A preliminary survey of lichen associated eukaryotes using pyrosequencing

AbstractAlthough various eukaryotic organisms, such as arthropods, endolichenic/lichenicolous fungi, and nematodes, have been isolated from lichens, the diversity and structure of eukaryotic communities associated with lichen thalli has not been well studied. In addressing this knowledge gap, we used bar-coded pyrosequencing of 18S rRNA genes to survey eukaryotes associated with thalli of three different lichen species. In addition to revealing an expected high abundance of lichen biont-related 18S genes, sequences recovered in our survey showed non-biont fungi from the Ascomycota also have a substantial presence in these thalli. Our samples additionally harboured fungi representing phyla (Blastocladiomycota, Chytridiomycota) that have not been isolated previously from lichens; however, their very low abundance indicates an incidental presence. The recovery of Alveolata, Metazoa, and Rhizaria sequences, along with recent work revealing the considerable bacterial diversity in these same samples, suggests lichens function as minute ecosystems in addition to being symbiotic organisms.

Download Full-text

Design of new universal PCR primers for detecting 18S rRNA genes of bacterivorous protozoa in the environment

Journal of Japan Society of Civil Engineers Ser G (Environmental Research) ◽

10.2208/jscejer.74.iii_239 ◽

2018 ◽

Vol 74 (7) ◽

pp. III_239-III_245

Author(s):

Kanji NAKAMURA ◽

Haruka OKUDA

Keyword(s):

18S Rrna ◽

Pcr Primers ◽

Rrna Genes ◽

18S Rrna Genes

Download Full-text

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

Journal of Helminthology ◽

10.1017/s0022149x21000110 ◽

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.

Download Full-text

Eucaryotic Diversity in a Hypersaline Microbial Mat

Applied and Environmental Microbiology ◽

10.1128/aem.01448-07 ◽

2007 ◽

Vol 74 (1) ◽

pp. 329-332 ◽

Cited By ~ 40

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.

Download Full-text

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

Helminthologia ◽

10.2478/helm-2020-0020 ◽

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.

Download Full-text

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

Kongunadu Research Journal ◽

10.26524/krj.2020.5 ◽

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.

Download Full-text

A Molecular Phylogeny of Bryophytes Based on the Nuclear Encoded 18S rRNA Genes

Journal of Plant Physiology ◽

10.1016/s0176-1617(11)81968-1 ◽

1995 ◽

Vol 146 (1-2) ◽

pp. 59-63 ◽

Cited By ~ 20

Author(s):

Ingrid Capesius

Keyword(s):

Molecular Phylogeny ◽

18S Rrna ◽

Rrna Genes ◽

18S Rrna Genes

Download Full-text

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

Applied and Environmental Microbiology ◽

10.1128/aem.00057-14 ◽

2014 ◽

Vol 80 (14) ◽

pp. 4363-4373 ◽

Cited By ~ 49

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.

Download Full-text

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

Applied and Environmental Microbiology ◽

10.1128/aem.01644-14 ◽

2014 ◽

Vol 80 (17) ◽

pp. 5515-5521 ◽

Cited By ~ 22

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.

Download Full-text

Molecular identification ofSarcocystisspp. helped to define the origin of green pythons (Morelia viridis) confiscated in Germany

Parasitology ◽

10.1017/s0031182013001960 ◽

2013 ◽

Vol 141 (5) ◽

pp. 646-651 ◽

Cited By ~ 9

Author(s):

GASTÓN MORÉ ◽

NIKOLA PANTCHEV ◽

DALAND C. HERRMANN ◽

MAJDA GLOBOKAR VRHOVEC ◽

SABINE ÖFNER ◽

...

Keyword(s):

18S Rrna ◽

Sequence Data ◽

18S Rrna Gene ◽

Rrna Genes ◽

Rrna Gene ◽

Intermediate Hosts ◽

Apicomplexan Parasites ◽

Large Numbers ◽

Wide Range ◽

18S Rrna Genes

SUMMARYSarcocystisspp. represent apicomplexan parasites. They usually have a heteroxenous life cycle. Around 200 species have been described, affecting a wide range of animals worldwide, including reptiles. In recent years, large numbers of reptiles have been imported into Europe as pets and, as a consequence, animal welfare and species protection issues emerged. A sample of pooled feces from four confiscated green pythons (Morelia viridis) containingSarcocystisspp. sporocysts was investigated. These snakes were imported for the pet trade and declared as being captive-bred. Full length 18S rRNA genes were amplified, cloned into plasmids and sequenced. Two differentSarcocystisspp. sequences were identified and registered asSarcocystissp. fromM. viridisin GenBank. Both showed a 95–97% sequence identity with the 18S rRNA gene ofSarcocystis singaporensis.Phylogenetic analysis positioned these sequences together with otherSarcocystisspp. from snakes and rodents as definitive and intermediate hosts (IH), respectively. Sequence data and also the results of clinical and parasitological examinations suggest that the snakes were definitive hosts forSarcocystisspp. that circulate in wild IH. Thus, it seems unlikely that the infected snakes had been legally bred. Our research shows that information on the infection of snakes withSarcocystisspp. may be used to assess compliance with regulations on the trade with wildlife species.

Download Full-text