  
18S Rrna ◽  
Sequence Data ◽  
Sequence Similarity ◽  
Hypervariable Region ◽  
Full Length ◽  
Rrna Genes ◽  
Data Sets ◽  
18S Rrna Genes

ABSTRACTNext-generation DNA sequencing (NGS) approaches are rapidly surpassing Sanger sequencing for characterizing the diversity of natural microbial communities. Despite this rapid transition, few comparisons exist between Sanger sequences and the generally much shorter reads of NGS. Operational taxonomic units (OTUs) derived from full-length (Sanger sequencing) and pyrotag (454 sequencing of the V9 hypervariable region) sequences of 18S rRNA genes from 10 global samples were analyzed in order to compare the resulting protistan community structures and species richness. Pyrotag OTUs called at 98% sequence similarity yielded numbers of OTUs that were similar overall to those for full-length sequences when the latter were called at 97% similarity. Singleton OTUs strongly influenced estimates of species richness but not the higher-level taxonomic composition of the community. The pyrotag and full-length sequence data sets had slightly different taxonomic compositions of rhizarians, stramenopiles, cryptophytes, and haptophytes, but the two data sets had similarly high compositions of alveolates. Pyrotag-based OTUs were often derived from sequences that mapped to multiple full-length OTUs at 100% similarity. Thus, pyrotags sequenced from a single hypervariable region might not be appropriate for establishing protistan species-level OTUs. However, nonmetric multidimensional scaling plots constructed with the two data sets yielded similar clusters, indicating that beta diversity analysis results were similar for the Sanger and NGS sequences. Short pyrotag sequences can provide holistic assessments of protistan communities, although care must be taken in interpreting the results. The longer reads (>500 bp) that are now becoming available through NGS should provide powerful tools for assessing the diversity of microbial eukaryotic assemblages.

scholarly journals Design and Validation of Four New Primers for Next-Generation Sequencing To Target the 18S rRNA Genes of Gastrointestinal Ciliate Protozoa

2014 ◽  
Vol 80 (17) ◽  
pp. 5515-5521 ◽  
Author(s):  
Suzanne L. Ishaq ◽  
André-Denis G. Wright
Keyword(s):  
18S Rrna ◽  
18S Rrna Gene ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Content Type ◽  
Hypervariable Regions ◽  
Blast Database ◽  
Primer Sets ◽  
18S Rrna Genes ◽  
Ciliate Protozoa

ABSTRACTFour new primers and one published primer were used to PCR amplify hypervariable regions within the protozoal 18S rRNA gene to determine which primer pair provided the best identification and statistical analysis. PCR amplicons of 394 to 498 bases were generated from three primer sets, sequenced using Roche 454 pyrosequencing with Titanium, and analyzed using the BLAST database (NCBI) and MOTHUR version 1.29. The protozoal diversity of rumen contents from moose in Alaska was assessed. In the present study, primer set 1, P-SSU-316F and GIC758R (amplicon of 482 bases), gave the best representation of diversity using BLAST classification, and the set amplifiedEntodinium simplexandOstracodiniumspp., which were not amplified by the other two primer sets. Primer set 2, GIC1080F and GIC1578R (amplicon of 498 bases), had similar BLAST results and a slightly higher percentage of sequences that were identified with a higher sequence identity. Primer sets 1 and 2 are recommended for use in ruminants. However, primer set 1 may be inadequate to determine protozoal diversity in nonruminants. The amplicons created by primer set 1 were indistinguishable for certain species within the generaBandia,Blepharocorys,Polycosta, andTetratoxumand betweenHemiprorodon gymnoprosthiumandProrodonopsiscoli, none of which are normally found in the rumen.

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