scholarly journals The differential expression of ribosomal 18S RNA paralog genes from the chaetognath Spadella cephaloptera

2007 ◽  
Vol 12 (4) ◽  
Author(s):  
Roxane-Marie Barthélémy ◽  
Michel Grino ◽  
Pierre Pontarotti ◽  
Jean-Paul Casanova ◽  
Eric Faure
Keyword(s):  
Physiological Role ◽  
Class Ii ◽  
Class I ◽  
Rrna Genes ◽  
Whole Body ◽  
Rrna Gene ◽  
28S Rrna ◽  
Cellular Functions ◽  
Intraindividual Variation ◽  
Spadella Cephaloptera

AbstractChaetognaths constitute a small marine phylum of approximately 120 species. Two classes of both 18S and 28S rRNA gene sequences have been evidenced in this phylum, even though significant intraindividual variation in the sequences of rRNA genes is unusual in animal genomes. These observations led to the hypothesis that this unusual genetic characteristic could play one or more physiological role(s). Using in situ hybridization on the frontal sections of the chaetognath Spadella cephaloptera, we found that the 18S Class I genes are expressed in the whole body, with a strong expression throughout the gut epithelium, whereas the expression of the 18S Class II genes is restricted to the oocytes. Our results could suggest that the paralog products of the 18S Class I genes are probably the “housekeeping” 18S rRNAs, whereas those of class II would only be essential in specific tissues. These results provide support for the idea that each type of 18S paralog is important for specific cellular functions and is under the control of selective factors.

The effect of transposon Pokey insertions on sequence variation in the 28S rRNA gene of Daphnia pulex

Genome ◽  
2008 ◽  
Vol 51 (12) ◽  
pp. 988-1000 ◽  
Author(s):  
Shiona K. Glass ◽  
Anna Moszczynska ◽  
Teresa J. Crease
Keyword(s):  
Sequence Variation ◽  
Insertion Site ◽  
Daphnia Pulex ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Intraindividual Variation ◽  
Rdna Array ◽  
The Impact ◽  
Host Genes

The goal of this study was to determine the impact of breeding system and the presence of the transposon Pokey on intraindividual variation in 28S rRNA genes. We PCR-amplified, cloned, and sequenced 1000 nucleotides downstream of the Pokey insertion site in genes with and without insertions from 10 obligately and 10 cyclically parthenogenetic isolates of Daphnia pulex. Variation among genes with Pokey insertions was higher than variation among genes without insertions in both cyclic and obligate isolates. Although the differences were not quite significant (p = 0.06 in both cases), the results suggest that Pokey insertions are likely to inhibit the homogenization of their host genes to some extent. We also observed that the complement of 28S rRNA alleles differed between genes with and without inserts in some isolates, suggesting that a particular inserted gene can persist for substantial periods of time and even spread within the rDNA array, despite the fact that insertions are deleterious. This apparently contradictory pattern can be explained if homogenization of rRNA genes occurs primarily by gene conversion, but copies with Pokey inserts can occasionally increase in frequency within arrays owing to unequal crossing over events that do not originate in the inserted genes themselves.

scholarly journals Testing the higher-level phylogenetic classification of Digenea (Platyhelminthes, Trematoda) based on nuclear rDNA sequences before entering the age of the ‘next-generation’ Tree of Life

2019 ◽  
Vol 93 (3) ◽  
pp. 260-276 ◽  
Author(s):  
G. Pérez-Ponce de León ◽  
D.I. Hernández-Mena
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
28S Rdna ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Next Generation ◽  
Phylogenetic Classification ◽  
Rdna Sequences

AbstractDigenea Carus, 1863 represent a highly diverse group of parasitic platyhelminths that infect all major vertebrate groups as definitive hosts. Morphology is the cornerstone of digenean systematics, but molecular markers have been instrumental in searching for a stable classification system of the subclass and in establishing more accurate species limits. The first comprehensive molecular phylogenetic tree of Digenea published in 2003 used two nuclear rRNA genes (ssrDNA = 18S rDNA and lsrDNA = 28S rDNA) and was based on 163 taxa representing 77 nominal families, resulting in a widely accepted phylogenetic classification. The genetic library for the 28S rRNA gene has increased steadily over the last 15 years because this marker possesses a strong phylogenetic signal to resolve sister-group relationships among species and to infer phylogenetic relationships at higher levels of the taxonomic hierarchy. Here, we have updated the database of 18S and 28S rRNA genes until December 2017, we have added newly generated 28S rDNA sequences and we have reassessed phylogenetic relationships to test the current higher-level classification of digeneans (at the subordinal and subfamilial levels). The new dataset consisted of 1077 digenean taxa allocated to 106 nominal families for 28S and 419 taxa in 98 families for 18S. Overall, the results were consistent with previous higher-level classification schemes, and most superfamilies and suborders were recovered as monophyletic assemblages. With the advancement of next-generation sequencing (NGS) technologies, new phylogenetic hypotheses from complete mitochondrial genomes have been proposed, although their power to resolve deep levels of trees remains controversial. Since data from NGS methods are replacing other widely used markers for phylogenetic analyses, it is timely to reassess the phylogenetic relationships of digeneans with conventional nuclear rRNA genes, and to use the new analysis to test the performance of genomic information gathered from NGS, e.g. mitogenomes, to infer higher-level relationships of this group of parasitic platyhelminths.

Conflict and congruence between morphological and molecular data: revision of the Merodon constans group (Diptera : Syrphidae)

2020 ◽  
Author(s):  
Ante Vujić ◽  
Snežana Radenković ◽  
Laura Likov ◽  
Andrijana Andrić ◽  
Marina Janković ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Distinct Species ◽  
Morphological Characters ◽  
Molecular Data ◽  
Species Group ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
The Status ◽  
Data Revision

We revise the Merodon constans species group of the genus Merodon Meigen, 1803 (Diptera: Syrphidae), provide morphological diagnosesand descriptions, as well as an illustrated key and a discussion on the different taxonomic characters used. In total, 15 species were studied, their geographic distributions are presented on maps, and nine new species are described. Two species are redefined and neotypes are designated, lectotypes are designated for five species, and onespeciesis reinstated as valid. Following a detailed study of type material in different entomological collections, the status of several species is revised and three new synonymies are proposed. The M. constans species group was resolved as being monophyletic within the M. albifrons lineage based on molecular analyses using COI and 28S rRNA gene sequences. Three species morphologically similar to M. constans (Rossi, 1794) but occurring outside its distributional rangewere supported as being valid and distinct species on the basis of molecular data, but they were not distinguishable based on morphological characters. By contrast, continental populations of M. analis Meigen, 1822 could not be separated from Mediterranean M. constans based on differences in COI or 28S rRNA genes. The same molecular markers could not discriminate between two other species pairs. We conclude that these molecular markers only partially resolve species within the M. constans group. Geometric morphometry of wing shape successfully separated M. analis and M. constans, as well as M. spineus Vujić, Šašić Zorić & Likov, sp. nov. in both species and population analyses.

Processing of truncated mouse or human rRNA transcribed from ribosomal minigenes transfected into mouse cells

1994 ◽  
Vol 14 (6) ◽  
pp. 4044-4056
Author(s):  
K V Hadjiolova ◽  
A Normann ◽  
J Cavaillé ◽  
E Soupène ◽  
S Mazan ◽  
...  
Keyword(s):  
18S Rrna ◽  
Processing System ◽  
Rrna Genes ◽  
In Vitro Assays ◽  
Rrna Gene ◽  
28S Rrna ◽  
Rrna Processing ◽  
Mouse Cells

The processing of pre-rRNA in eukaryotic cells involves a complex pattern of nucleolytic reactions taking place in preribosomes with the participation of several nonribosomal proteins and small nuclear RNAs. The mechanism of these reactions remains largely unknown, mainly because of the absence of faithful in vitro assays for most processing steps. We have developed a pre-rRNA processing system using the transient expression of ribosomal minigenes transfected into cultured mouse cells. Truncated mouse or human rRNA genes are faithfully transcribed under the control of mouse promoter and terminator signals. The fate of these transcripts is analyzed by the use of reporter sequences flanking the rRNA gene inserts. Both mouse and human transcripts, containing the 3' end of 18S rRNA-encoding DNA (rDNA), internal transcribed spacer (ITS) 1, 5.8S rDNA, ITS 2, and the 5' end of 28S rDNA, are processed predominantly to molecules coterminal with the natural mature rRNAs plus minor products corresponding to cleavages within ITS 1 and ITS 2. To delineate cis-acting signals in pre-rRNA processing, we studied series of more truncated human-mouse minigenes. A faithful processing at the 18S rRNA/ITS 1 junction can be observed with transcripts containing only the 60 3'-terminal nucleotides of 18S rRNA and the 533 proximal nucleotides of ITS 1. However, further truncation of 18S rRNA (to 8 nucleotides) or of ITS 1 (to 48 nucleotides) abolishes the cleavage of the transcript. Processing at the ITS 2/28S rRNA junction is observed with truncated transcripts lacking the 5.8S rRNA plus a major part of ITS 2 and containing only 502 nucleotides of 28S rRNA. However, further truncation of the 28S rRNA segment to 217 nucleotides abolishes processing. Minigene transcripts containing most internal sequences of either ITS 1 or ITS 2, but devoid of ITS/mature rRNA junctions, are not processed, suggesting that the cleavages in vivo within either ITS segment are dependent on the presence in cis of mature rRNA sequences. These results show that the major cis signals for pre-rRNA processing at the 18S rRNA/ITS 1 or the ITS2/28S rRNA junction involve solely a limited critical length of the respective mature rRNA and adjacent spacer sequences.

scholarly journals Combined Molecular and Biochemical Approach Identifies Aspergillus japonicus and Aspergillus aculeatus as Two Species

2001 ◽  
Vol 67 (2) ◽  
pp. 521-527 ◽  
Author(s):  
Lucie Pařenicová ◽  
Pernille Skouboe ◽  
Jens Frisvad ◽  
Robert A. Samson ◽  
Lone Rossen ◽  
...  
Keyword(s):  
Secondary Metabolite ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Aspergillus Aculeatus ◽  
Aspergillus Japonicus ◽  
5.8S Rrna Gene ◽  
Black Aspergilli ◽  
5.8S Rrna ◽  
Metabolite Profiles

ABSTRACT We examined nine Aspergillus japonicus isolates and 10Aspergillus aculeatus isolates by using molecular and biochemical markers, including DNA sequences of the ITS1-5.8S rRNA gene-ITS2 region, restriction fragment length polymorphisms (RFLP), and secondary-metabolite profiles. The DNA sequence of the internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene could not be used to distinguish between A. japonicus and A. aculeatus but did show that these two taxa are more closely related to each other than to other species of black aspergilli.Aspergillus niger pyruvate kinase (pkiA) and pectin lyase A (pelA) and Agaricus bisporus 28S rRNA genes, which were used as probes in the RFLP analysis, revealed clear polymorphism between these two taxa. The A. niger pkiA and pelA probes placed six strains in anA. japonicus group and 12 isolates in an A. aculeatus group, which exhibited intraspecific variation when they were probed with the pelA gene. The secondary-metabolite profiles supported division of the isolates into the two species and differed from those of other black aspergilli. The strains classified as A. japonicus produced indole alkaloids and a polar metabolite, while the A. aculeatusisolates produced neoxaline, okaramins, paraherquamidelike compounds, and secalonic acid. A. aculeatus CBS 114.80 showed specific RFLP patterns for all loci examined. The secondary-metabolite profile of strain CBS 114.80 also differed from those of A. japonicus and A. aculeatus. Therefore, this strain probably represents a third taxon. This study provides unambiguous criteria for establishing the taxonomic positions of isolates of black aspergilli, which are important in relation to industrial use and legal protection of these organisms.

Morphological and molecular characterisation of several Paratylenchus Micoletzky, 1922 (Tylenchida: Paratylenchidae) species from South Africa and USA, together with some taxonomic notes

Nematology ◽  
2014 ◽  
Vol 16 (3) ◽  
pp. 323-358 ◽  
Author(s):  
Esther Van den Berg ◽  
Esther Van den Berg ◽  
Louwrens R. Tiedt ◽  
Esther Van den Berg ◽  
Louwrens R. Tiedt ◽  
...  
Keyword(s):  
South Africa ◽  
Rrna Genes ◽  
Morphological Identification ◽  
Rrna Gene ◽  
28S Rrna ◽  
Molecular Characterisation ◽  
Electron Microscopic ◽  
Wide Range ◽  
Its Rrna Gene ◽  
Its Rrna

Pin nematodes of the genus Paratylenchus are widely distributed across the world and associated with many plant species. Morphological identification of Paratylenchus species is a difficult task because it relies on many characters with a wide range of intraspecific variation. In this study we provide morphological and molecular characterisation of several pin nematodes: Paratylenchus aquaticus, P. dianthus, P. hamatus, P. nanus and P. straeleni, collected in different states of the USA and South Africa. Paratylenchus aquaticus is reported from South Africa and Hawaii and P. nanus is found from South Africa for the first time. Morphological descriptions, morphometrics, light and scanning electron microscopic photos and drawings are given for these species. Molecular characterisation of nematodes using the D2-D3 of 28S rRNA and ITS rRNA gene sequence revealed that samples morphologically identified as P. aquaticus, P. hamatus and P. nanus indeed represent species complexes containing several species. Sequences of the rRNA genes are also provided for several unidentified Paratylenchus. Phylogenetic relationships within the genus Paratylenchus are given as inferred from the analyses of the D2-D3 of 28S rRNA and ITS rRNA gene sequences. We present here the most complete phylogenetic analysis of the genus.

scholarly journals Molecular identification of parasitoid, Encarsia formosa gahan in Bemisia tabaci (Gennadius) and determination of its secondary endosymbionts

2015 ◽  
Vol 39 (4) ◽  
pp. 563-578
Author(s):  
SMH Jahan ◽  
KY Lee ◽  
MIA Howlader ◽  
HM Bashar ◽  
GN Hasan
Keyword(s):  
Research Work ◽  
Pcr Amplification ◽  
Rrna Genes ◽  
Gene Region ◽  
Molecular Technique ◽  
Rrna Gene ◽  
28S Rrna ◽  
Encarsia Formosa ◽  
Molecular Physiology

In this study two pairs of primers based on mitochondrial cytochrome oxidase subunit 1 (mtCOI) region and 28S ribosomal RNA (rRNA) gene region were used for identifying very tiny and morphologically indistinguishable parasitoid Encarsia formosa (Gahan) which are specific to this insect. The fragment amplified by these primer pairs were 860 and 650 bp in length. Species specificity test showed that all E. formosa specimens were detected with no cross reactions with other aphelinid species, including E. sophia (Girault & Dodd), E. luteola, E. Inaron and E. Nigricephala. Using phylogenetic cladogram by the sequences analysis of both mtCOI and 28S rRNA genes could be detected in E. formosa accurately in all replicates. Cardinium and Wolbachia secondary endosymbiont were also detected in E. Formosa used by PCR amplification as well as sequence analysis of 16S-23S rDNA gene region. The molecular technique developed here would be useful for rapid and precise species identification, determination of the host spectrum and more effective utilization of E. formosa. This research work has been performed from January 2011 to June 2012 at the insect molecular physiology lab in the Republic of Korea. DOI: http://dx.doi.org/10.3329/bjar.v39i4.22532 Bangladesh J. Agril. Res. 39(4): 563-578, December 2014

scholarly journals From 18S to 28S rRNA Gene: An Improved Targeted Sarcocystidae PCR Amplification, Species Identification with Long DNA Sequences

2021 ◽  
Vol 104 (4) ◽  
pp. 1388-1393
Author(s):  
Florence C. H. Lee ◽  
Vickneshwaran Muthu
Keyword(s):  
Species Identification ◽  
Dna Sequence ◽  
Dna Sequences ◽  
Environmental Samples ◽  
Pcr Amplification ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Index Test ◽  
Identity Matching

ABSTRACTSarcocystosis outbreaks in Tioman and Pangkor islands of Malaysia between 2011 and 2014 have raised the need to improve Sarcocystis species detection from environmental samples. In-house works found that published primers amplifying the 18S rRNA gene of Sarcocystis either could not produce the target from environmental samples or produced Sarcocystis DNA sequence that was insufficient for species identification. Using the primer pair of 18S S5 F (published) and 28S R6 R (new), this study improved the PCR amplification of Sarcocystidae to overcome these two difficulties. The PCR product spanned from the 18S to 28S rRNA genes, providing more information for species identification. The long DNA sequence allowed comparison between the “Ident” and “Query Cover” sorting in GenBank identity matching. This revealed the ambiguity in identity matching caused by different lengths of reference DNA sequences, which is seldom discussed in the literature. Using the disparity index test, a measurement of homogeneity in nucleotide substitution pattern, it is shown that the internal transcribed spacer (ITS)1-5.8S-ITS2 and 28S genes are better than the 18S gene in indicating nucleotide variations, implying better potentials for species identification. The example given by the handful of Sarcocystidae long DNA sequences reported herein calls for the need to report DNA sequence from the 18S to the 28S rRNA genes for species identification, especially among emerging pathogens. DNA sequence reporting should include the hypervariable 5.8S and ITS2 regions where applicable, and not be limited to single gene, per the current general trend.

scholarly journals Widespread germline genetic heterogeneity of human ribosomal RNA genes

2021 ◽  
Author(s):  
Wenjun Fan ◽  
Eetu Eklund ◽  
Rachel M Sherman ◽  
Hester Liu ◽  
Stephanie Pitts ◽  
...  
Keyword(s):  
Ribosomal Rna ◽  
Variant Calling ◽  
Chromosome 21 ◽  
Interindividual Variation ◽  
Reference Sequence ◽  
Rrna Genes ◽  
Rrna Gene ◽  
28S Rrna ◽  
Coding Region ◽  
Bioinformatics Pipeline

Polymorphism drives survival under stress and provides adaptability. Genetic polymorphism of ribosomal RNA (rRNA) genes derives from internal repeat variation of this multicopy gene, and from interindividual variation. A considerable amount of rRNA sequence heterogeneity has been proposed but has been challenging to estimate given the scarcity of accurate reference sequences. We identified four rDNA copies on chromosome 21 (GRCh38) with 99% similarity to recently introduced reference sequence KY962518.1. Pairwise alignment of the rRNA coding sequences of these copies showed differences in sequence and length. We customized a GATK bioinformatics pipeline using the four rDNA loci, spanning a total 145 kb, for variant calling. We employed whole genome sequencing (WGS) data from the 1000 Genomes Project phase 3 and analyzed variants in 2,504 individuals from 26 populations. Using the pipeline, we identified a total of 3,790 variant positions. The variants positioned non-randomly on the rRNA gene. Invariant regions included the promoter, early 5' ETS, 5.8S, ITS1 and certain regions of the 28S rRNA, and large areas of the intragenic spacer. 18S rRNA coding region had very few variants, while a total of 470 variant positions were observed on 28S rRNA. The majority of the 28S rRNA variants located on highly flexible human-expanded rRNA helical folds ES7L and ES27L, suggesting that these represent positions of diversity and are potentially under continuous evolution. These findings provide a genetic view for rRNA heterogeneity and raise the need to functional assess how the 28S rRNA variants affect ribosome functions.

scholarly journals Molecular organization of 5S rDNA in sharks of the genusRhizoprionodon: insights into the evolutionary dynamics of 5S rDNA in vertebrate genomes

2009 ◽  
Vol 91 (1) ◽  
pp. 61-72 ◽  
Author(s):  
DANILLO PINHAL ◽  
CARLOS S. ARAKI ◽  
OTTO B. F. GADIG ◽  
CESAR MARTINS
Keyword(s):  
Comparative Analysis ◽  
5S Rdna ◽  
Class Ii ◽  
Molecular Organization ◽  
Class I ◽  
Rrna Gene ◽  
Shark Species ◽  
Coding Region ◽  
Fish Genome ◽  
Repeat Class

SummaryIn this study, we attempted a molecular characterization of the 5S rDNA in two closely related species of carcharhiniform sharks,Rhizoprionodon lalandiiandRhizoprionodon porosus, as well as a further comparative analysis of available data on lampreys, several fish groups and other vertebrates. Our data show thatRhizoprionodonsharks carry two 5S rDNA classes in their genomes: a short repeat class (termed class I) composed of ~185 bp repeats, and a large repeat class (termed class II) arrayed in ~465 bp units. These classes were differentiated by several base substitutions in the 5S coding region and by completely distinct non-transcribed spacers (NTS). In class II, both species showed a similar composition for both the gene coding region and the NTS region. In contrast, class I varied extensively both within and between the two shark species. A comparative analysis of 5S rRNA gene sequences of elasmobranchs and other vertebrates showed that class I is closely related to the bony fishes, whereas the class II gene formed a separate cartilaginous clade. The presence of two variant classes of 5S rDNA in sharks likely maintains the tendency for dual ribosomal classes observed in other fish species. The present data regarding the 5S rDNA organization provide insights into the dynamics and evolution of this multigene family in the fish genome, and they may also be useful in clarifying aspects of vertebrate genome evolution.

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