scholarly journals SCAR Marker for Identification and Discrimination of Commiphora wightii and C. myrrha

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Pramod Kumar Sairkar ◽  
Anjana Sharma ◽  
N. P. Shukla
Keyword(s):  
Rapid Identification ◽  
Scar Markers ◽  
Specific Sequence ◽  
Closely Related Species ◽  
Commiphora Wightii ◽  
Drought Tolerant ◽  
Commercially Important ◽  
Sequence Characterized Amplified Regions ◽  
Species Specific ◽  
Study Species

Commercially important Commiphora species are drought-tolerant plants and they are leafless for most of the year. Therefore, it is necessary to develop some molecular marker for the identification. Intended for that, in the present study, species-specific, sequence-characterized amplified regions (SCAR) markers were developed for proficient and precise identification of closely related species Commiphora wightii and C. myrrha, which may ensure the quality, safety, and efficacy of medicines made from these plants through adulterous mixing of these plants. Two species-specific RAPD amplicons were selected, gel-purified, cloned, and sequenced after screening of 20 RAPD primers. The sequence of 979 and 590 nucleotides (Genebank accession numbers K90051 and K90052) was used for development of 4 SCAR markers, namely, Sc1P, Sc1Pm, Sc2P, and Sc2Pm. Out of them, the Sc1Pm was specific for C. wightii, while Sc2P discriminated both the Commiphora species. These markers are first reported and will be useful for rapid identification of closely related Commiphora wightii and C. myrrha species.

scholarly journals Development of Pathotype-Specific SCAR Markers for Detection of Verticillium albo-atrum Isolates from Hop

Plant Disease ◽  
2004 ◽  
Vol 88 (10) ◽  
pp. 1115-1122 ◽  
Author(s):  
Sebastjan Radišek ◽  
Jernej Jakše ◽  
Branka Javornik
Keyword(s):  
Rapid Identification ◽  
Aflp Markers ◽  
Scar Markers ◽  
Specific Primer ◽  
Specific Sequence ◽  
Sequence Characterized Amplified Region ◽  
Wide Range ◽  
Rapid Polymerase Chain Reaction ◽  
Production Areas ◽  
Verticillium Albo Atrum

Rapid polymerase chain reaction (PCR) assays were developed for the identification and detection of Verticillium albo-atrum hop pathotypes PG1 and PG2 from Slovenia. Of 17 pathotype-linked amplified fragment length polymorphism (AFLP) markers, 11 were cloned successfully and sequenced. To convert polymorphic AFLP markers into pathotype-specific sequence-characterized amplified region (SCAR) markers, 22 PG2- and 10 PG1-specific primer pairs were designed from 16 sequences. When primer specificity was tested on a wide range of Verticillium isolates, 10 PG2- and 6 PG1-specific primer pairs retained amplification specificity for V. albo-atrum Slovene hop isolates, but also amplified sequences in V. albo-atrum and V. dahliae hop isolates from different hop production areas in Europe, as well as in some isolates from other hosts. Primer combinations obtained from the AFLP-9-1 marker were specific only for V. albo-atrum PG2 isolates. The highly specific primers were used in multiplex PCR and a nested PCR to detect the V. albo-atrum PG2 pathotype in xylem tissue of hop plants. These new SCAR markers provide a valuable tool for rapid identification of V. albo-atrum PG1 and PG2 hop pathotypes.

scholarly journals Species-Specific Monoclonal Antibodies for Rapid Identification of Bartonella quintana

2000 ◽  
Vol 7 (1) ◽  
pp. 21-24 ◽  
Author(s):  
Zhongxing Liang ◽  
Didier Raoult
Keyword(s):  
Monoclonal Antibodies ◽  
Bartonella Henselae ◽  
Low Cost ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Rapid Identification ◽  
Closely Related Species ◽  
Bartonella Quintana ◽  
Species Specific ◽  
Body Lice

ABSTRACT Seven species-specific monoclonal antibodies (MAbs) toBartonella quintana were produced and characterized. The MAbs were of the immunoglobulin G class and reacted only with 13B. quintana strains in indirect microimmunofluorescence and Western immunoblotting assays. They did not react with eight otherBartonella spp., including Bartonella henselae, the most closely related species, and a selected MAb did also not react with nine other strains of gram-negative bacteria. The MAbs reacted mainly with a 34-kDa protein epitope of B. quintana which was shown to be species specific by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Four of five body lice experimentally infected with B. quintana were found to be positive for the organism in microimmunofluorescence assays with one MAb. These MAbs may provide a specific, simple, rapid, and low-cost tool for the identification of B. quintana and the diagnosis of infections due to the microorganism.

scholarly journals Authentication of commercially important tuna species landed in Tuticorin coast of Tamil Nadu, India by SE-AFLP method

2017 ◽  
Vol 64 ◽  
Author(s):  
G. Jeyasekaran ◽  
G. Arunkumar ◽  
P. Senthil Kumar ◽  
R. Jeya Shakila ◽  
D. Sukumar
Keyword(s):  
Tamil Nadu ◽  
Thunnus Albacares ◽  
Katsuwonus Pelamis ◽  
Closely Related Species ◽  
Important Species ◽  
Fish Meat ◽  
Thunnus Obesus ◽  
Commercially Important ◽  
Euthynnus Affinis ◽  
Species Specific

Seafood serves as a valuable protein source for human population. Among the seafood, tuna is considered as one of the commercially important species worldwide. Five tuna species namely Euthynnus affinis, Auxis thazard, Katsuwonus pelamis, Thunnus albacares and Thunnus obesus are commonly landed in the Tuticorin coast of Tamil Nadu. Among the five species, the exportable quality and grade of the meat is as follows: T. albacares> T. obesus> K. pelamis> E. affinis> A. thazard. In recent years, mislabeling is done by replacing high value tuna meat with low value tuna meat or with other low value fish meat to earn illegally. Usually, the species identification is done based on the morphological features, but this cannot be applied for the processed fish. PCR based identification methods have gained importance in the identification of fish species. PCR-AFLP is one of the molecular based methods, which can differentiate even closely related species. In this study, SE-AFLP method was employed to differentiate the above five tuna species viz., E. affinis, A. thazard, K. pelamis, T. albacares and T. obesus. Species specific AFLP marker was obtained in the primer combination of EcoR1 for fresh tuna. Band Sharing Index (BSI) analysis was also performed to find the similarities and variation among the five tuna species. AFLP profile of unknown tuna products was compared with the standard AFLP profile and the tuna species authentication was done by analysing BSI score.

scholarly journals A Comparative Study of 5S rDNA Non-Transcribed Spacers in Elaeagnaceae Species

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 4
Author(s):  
Oleg S. Alexandrov ◽  
Olga V. Razumova ◽  
Gennady I. Karlov
Keyword(s):  
Polymerase Chain Reaction ◽  
Molecular Markers ◽  
Dna Markers ◽  
5S Rdna ◽  
Chain Reaction ◽  
Closely Related Species ◽  
Pcr Products ◽  
Polymerase Chain ◽  
Species Specific ◽  
Shepherdia Canadensis

5S rDNA is organized as a cluster of tandemly repeated monomers that consist of the conservative 120 bp coding part and non-transcribed spacers (NTSs) with different lengths and sequences among different species. The polymorphism in the 5S rDNA NTSs of closely related species is interesting for phylogenetic and evolutional investigations, as well as for the development of molecular markers. In this study, the 5S rDNA NTSs were amplified with universal 5S1/5S2 primers in some species of the Elaeagnaceae Adans. family. The polymerase chain reaction (PCR) products of five Elaeagnus species had similar lengths near 310 bp and were different from Shepherdia canadensis (L.) Nutt. and Sh. argentea (Pusch.) Nutt. samples (260 bp and 215 bp, respectively). The PCR products were cloned and sequenced. An analysis of the sequences revealed that intraspecific levels of NTS identity are high (approximately 95–96%) and similar in the Elaeagnus L. species. In Sh. argentea, this level was slightly lower due to the differences in the poly-T region. Moreover, the intergeneric and intervarietal NTS identity levels were studied and compared. Significant differences between species (except E. multiflora Thunb. and E. umbellata Thunb.) and genera were found. Herein, a range of the NTS features is discussed. This study is another step in the investigation of the molecular evolution of Elaeagnaceae and may be useful for the development of species-specific DNA markers in this family.

A species-specific satellite DNA from the entomopathogenic nematode Heterorhabditis indicus

Genome ◽  
1998 ◽  
Vol 41 (2) ◽  
pp. 148-153 ◽  
Author(s):  
Monique Abadon ◽  
Eric Grenier ◽  
Christian Laumond ◽  
Pierre Abad
Keyword(s):  
Dna Sequence ◽  
Satellite Dna ◽  
Tandem Repeats ◽  
Sequence Data ◽  
Entomopathogenic Nematode ◽  
Consensus Sequence ◽  
Repeated Sequence ◽  
Nucleotide Sequence Analysis ◽  
Specific Sequence ◽  
Species Specific

An AluI satellite DNA family has been cloned from the entomopathogenic nematode Heterorhabditis indicus. This repeated sequence appears to be an unusually abundant satellite DNA, since it constitutes about 45% of the H. indicus genome. The consensus sequence is 174 nucleotides long and has an A + T content of 56%, with the presence of direct and inverted repeat clusters. DNA sequence data reveal that monomers are quite homogeneous. Such homogeneity suggests that some mechanism is acting to maintain the homogeneity of this satellite DNA, despite its abundance, or that this repeated sequence could have appeared recently in the genome of H. indicus. Hybridization analysis of genomic DNAs from different Heterorhabditis species shows that this satellite DNA sequence is specific to the H. indicus genome. Considering the species specificity and the high copy number of this AluI satellite DNA sequence, it could provide a rapid and powerful tool for identifying H. indicus strains.Key words: AluI repeated DNA, tandem repeats, species-specific sequence, nucleotide sequence analysis.

ISSR-Derived Species-Specific SCAR Marker for Rapid and Accurate Authentication of Ocimum tenuiflorum L.

Planta Medica ◽  
2017 ◽  
Vol 84 (02) ◽  
pp. 117-122 ◽  
Author(s):  
Amit Kumar ◽  
Vereena Rodrigues ◽  
Priyanka Mishra ◽  
Kuppusamy Baskaran ◽  
Ashutosh Shukla ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
High Volume ◽  
Inter Simple Sequence Repeat ◽  
Rapid Identification ◽  
Medicinal Species ◽  
Accurate Identification ◽  
Sequence Characterized Amplified Region ◽  
Medicinal Value ◽  
Ocimum Tenuiflorum ◽  
Species Specific

Abstract Ocimum tenuiflorum has been widely used in traditional medicine and has high medicinal value. High volume trade of this potential medicinal plant species led to unscrupulous adulteration of both crude drugs as well as formulations. Morphology-based authentication is difficult in cases of incomplete or damaged samples and in dried herbal materials. In such cases, PCR-based molecular methods may aid in accurate identification. The present study aimed at developing species-specific DNA marker(s) for the authentication of O. tenuiflorum. A species-specific amplicon (279 bp) generated through an inter-simple sequence repeat marker (UBC 835) in all individuals of O. tenuiflorum was cloned, sequenced, and a primer pair was developed (designated as CIM-OT-835F/CIM-OT-835R). The newly developed sequence characterized amplified region marker was validated through PCR amplification in all available seven species of Ocimum, and its specificity for O. tenuiflorum was confirmed with the consistent generation of an amplicon of 177 bp. The developed marker can be used for accurate and rapid identification of the species for certification purposes and will be useful in quality control of medicinal preparations containing this important medicinal species.

scholarly journals Repeated evolution of asymmetric genitalia and right-sided mating behavior in theDrosophila nannopteraspecies group

2019 ◽  
Author(s):  
Andrea Acurio ◽  
Flor T. Rhebergen ◽  
Sarah Paulus ◽  
Virginie Courtier-Orgogozo ◽  
Michael Lang
Keyword(s):  
Related Species ◽  
Current Data ◽  
The Other ◽  
Genital Morphology ◽  
Closely Related Species ◽  
Outgroup Species ◽  
Repeated Evolution ◽  
Drosophila Pachea ◽  
Species Specific ◽  
Group Species

AbstractBackgroundMale genitals have repeatedly evolved left-right asymmetries, and the causes of such evolution remain unclear. TheDrosophila nannopteragroup contains four species, among which three exhibit left-right asymmetries of distinct genital organs. In the most studied species,Drosophila pachea, males display asymmetric genital lobes and they mate right-sided on top of the female. Copulation position of the other species is unknown.ResultsTo assess whether the evolution of genital asymmetry could be linked to the evolution of one-sided mating, we examined phallus morphology and copulation position inD. pacheaand closely related species. The phallus was found to be symmetric in all investigated species exceptD. pachea, which display an asymmetric phallus with a right-sided gonopore, andD. acanthoptera, which harbor an asymmetrically bent phallus. In all examined species, males were found to position themselves symmetrically on top of the female, except inD. pacheaandD. nannoptera, where males mated right-sided, in distinctive, species-specific positions. In addition, the copulation duration was found to be increased innannopteragroup species compared to closely related outgroup species.ConclusionOur study shows that gains, and possibly losses, of asymmetry in genital morphology and mating position have evolved repeatedly in thenannopteragroup. Current data does not allow us to conclude whether genital asymmetry has evolved in response to changes in mating position, or vice versa.

scholarly journals Nanopore amplicon sequencing reveals molecular convergence and local adaptation of opsin genes

2020 ◽  
Author(s):  
Katherine M. Eaton ◽  
Moisés A. Bernal ◽  
Nathan J.C. Backenstose ◽  
Trevor J. Krabbenhoft
Keyword(s):  
Local Adaptation ◽  
Environmental Gradients ◽  
Parallel Evolution ◽  
Amplicon Sequencing ◽  
Species Flock ◽  
Closely Related Species ◽  
Oxford Nanopore ◽  
Opsin Genes ◽  
Potential Case ◽  
Species Specific

AbstractLocal adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined a potential case of adaptation to novel visual environments in a species flock (Great Lakes salmonids, genus Coregonus) using a new amplicon genotyping protocol on the Oxford Nanopore Flongle. Five visual opsin genes were amplified for individuals of C. artedi, C. hoyi, C. kiyi, and C. zenithicus. Comparisons revealed species-specific differences in the coding sequence of rhodopsin (Tyr261Phe substitution), suggesting local adaptation by C. kiyi to the blue-shifted depths of Lake Superior. Parallel evolution and “toggling” at this amino acid residue has occurred several times across the fish tree of life, resulting in identical changes to the visual systems of distantly related taxa across replicated environmental gradients. Our results suggest that ecological differences and local adaptation to distinct visual environments are strong drivers of both evolutionary parallelism and diversification.

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