scholarly journals Development of SCAR Markers for Species Identification in the Genus Shorea (Dipterocarpaceae)

2010 ◽  
Vol 59 (1-6) ◽  
pp. 249-257 ◽  
Author(s):  
H. S. Nuroniah ◽  
O. Gailing ◽  
R. Finkeldey
Keyword(s):  
Species Identification ◽  
Rflp Markers ◽  
Scar Markers ◽  
Closely Related Species ◽  
Tropical Timber ◽  
Sequence Characterized Amplified Region ◽  
Cpdna Region ◽  
Pcr Rflp ◽  
Primer Sets ◽  
Good Agreement

AbstractThe development of molecular markers unambiguously distinguishing groups at different taxonomic levels has numerous forensic applications. The identification of tropical timber is of particular interest in this context. We describe the development of SCAR (Sequence Characterized Amplified Region) markers for forensic applications taking the example of two closely related species of the tropical tree family Shorea (Dipterocarpaceae). Two AFLP (Amplified Fragment Length Polymorphism) fragments have been described earlier showing strong differentiation between S. leprosula and S. parvifolia. The AFLP markers were isolated from a gel, re-amplified, cloned and sequenced. Primer sets were designed from these sequences and AFLP fragments were converted into SCAR markers. The SCAR markers and PCR-RFLP markers of the chloroplast region trnLF digested with HinfI were used to screen in total 557 samples of S. parvifolia and S. leprosula from nineteen widely separated populations in Indonesia. Complete genetic differentiation between species was observed based on the putatively nuclear SCAR marker and the PCR-RFLP of the cpDNA region. We found a good agreement between leaf morphological variation and species identification based on both marker types and no indication for interspecific hybridization.

scholarly journals Comparison between single and multi-locus approaches for specimen identification in Mytilus mussels

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
María Angélica Larraín ◽  
Pía González ◽  
Claudio Pérez ◽  
Cristián Araneda
Keyword(s):  
Species Identification ◽  
Dna Marker ◽  
Morphological Characteristics ◽  
Rflp Markers ◽  
Identification Performance ◽  
As Species ◽  
Pcr Rflp ◽  
Food Quality And Safety ◽  
Genomic Regions ◽  
Specimen Identification

AbstractMytilus mussels have been the object of much research given their sentinel role in coastal ecosystems and significant value as an aquaculture resource appreciated for both, its flavour and nutritional content. Some of the most-studied Mytilus species are M. edulis, M. galloprovincialis, M. chilensis and M. trossulus. As species identification based on morphological characteristics of Mytilus specimens is difficult, molecular markers are often used. Single-locus markers can give conflicting results when used independently; not all markers differentiate among all species, and the markers target genomic regions with different evolutionary histories. We evaluated the concordance between the PCR-RFLP markers most commonly-used for species identification in mussels within the Mytilus genus (Me15-16, ITS, mac-1, 16S rRNA and COI) when used alone (mono-locus approach) or together (multi-locus approach). In this study, multi-locus strategy outperformed the mono-locus methods, clearly identifying all four species and also showed similar specimen identification performance than a 49 SNPs panel. We hope that these findings will contribute to a better understanding of DNA marker-based analysis of Mytilus taxa. These results support the use of a multi-locus approach when studying this important marine resource, including research on food quality and safety, sustainable production and conservation.

scholarly journals Rapid and Simple Species Identification of Cicada Exuviae Using COI-Based SCAR Assay

Insects ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 168 ◽  
Author(s):  
Pureum Noh ◽  
Wook Jin Kim ◽  
Jun-Ho Song ◽  
Inkyu Park ◽  
Goya Choi ◽  
...  
Keyword(s):  
Species Identification ◽  
Scar Markers ◽  
Pharmacological Effects ◽  
Mitochondrial Cytochrome ◽  
Powder Form ◽  
Sequence Alignments ◽  
Republic Of China ◽  
Sequence Characterized Amplified Region ◽  
Anticancer Effects ◽  
Reproducible Method

Cicadidae periostracum (CP), the medicinal name of cicada exuviae, is well-known insect-derived traditional medicine with various pharmacological effects, e.g., anticonvulsive, anti-inflammatory, antitussive, and anticancer effects; it is also beneficial for the treatment of Parkinson’s disease. For appropriate CP application, accurate species identification is essential. The Korean pharmacopoeia and the pharmacopoeia of the People’s Republic of China define Cryptotympana atrata as the only authentic source of CP. Species identification of commercially distributed CP based on morphological features, however, is difficult because of the combined packaging of many cicada exuviae in markets, damage during distribution, and processing into powder form. DNA-based molecular markers are an excellent alternative to morphological detection. In this study, the mitochondrial cytochrome c oxidase subunit I sequences of C. atrata, Meimuna opalifera, Platypleura kaempferi, and Hyalessa maculaticollis were analyzed. On the basis of sequence alignments, we developed sequence-characterized amplified-region (SCAR) markers for efficient species identification. These markers successfully discriminated C. atrata from the three other cicada species, and detected the adulteration of market CP samples. This SCAR assay is a rapid, simple, cheap, reliable, and reproducible method for species identification, regardless of sample form and status, and contributes to CP quality control.

Molecular typing of Staphylococcus aureus based on PCR-RFLP of coa gene and RAPD analysis

2011 ◽  
Vol 14 (2) ◽  
pp. 285-286 ◽  
Author(s):  
J. Karakulska ◽  
A. Pobucewicz ◽  
P. Nawrotek ◽  
M. Muszyńska ◽  
A. Furowicz ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Species Identification ◽  
Genetic Relationship ◽  
Molecular Typing ◽  
Rapd Analysis ◽  
Milk Samples ◽  
Rapd Pcr ◽  
Pcr Rflp ◽  
Mastitic Milk ◽  
Coa Gene

Molecular typing ofStaphylococcus aureusbased on PCR-RFLP ofcoagene and RAPD analysisThe aim of this study was molecular identification ofS. aureusstrains isolated from mastitic milk samples and establishing the genetic relationship between strains isolated from cows belonging to the same herd. In all 43 isolated strains thegapgene (930 bp) was amplified, which enabled their affiliation to theStaphylococcusgenus to be established. PCR-RFLP withAluI endonuclease of thegapgene as well asnuc(450 bp) andcoa(1130 bp) gene amplification allowed preciseS. aureusspecies identification. One hundred percent of the genetic relationship between strains was establishedviaRAPD-PCR and coa-typing.

Species identification of four economically important Pangasiid catfishes and closely related species using SSCP markers

Aquaculture ◽  
2010 ◽  
Vol 308 ◽  
pp. S47-S50 ◽  
Author(s):  
Kednapat Sriphairoj ◽  
Sirawut Klinbu-nga ◽  
Wongpathom Kamonrat ◽  
Uthairat Na-Nakorn
Keyword(s):  
Species Identification ◽  
Related Species ◽  
Closely Related Species

Distribution of Puccinia striiformis f. sp. tritici races and virulence in wheat growing regions of Kenya from 1970 TO 2014

Plant Disease ◽  
2021 ◽  
Author(s):  
Mercy Wamalwa ◽  
Ruth Wanyera ◽  
Julian Rodriguez-Algaba ◽  
Lesley Boyd ◽  
James Owuoche ◽  
...  
Keyword(s):  
Stripe Rust ◽  
Fungal Pathogen ◽  
Puccinia Striiformis ◽  
Yellow Rust ◽  
Stripe Rust Resistance ◽  
Scar Markers ◽  
Seedling Resistance ◽  
Sequence Characterized Amplified Region ◽  
Triticum Spp ◽  
Virulence Diversity

Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is a major threat to wheat (Triticum spp.) production worldwide. The objective of this study was to determine the virulence of Pst races prevalent in the main wheat growing regions of Kenya, which includes Mt. Kenya, Eastern Kenya, and the Rift Valley (Central, Southern, and Northern Rift). Fifty Pst isolates collected from 1970 to 1992 and from 2009 to 2014 were virulence phenotyped using stripe rust differential sets, and 45 isolates were genotyped with sequence characterized amplified region (SCAR) markers to differentiate among the isolates and identify aggressive strains PstS1 and PstS2. Virulence corresponding to stripe rust resistance genes Yr1, Yr2, Yr3, Yr6, Yr7, Yr8, Yr9, Yr17, Yr25, Yr27 and the seedling resistance in genotype Avocet S were detected. Ten races were detected in the Pst samples obtained from 1970 to 1992, and three additional races were detected from 2009 to 2014, with a single race being detected in both periods. The SCAR markers detected both Pst1 and Pst2 strains in the collection. Increasing Pst virulence was found in the Kenyan Pst population, and that diverse Pst race groups dominated different wheat growing regions. Moreover, recent Pst races in east Africa indicated possible migration of some race groups into Kenya from other regions. This study is important in understanding Pst evolution and virulence diversity and useful in breeding wheat cultivars with effective resistance to stripe rust. Keywords: pathogenicity, Puccinia f. sp. tritici stripe (yellow) rust, Triticum aestivum

scholarly journals Species Identification of Pinus Pollen Found in Belukha Glacier, Russian Altai Mountains, Using a Whole-Genome Amplification Method

Forests ◽  
2018 ◽  
Vol 9 (8) ◽  
pp. 444
Author(s):  
Fumio Nakazawa ◽  
Yoshihisa Suyama ◽  
Satoshi Imura ◽  
Hideaki Motoyama
Keyword(s):  
Species Identification ◽  
Whole Genome Amplification ◽  
Pollen Grains ◽  
Pollen Grain ◽  
Pinus Sibirica ◽  
Whole Genome ◽  
Accurate Identification ◽  
Closely Related Species ◽  
Genome Amplification ◽  
Amplification Method

Pollen taxa in sediment samples can be identified based on morphology. However, closely related species do not differ substantially in pollen morphology, and accurate identification is generally limited to genera or families. Because many pollen grains in glaciers contain protoplasm, genetic information obtained from pollen grains should enable the identification of plant taxa at the species level. In the present study, species identification of Pinus pollen grains was attempted using whole-genome amplification (WGA). We used pollen grains extracted from surface snow (depth, 1.8–1.9 m) from the Belukha glacier in the summer of 2003. WGA was performed using a single pollen grain. Some regions of the chloroplast genome were amplified by PCR, and the DNA products were sequenced to identify the pollen grain. Pinus includes approximately 111 recognized species in two subgenera, four sections, and 11 subsections. The tree species Pinus sibirica and P. sylvestris are currently found at the periphery of the glacier. We identified the pollen grains from the Belukha glacier to the level of section or subsection to which P. sibirica and P. sylvestris belong. Moreover, we specifically identified two pollen grains as P. sibirica or P. cembra. Fifteen species, including P. sibirica, were candidates for the remaining pollen grain.

Evidence of the three main clonalToxoplasma gondiilineages from wild mammalian carnivores in the UK

Parasitology ◽  
2013 ◽  
Vol 140 (14) ◽  
pp. 1768-1776 ◽  
Author(s):  
A. BURRELLS ◽  
P. M. BARTLEY ◽  
I. A. ZIMMER ◽  
S. ROY ◽  
A. C. KITCHENER ◽  
...  
Keyword(s):  
Toxoplasma Gondii ◽  
Rflp Markers ◽  
Type I ◽  
Type Ii ◽  
Red Foxes ◽  
Mammal Species ◽  
Tissue Samples ◽  
Pcr Rflp ◽  
Few Data ◽  
The Uk

SUMMARYToxoplasma gondiiis a zoonotic pathogen defined by three main clonal lineages (types I, II, III), of which type II is most common in Europe. Very few data exist on the prevalence and genotypes ofT. gondiiin the UK. Wildlife can act as sentinel species forT. gondiigenotypes present in the environment, which may subsequently be transmitted to livestock and humans. DNA was extracted from tissue samples of wild British carnivores, including 99 ferrets, 83 red foxes, 70 polecats, 65 mink, 64 badgers and 9 stoats. Parasite DNA was detected using a nested ITS1 PCR specific forT. gondii, PCR positive samples were subsequently genotyped using five PCR–RFLP markers.Toxoplasma gondiiDNA was detected within all these mammal species and prevalence varied from 6·0 to 44·4% depending on the host. PCR–RFLP genotyping identified type II as the predominant lineage, but type III and type I alleles were also identified. No atypical or mixed genotypes were identified within these animals. This study demonstrates the presence of alleles for all three clonal lineages with potential for transmission to cats and livestock. This is the first DNA-based study ofT. gondiiprevalence and genotypes across a broad range of wild British carnivores.

scholarly journals Species Identification of Five Penaeid Shrimps Using PCR-RFLP and SSCP Analyses of 16S Ribosomal DNA

BMB Reports ◽  
2005 ◽  
Vol 38 (4) ◽  
pp. 491-499 ◽  
Author(s):  
Bavornlak Khamnamtong ◽  
Sirawut Klinbunga ◽  
Piamsak Menasveta
Keyword(s):  
Species Identification ◽  
Ribosomal Dna ◽  
16S Ribosomal Dna ◽  
Pcr Rflp ◽  
Penaeid Shrimps

NIRS IDENTIFICATION OF SWIETENIA MACROPHYLLA IS ROBUST ACROSS SPECIMENS FROM 27 COUNTRIES

IAWA Journal ◽  
2016 ◽  
Vol 37 (3) ◽  
pp. 420-430 ◽  
Author(s):  
Maria C.J. Bergo ◽  
Tereza C.M. Pastore ◽  
Vera T.R. Coradin ◽  
Alex C. Wiedenhoeft ◽  
Jez W.B. Braga
Keyword(s):  
Species Identification ◽  
Near Infrared ◽  
Similar Species ◽  
Timber Species ◽  
Cedrela Odorata ◽  
Swietenia Macrophylla ◽  
Classification Rate ◽  
Tropical Timber ◽  
Carapa Guianensis ◽  
Country Level

Big-leaf mahogany is the world’s most valuable widely traded tropical timber species and Near Infrared Spectroscopy (NIRS) has been applied as a tool for discriminating its wood from similar species using multivariate analysis. In this study four look-alike timbers of Swietenia macrophylla (mahogany or big-leaf mahogany), Carapa guianensis (crabwood), Cedrela odorata (cedar or cedro) and Micropholis melinoniana (curupixá) have been successfully discriminated using NIRS and Partial Least Squares for Discriminant Analysis using solid block and milled samples. Species identification models identified 155 samples of S. macrophylla from 27 countries with a correct classification rate higher than 96.8%. For these specimens, the NIRS spectrum variation was more powerful for species identification than for determining provenance of S. macrophylla at the country level.

scholarly journals A PCR Method That Can Be Further Developed into PCR-RFLP Assay for Eight Animal Species Identification

2018 ◽  
Vol 2018 ◽  
pp. 1-6 ◽  
Author(s):  
Feng Guan ◽  
Yu-Ting Jin ◽  
Jin Zhao ◽  
Ai-Chun Xu ◽  
Yuan-Yuan Luo
Keyword(s):  
Species Identification ◽  
Animal Species ◽  
Limit Of Detection ◽  
Cost Effective ◽  
Universal Primers ◽  
Universal Primer ◽  
Routine Identification ◽  
Pcr Rflp ◽  
Fast Processing ◽  
Rflp Assay

There are many PCR-based methods for animal species identification; however, their detection numbers are limited or could not identify unknown species. We set out to solve this problem by developing a universal primer PCR assay for simultaneous identification of eight animal species, including goat, sheep, deer, buffalo, cattle, yak, pig, and camel. In this assay, the variable lengths of mitochondrial DNA were amplified using a pair of universal primers. PCR amplifications yielded 760 bp, 737 bp, 537 bp, 486 bp, 481 bp, 464 bp, 429 bp, and 359 bp length fragments for goat, sheep, deer, buffalo, cattle, yak, pig, and camel, respectively. This primer pair had no cross-reaction with other common domestic animals and fish. The limit of detection varied from 0.01 to 0.05 ng of genomic DNA for eight animal species in a 20 µl PCR mixture. Each PCR product could be further digested into fragments with variable sizes and qualitative analysis by SspI restriction enzyme. This developed PCR-RFLP assay was sufficient to distinguish all targeted species. Compared with the previous published related methods, this approach is simple, with high throughput, fast processing rates, and more cost-effective for routine identification of meat in foodstuffs.

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