Unusually high numbers of ribosomal RNA genes in copepods (Arthropoda: Crustacea) and their relationship to genome size

Genome ◽  
1995 ◽  
Vol 38 (1) ◽  
pp. 97-104 ◽  
Author(s):  
G. A. Wyngaard ◽  
I. A. McLaren ◽  
M. M. White ◽  
J.-M. Sévigny
Keyword(s):  
Genome Size ◽  
Ribosomal Rna ◽  
Copy Number ◽  
18S Rrna ◽  
Marine Species ◽  
18S Rrna Gene ◽  
Gene Copy ◽  
Rrna Gene ◽  
Copy Numbers ◽  
Rna Genes

We report on copy numbers of 18S ribosomal RNA genes in three species of copepods (Crustacea: Copepoda), two of which possess an unusual arrangement in which 5S genes are included within the 18S–5.8S–28S repeat unit. Slot blots of genomic and standard DNA were hybridized with an 18S rRNA gene probe constructed from one of the marine species and hybridization was quantified using chemiluminescence. Diploid 18S rRNA gene copy numbers are estimated as ca. 15 300 and 33 500 in the marine species Calanus finmarchicus (13.0 pg DNA in 2C adult nuclei) and C. glacialis (24.2 pg DNA), respectively, and ca. 840 and 730 in two freshwater populations of Mesocyclops edax (both ca. 3 pg DNA) from Virginia and Nova Scotia, respectively. The roughly proportional relationship between 2C somatic nuclear DNA contents and rRNA gene copy number in the sibling species C. finmarchicus and C. glacialis may reflect polytenic replication of entire genomes during abrupt speciation events. Copy numbers may also reflect differential losses during embryonic chromatin diminution.Key words: rRNA genes, copy number, genome size, Calanus, Mesocyclops.

scholarly journals The Responding Site of the Rex Locus of Drosophila melanogaster

Genetics ◽  
1987 ◽  
Vol 115 (2) ◽  
pp. 271-276
Author(s):  
Ellen E Swanson
Keyword(s):  
Drosophila Melanogaster ◽  
X Chromosome ◽  
Ribosomal Rna ◽  
Maternal Effect ◽  
Copy Number ◽  
Mitotic Chromosome ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Rrna Gene ◽  
Chromosome Behavior

ABSTRACT Rex is a dominant, maternal-effect locus in the heterochromatin of the X chromosome Drosophila melanogaster. It causes an early mitotic exchange-like event between heterochromatic elements of an attached- XY in X/attached-XY embryos of Rex mothers. Evidence is presented here that the site of Rex action is the ribosomal RNA gene cluster (the bb locus) only; no other heterochromatin is affected. The Rex locus may be useful in studying regulation of rRNA-gene copy number, mitotic chromosome behavior and heterochromatic function.

scholarly journals Quantitative Detection of the Free-Living Amoeba Hartmannella vermiformis in Surface Water by Using Real-Time PCR

2006 ◽  
Vol 72 (9) ◽  
pp. 5750-5756 ◽  
Author(s):  
Melanie W. Kuiper ◽  
Rinske M. Valster ◽  
Bart A. Wullings ◽  
Harry Boonstra ◽  
Hauke Smidt ◽  
...  
Keyword(s):  
Real Time ◽  
Real Time Pcr ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Quantitative Detection ◽  
Rrna Gene ◽  
Free Living ◽  
Copy Numbers ◽  
Free Living Amoeba ◽  
Hartmannella Vermiformis

ABSTRACT A real-time PCR-based method targeting the 18S rRNA gene was developed for the quantitative detection of Hartmannella vermiformis, a free-living amoeba which is a potential host for Legionella pneumophila in warm water systems and cooling towers. The detection specificity was validated using genomic DNA of the closely related amoeba Hartmannella abertawensis as a negative control and sequence analysis of amplified products from environmental samples. Real-time PCR detection of serially diluted DNA extracted from H. vermiformis was linear for microscopic cell counts between 1.14 � 10−1 and 1.14 � 104 cells per PCR. The genome of H. vermiformis harbors multiple copies of the 18S rRNA gene, and an average number (with standard error) of 1,330 � 127 copies per cell was derived from real-time PCR calibration curves for cell suspensions and plasmid DNA. No significant differences were observed between the 18S rRNA gene copy numbers for trophozoites and cysts of strain ATCC 50237 or between the copy numbers for this strain and strain KWR-1. The developed method was applied to water samples (200 ml) collected from a variety of lakes and rivers serving as sources for drinking water production in The Netherlands. Detectable populations were found in 21 of the 28 samples, with concentrations ranging from 5 to 75 cells/liter. A high degree of similarity (≥98%) was observed between sequences of clones originating from the different surface waters and between these clones and the reference strains. Hence, H. vermiformis, which is highly similar to strains serving as hosts for L. pneumophila, is a common component of the microbial community in fresh surface water.

Mixia osmundae: transfer from the Ascomycota to the Basidiomycota based on evidence from molecules and morphology

1995 ◽  
Vol 73 (S1) ◽  
pp. 660-666 ◽  
Author(s):  
Hiromi Nishida ◽  
Katsuhiko Ando ◽  
Yasuo Ando ◽  
Aiko Hirata ◽  
Junta Sugiyama
Keyword(s):  
Ribosomal Rna ◽  
18S Rrna ◽  
Morphological Characters ◽  
Small Subunit ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Phylogenetic Placement ◽  
Fungal Evolution ◽  
Sporobolomyces Roseus ◽  
Sporidiobolus Johnsonii

To determine phylogenetic placement of Mixia osmundae (T. Nishida) Kramer (Mixiaceae, Protomycetales), we sequenced the nuclear small subunit ribosomal RNA (18S rRNA) gene from M. osmundae IFO-32408 and compared it with that from 4 archiascomycetes (Ascomycota) and 24 basidiomycetes. Our molecular phylogeny indicates that M. osmundae and the basidiomycetes Rhodosporidium toruloides, Leucosporidium scottii, Sporobolomyces roseus, Sporidiobolus johnsonii, Cronartium ribicola, Peridermium harknessii, and Erythrobasidium hasegawianum group together in 100% of bootstrap replicates. The M. osmundae spores on the host fern Osmunda japonica have been regarded as ascospores (i.e., endogenously produced within an ascus), but our light microscopic, SEM, and TEM observations for fresh materials of M. osmundae on O. japonica in Japan clearly demonstrated that these are produced exogenously, blastically, and simultaneously from the sporogenous cell. Evidence from both molecular and morphological characters suggests that M. osmundae is not a member of the ascomycetes and is not related to either the Taphrinales or Protomycetales. Obviously Mixia osmundae is a member of the basidiomycetes and placed within the simple septate basidiomycete lineage. Key words: fungal evolution, basidiomycete phylogeny, Mixia osmundae, Taphrinales, Protomycetales, 18S rRNA.

scholarly journals From the sxtA4 Gene to Saxitoxin Production: What Controls the Variability Among Alexandrium minutum and Alexandrium pacificum Strains?

2021 ◽  
Vol 12 ◽  
Author(s):  
Solène Geffroy ◽  
Marc-Marie Lechat ◽  
Mickael Le Gac ◽  
Georges-Augustin Rovillon ◽  
Dominique Marie ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genome Size ◽  
Copy Number ◽  
Gene Copy Number ◽  
Toxin Production ◽  
Gene Copy ◽  
Alexandrium Minutum ◽  
Copy Numbers ◽  
Gene Copies ◽  
Paralytic Shellfish

Paralytic shellfish poisoning (PSP) is a human foodborne syndrome caused by the consumption of shellfish that accumulate paralytic shellfish toxins (PSTs, saxitoxin group). In PST-producing dinoflagellates such as Alexandrium spp., toxin synthesis is encoded in the nuclear genome via a gene cluster (sxt). Toxin production is supposedly associated with the presence of a 4th domain in the sxtA gene (sxtA4), one of the core genes of the PST gene cluster. It is postulated that gene expression in dinoflagellates is partially constitutive, with both transcriptional and post-transcriptional processes potentially co-occurring. Therefore, gene structure and expression mode are two important features to explore in order to fully understand toxin production processes in dinoflagellates. In this study, we determined the intracellular toxin contents of twenty European Alexandrium minutum and Alexandrium pacificum strains that we compared with their genome size and sxtA4 gene copy numbers. We observed a significant correlation between the sxtA4 gene copy number and toxin content, as well as a moderate positive correlation between the sxtA4 gene copy number and genome size. The 18 toxic strains had several sxtA4 gene copies (9–187), whereas only one copy was found in the two observed non-toxin producing strains. Exploration of allelic frequencies and expression of sxtA4 mRNA in 11 A. minutum strains showed both a differential expression and specific allelic forms in the non-toxic strains compared with the toxic ones. Also, the toxic strains exhibited a polymorphic sxtA4 mRNA sequence between strains and between gene copies within strains. Finally, our study supported the hypothesis of a genetic determinism of toxin synthesis (i.e., the existence of several genetic isoforms of the sxtA4 gene and their copy numbers), and was also consistent with the hypothesis that constitutive gene expression and moderation by transcriptional and post-transcriptional regulation mechanisms are the cause of the observed variability in the production of toxins by A. minutum.

Identification of new 18S rRNA strains of Babesia canis isolated from dogs with subclinical babesiosis

2015 ◽  
Vol 18 (3) ◽  
pp. 573-577 ◽  
Author(s):  
P. Łyp ◽  
Ł. Adaszek ◽  
B. Furmaga ◽  
S. Winiarczyk
Keyword(s):  
Ribosomal Rna ◽  
18S Rrna ◽  
Venous Blood ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Babesia Canis ◽  
Gene Fragment ◽  
Nucleotide Substitutions ◽  
New Variant ◽  
Pcr Products

Abstract In this study, we used PCR to detect and characterize B. canis from naturally infected dogs in Poland with subclinical babesiosis by amplifying and sequencing a portion of the 18S ribosomal RNA (rRNA) gene. Venous blood samples were collected from ten dogs with subclinical babesiosis. A 559-bp fragment of the B. canis 18S rRNA gene was amplified by PCR. Sequencing of the PCR products led to the identification of a new variant of Babesia canis, differing from the previously detected protozoa genotypes (18S rRNA-A and 18S rRNA-B) with nucleotide substitutions in positions 150 and 151 of the tested gene fragment. The results indicate the emergence within the Polish territory of a new, previously unencountered Babesia canis genotype responsible for the development of subclinical babesiosis.

scholarly journals Iron encrustations on filamentous algae colonized by <i>Gallionella</i>-related bacteria in a metal-polluted freshwater stream

2015 ◽  
Vol 12 (10) ◽  
pp. 7705-7737
Author(s):  
J. F. Mori ◽  
T. R. Neu ◽  
S. Lu ◽  
M. Händel ◽  
K. U. Totsche ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Green Algae ◽  
Brown Algae ◽  
18S Rrna ◽  
18S Rrna Gene ◽  
Laser Scanning Microscopy ◽  
Gene Copy ◽  
Rrna Gene ◽  
Sequencing Analysis

Abstract. Filamentous macroscopic algae were observed in slightly acidic to circumneutral (pH 5.9~6.5) metal-rich stream water that leaked out in a former uranium-mining district (Ronneburg, Germany). These algae differ in color and morphology and were encrusted with Fe-deposits. To elucidate the potential interaction with Fe(II)-oxidizing bacteria (FeOB), we collected algal samples at three time points during summer 2013 and studied the algae-bacteria-mineral compositions via confocal laser scanning microscopy (CLSM), scanning electronic microscopy, Fourier transform infrared spectra, and a 16S and 18S rRNA gene based bacterial and algae community analysis. Surprisingly, sequencing analysis of 18S rRNA gene regions of green and brown algae revealed high homologies with the yellow-green freshwater algae Tribonema (99.9~100%). CLSM imaging indicates a loss of active chloroplasts in the algae cells, which may be responsible for the change in color in Tribonema. Fe(III)-precipitates on algal cells identified as ferrihydrite and schwertmannite were associated with microbes and extracellular polymeric substances (EPS)-like glycoconjugates. While the green algae were fully encrusted with Fe-precipitates, the brown algae often exhibited discontinuous series of precipitates. This pattern was likely due to the intercalary growth of algal filaments which allowed them to avoid fatal encrustation. 16S rRNA gene targeted studies based on DNA and RNA revealed that Gallionella-related FeOB dominated the bacterial RNA and DNA communities (70–97 and 63–96%, respectively) suggesting their contribution to Fe(II) oxidation. Quantitative PCR revealed higher Gallionella-related 16S rRNA gene copy numbers on the surface of green algae compared to the brown algae. The latter harbored a higher microbial diversity, including some putative predators of algae. Lower photosynthetic activities of the brown algae lead to reduced EPS production which may have enabled predator colonization. The differences observed between green and brown algae suggest that metal-tolerant Tribonema sp. provide suitable microenvironments for microaerophilic Fe-oxidizing bacteria. However, high levels of iron orchres can be fatal to the alga.

Small subunit (18S) ribosomal RNA gene divergence in the genus Schistosoma

Parasitology ◽  
1993 ◽  
Vol 107 (2) ◽  
pp. 147-156 ◽  
Author(s):  
D. A. Johnston ◽  
R. A. Kane ◽  
D. Rollinson
Keyword(s):  
Ribosomal Rna ◽  
18S Rrna ◽  
Gene Sequence ◽  
Small Subunit ◽  
18S Rrna Gene ◽  
Rrna Genes ◽  
Rrna Gene ◽  
18S Ribosomal Rna Gene ◽  
Species Groups ◽  
18S Rrna Genes

SUMMARYAn entire 18S rRNA gene sequence from Schistosoma spindale (1990 bases) and partial 18S rRNA gene sequences from S. haematobium (1950 bases) and S. japonicum (1648 bases) have been determined. Together with the previously published sequence for the S. mansoni 18S rRNA gene, these data encompass the 4 recognized Schistosoma species groups. Although Schistosoma 18S rRNA genes are highly conserved, the sequences permit a preliminary molecular phylogeny to be established for the genus. This identifies S. haematobium and S. spindale as sister taxa in a clade with S. mansoni. S. japonicum does not appear to be closely related to this clade. Much of the observed variation occurs within a ‘hypervariable’ stretch of the gene corresponding to part of the V4 region of 18S rRNA. Despite this variation, the 3 new sequences fit models of 18S rRNA secondary structure predicted from the S. mansoni sequence.The sequences reported in this paper have been submitted to the EMBL Database under accession numbers Z11976 (S. haematobium), Z11590 (S. japonicum) and Z11979 (S. spindale).

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.

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