scholarly journals Species-specific amplification of tRNA-derived short interspersed repetitive elements (SINEs) by retroposition: a process of parasitization of entire genomes during the evolution of salmonids.

1994 ◽  
Vol 91 (21) ◽  
pp. 10153-10157 ◽  
Author(s):  
N. Takasaki ◽  
S. Murata ◽  
M. Saitoh ◽  
T. Kobayashi ◽  
L. Park ◽  
...  
Keyword(s):  
Repetitive Elements ◽  
Specific Amplification ◽  
Species Specific

scholarly journals Development of species-specific Cichla species eDNA primers for alien invasive species (AIS) monitoring in Malaysia

2021 ◽  
Vol 4 ◽  
Author(s):  
O. Nurul Fizatul Nabilah ◽  
A. R. Ramizah ◽  
A. B. Adibah ◽  
S. Syazwan ◽  
A.G. Intan Faraha ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Environmental Dna ◽  
Coi Gene ◽  
Alien Invasive Species ◽  
Survey Method ◽  
Specific Primers ◽  
Invasive Fishes ◽  
Specific Amplification ◽  
Species Specific ◽  
High Level

Peacock bass or the cichlids are known locally as top predator fishes which are invasive in Malaysia freshwater system. Detection probabilities for these fishes are typically low, especially using conventional capture-survey method due to the fish’s behaviour of hiding beneath the water’s surface. Hence, the environmental DNA (eDNA) monitoring is a relatively new approach that can be used to assess the distribution of these invasive fishes. Here, we report the strategy to develop small fragment (280- 400 bp) specific-specific primers for three selected invasive Cichla species namely, C. ocellaris, C. monoculus, and C. kelberi based on mitochondrial DNA (mtDNA) sequences. Current research showed that the developed species-specific primers from cytochrome oxidase I (COI) gene has high resolution at species level. Species-specific amplification tests also proved the specificity of the developed primers, securing the high- level species identification potential which may help in controlling the spread of alien invasive fish species.

Species-specific amplification by PCR of ribosomal DNA from some equine strongyles

Parasitology ◽  
1999 ◽  
Vol 119 (1) ◽  
pp. 69-80 ◽  
Author(s):  
G.-C. HUNG ◽  
R. B. GASSER ◽  
I. BEVERIDGE ◽  
N. B. CHILTON
Keyword(s):  
Ribosomal Dna ◽  
Anthelmintic Resistance ◽  
Pcr Assay ◽  
Strongylus Vulgaris ◽  
Faecal Samples ◽  
Faecal Egg Count ◽  
Specific Amplification ◽  
Internal Transcribed Spacer Sequences ◽  
Second Internal Transcribed Spacer ◽  
Species Specific

The first and second internal transcribed spacer sequences of 28 morphologically-defined species of horse strongyle were characterized, and specific oligonucleotide primers were designed for some species based on the nucleotide differences. Utilizing these primers, a PCR approach was developed for the specific amplification of ribosomal DNA of Strongylus vulgaris, Cyathostomum catinatum, Cylicocyclus nassatus, Cylicostephanus longibursatus or Cylicostephanus goldi. The method allowed the species-specific amplification of parasite DNA derived from faecal samples and/or copro-cultures, demonstrating the potential of the approach for the diagnosis of equine strongyloidosis. The establishment of this PCR assay also has implications for studying the biology and epidemiology of equine strongyles and anthelmintic resistance using faecal egg count reduction tests.

scholarly journals Malus ×oxysepala (M. domestica Borkh. × M. sylvestris Mill.) – a new spontaneous apple hybrid

2013 ◽  
Vol 82 (2) ◽  
pp. 147-156 ◽  
Author(s):  
Aneta Czarna ◽  
Renata Nowińska ◽  
Barbara Gawrońska
Keyword(s):  
Quantitative Traits ◽  
Profile Analysis ◽  
Diagnostic Feature ◽  
Hybrid Species ◽  
Molecular Investigation ◽  
Specific Amplification ◽  
Periclinal Walls ◽  
Species Specific ◽  
Genetic Profiles ◽  
Seed Testa

<p>A study of the three <em>Malus</em> species (<em>M. domestica</em>, <em>M. sylvestris</em>, and a hybrid species, <em>M. domestica</em> × <em>M. sylvestris</em>, which was named <em>M.</em> ×<em>oxysepala</em>) was carried out based on the morphological and micromorphological features and molecular investigation. Observations performed for 47 quantitative traits showed that this hybrid species exhibits intermediate values between <em>M. domestica</em> and <em>M. sylvestris</em>, or are similar to traits of one of the parents. Sepals proved to be the best diagnostic feature because they were acuminate and much longer than sepals in <em>M. domestica</em> and <em>M. sylvestris</em>. Seed testa cells are distinct, rimmed with straight anticlinal walls and strongly bulged periclinal walls. Simultaneous genetic analyses based on PCR RAPD reactions fully confirmed earlier morphological observations. Genetic profiles of the hybrid obtained with the use of 30 primers, next to species-specific amplification products, contain common products with each of the parents. However, both the profile analysis and the dendrogram constructed on its basis showed that the hybrid is genetically closer to <em>M. sylvestris</em>.</p>

scholarly journals Association analysis of repetitive elements and R-loop formation across species

2020 ◽  
Author(s):  
Chao Zeng ◽  
Masahiro Onoguchi ◽  
Michiaki Hamada
Keyword(s):  
Fruit Fly ◽  
Low Complexity ◽  
Repetitive Elements ◽  
S2 Cells ◽  
Loop Formation ◽  
Long Terminal Repeats ◽  
Long Interspersed Nuclear Elements ◽  
Regulatory Effects ◽  
Species Specific ◽  
Simple Repeats

ABSTRACTGenomes are known to have a large number of repetitive elements. Emerging evidence suggests that these non-coding elements may play an important regulatory role. However, few studies have investigated the effect of repetitive elements on R-loop formation. In this study, we found different repetitive elements related to R-loop formation in various species. By controlling length and genomic distributions, we observed that satellites, long interspersed nuclear elements (LINEs), and DNAs were each specifically enriched for R-loops in humans, fruit flies, and Arabidopsis thaliana, respectively. R-loops also tended to arise in regions of low-complexity or simple repeats across species. We also found that the repetitive elements associated with R-loop formation differ according to developmental stage. For instance, LINEs and long terminal repeats (LTRs) are more likely to contain R-loops in embryos (fruit fly) and then turn out to be low-complexity and simple repeats in post-developmental S2 cells. Our results indicate that repetitive elements may have species-specific or development-specific regulatory effects on R-loop formation. This work advances our understanding of repetitive elements and R-loop biology.

scholarly journals Genetic Analysis and Species Specific Amplification of the Artemisinin Resistance-Associated Kelch Propeller Domain in P. falciparum and P. vivax

PLoS ONE ◽  
2015 ◽  
Vol 10 (8) ◽  
pp. e0136099 ◽  
Author(s):  
Eldin Talundzic ◽  
Stella M. Chenet ◽  
Ira F. Goldman ◽  
Dhruviben S. Patel ◽  
Julia A. Nelson ◽  
...  
Keyword(s):  
Genetic Analysis ◽  
Artemisinin Resistance ◽  
Specific Amplification ◽  
Species Specific

scholarly journals Association analysis of repetitive elements and R-loop formation across species

Mobile DNA ◽  
2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chao Zeng ◽  
Masahiro Onoguchi ◽  
Michiaki Hamada
Keyword(s):  
Fruit Fly ◽  
Low Complexity ◽  
Wide Distribution ◽  
Long Terminal Repeat Retrotransposons ◽  
Repetitive Elements ◽  
Loop Formation ◽  
Genome Wide ◽  
Regulatory Effects ◽  
Species Specific ◽  
Simple Repeats

Abstract Background Although recent studies have revealed the genome-wide distribution of R-loops, our understanding of R-loop formation is still limited. Genomes are known to have a large number of repetitive elements. Emerging evidence suggests that these sequences may play an important regulatory role. However, few studies have investigated the effect of repetitive elements on R-loop formation. Results We found different repetitive elements related to R-loop formation in various species. By controlling length and genomic distributions, we observed that satellite, long interspersed nuclear elements (LINEs), and DNA transposons were each specifically enriched for R-loops in humans, fruit flies, and Arabidopsis thaliana, respectively. R-loops also tended to arise in regions of low-complexity or simple repeats across species. We also found that the repetitive elements associated with R-loop formation differ according to developmental stage. For instance, LINEs and long terminal repeat retrotransposons (LTRs) are more likely to contain R-loops in embryos (fruit fly) and then turn out to be low-complexity and simple repeats in post-developmental S2 cells. Conclusions Our results indicate that repetitive elements may have species-specific or development-specific regulatory effects on R-loop formation. This work advances our understanding of repetitive elements and R-loop biology.

scholarly journals Clonal Stability of RAPD Markers in Three Rhododendron Species

1995 ◽  
Vol 13 (1) ◽  
pp. 43-46 ◽  
Author(s):  
M. Javed Iqbal ◽  
D. W. Paden ◽  
A. Lane Rayburn
Keyword(s):  
Dna Sequences ◽  
Rapd Markers ◽  
Cultivar Identification ◽  
Rapd Analysis ◽  
Randomly Amplified Polymorphic Dna ◽  
Plant Identification ◽  
Specific Amplification ◽  
Polymerase Chain ◽  
The Individual ◽  
Species Specific

Abstract Amplification profiles produced by polymerase chain reaction (PCR) using randomly amplified polymorphic DNA sequences (RAPD) have the potential for species and cultivar identification. Since most rhododendron plants are vegetatively propagated, it is imperative that RAPD profiles be stable during this propagation. Three species of rhododendron, Rhododendron arborescens, R. atlanticum and R. yedoense var. poukhanense were used to produce species specific amplification profiles. Stability of amplification profiles among individually cloned plants of each species were studied. Ten plants of R. atlanticum, 9 of R. arborescens, and 10 of R. yedoense var. poukhanense were studied with 10 random primers. No polymorphism was observed among individual plants of R. atlanticum and R. arborescens with all the primers. The amplification product of one plant of R. yedoense var. poukhanense showed a difference of one band with one primer. The rest of the profiles with 9 primers were identical in all plants of this species. In order to ascertain that RAPD markers can indeed reveal real genetic differences among plants, F2 plants of two hybrids were analyzed. In contrast to the clonally propagated plants, extensive polymorphisms were observed among the individual F2 plants. Thus, RAPD analysis can be used to detect genetic variability. This stability of RAPD profiles in clonally propagated rhododendron indicates the usefulness of these markers in plant identification.

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