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 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.

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.

scholarly journals Oligonucleotide Microarray for 16S rRNA Gene-Based Detection of All Recognized Lineages of Sulfate-Reducing Prokaryotes in the Environment

2002 ◽  
Vol 68 (10) ◽  
pp. 5064-5081 ◽  
Author(s):  
Alexander Loy ◽  
Angelika Lehner ◽  
Natuschka Lee ◽  
Justyna Adamczyk ◽  
Harald Meier ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Pcr Amplification ◽  
Oligonucleotide Microarray ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Clinical Samples ◽  
Rrna Gene ◽  
Sulfate Reducing ◽  
Specific Pcr

ABSTRACT For cultivation-independent detection of sulfate-reducing prokaryotes (SRPs) an oligonucleotide microarray consisting of 132 16S rRNA gene-targeted oligonucleotide probes (18-mers) having hierarchical and parallel (identical) specificity for the detection of all known lineages of sulfate-reducing prokaryotes (SRP-PhyloChip) was designed and subsequently evaluated with 41 suitable pure cultures of SRPs. The applicability of SRP-PhyloChip for diversity screening of SRPs in environmental and clinical samples was tested by using samples from periodontal tooth pockets and from the chemocline of a hypersaline cyanobacterial mat from Solar Lake (Sinai, Egypt). Consistent with previous studies, SRP-PhyloChip indicated the occurrence of Desulfomicrobium spp. in the tooth pockets and the presence of Desulfonema- and Desulfomonile-like SRPs (together with other SRPs) in the chemocline of the mat. The SRP-PhyloChip results were confirmed by several DNA microarray-independent techniques, including specific PCR amplification, cloning, and sequencing of SRP 16S rRNA genes and the genes encoding the dissimilatory (bi)sulfite reductase (dsrAB).

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 Legionella Species Diversity in an Acidic Biofilm Community in Yellowstone National Park

2005 ◽  
Vol 71 (1) ◽  
pp. 507-511 ◽  
Author(s):  
Kathy B. Sheehan ◽  
Joan M. Henson ◽  
Michael J. Ferris
Keyword(s):  
Yellowstone National Park ◽  
National Park ◽  
Pcr Amplification ◽  
18S Rrna Gene ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Thermal Gradients ◽  
Legionella Species ◽  
Legionella Micdadei

ABSTRACT Legionella species are frequently detected in aquatic environments, but their occurrence in extreme, acidic, geothermal habitats has not been explored with cultivation-independent methods. We investigated a predominately eukaryotic algal mat community in a pH 2.7 geothermal stream in Yellowstone National Park for the presence of Legionella and potential host amoebae. Our analyses, using PCR amplification with Legionella-specific primers targeting 16S rRNA genes, detected four known Legionella species, as well as Legionella sequences from species that are not represented in sequence databases, in mat samples and cultivated isolates. The nonrandom occurrence of sequences detected at lower (30�C) and higher (35 to 38�C) temperatures suggests that natural thermal gradients in the stream influence Legionella species distributions in this mat community. We detected only one sequence, Legionella micdadei, from cultivated isolates. We cultured and sequenced partial 18S rRNA gene regions from two potential hosts, Acanthamoeba and Euglena species.

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 Selective and Sensitive Method for PCR Amplification of Escherichia coli 16S rRNA Genes in Soil

2000 ◽  
Vol 66 (2) ◽  
pp. 844-849 ◽  
Author(s):  
G. Sabat ◽  
P. Rose ◽  
W. J. Hickey ◽  
J. M. Harkin
Keyword(s):  
Escherichia Coli ◽  
16S Rrna ◽  
Pcr Amplification ◽  
Pcr Primers ◽  
Enteric Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Selective Amplification ◽  
E Coli

ABSTRACT A set of PCR primers targeting 16S rRNA gene sequences was designed, and PCR parameters were optimized to develop a robust and reliable protocol for selective amplification of Escherichia coli 16S rRNA genes. The method was capable of discriminatingE. coli from other enteric bacteria, including its closest relative, Shigella. Selective amplification of E. coli occurred only when the annealing temperature in the PCR was elevated to 72°C, which is 10°C higher than the optimum for the primers. Sensitivity was retained by modifying the length of steps in the PCR, by increasing the number of cycles, and most importantly by optimizing the MgCl2 concentration. The PCR protocol developed can be completed in less then 2 h and, by using Southern hybridization, has a detection limit of ca. 10 genomic equivalents per reaction. The method was demonstrated to be effective for detectingE. coli DNA in heterogeneous DNA samples, such as those extracted from soil.

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.

Sign in / Sign up

Export Citation Format

Share Document