scholarly journals Identification of Burseraceae trees from Peru: a comparison of the nuclear DNA marker ITS and the plastid DNA marker rbcL for DNA barcoding

2012 ◽  
Vol 16 (2) ◽  
Author(s):  
Elias Elbogen
Keyword(s):  
Dna Barcoding ◽  
Nuclear Dna ◽  
Dna Marker ◽  
Plastid Dna

scholarly journals Karyological Analysis and DNA Barcoding of Pompia Citron: A First Step toward the Identification of Its Relatives

Plants ◽  
2019 ◽  
Vol 8 (4) ◽  
pp. 83 ◽  
Author(s):  
Grazia Viglietti ◽  
Giulio Galla ◽  
Andrea Porceddu ◽  
Gianni Barcaccia ◽  
Franck Curk ◽  
...  
Keyword(s):  
Dna Barcoding ◽  
Dna Content ◽  
Nuclear Dna ◽  
Genetic Relationships ◽  
Citrus Fruit ◽  
Plastid Dna ◽  
Molecular Data ◽  
Dna Polymorphisms ◽  
Citrus Species ◽  
Chloroplast Markers

Pompia is a citrus fruit endemic of Sardinia, Italy, with an essential oil profile showing outstanding anti-inflammatory and anti-microbic properties. Despite its remarkable pharmaceutical potential, little taxonomic and genetic information is available for this species. We applied flow cytometry and classical cytogenetic techniques to assess the DNA content and to reconstruct the karyotype of several Pompia accessions. Molecular data from plastid DNA barcoding and nuclear DNA sequencing were used to study the genetic distance between Pompia and other citrus species. Flow cytometric estimates of DNA content and somatic chromosome counts suggest that Pompia is a regular diploid Citrus species. DNA polymorphisms of nuclear and chloroplast markers allowed us to investigate the genetic relationships between Pompia accessions and other Citrus species. Based on DNA polymorphism data we propose that Pompia is a very recent interspecific hybrid generated by a cross between C. aurantium (as seed bearer) and C. medica (as pollen donor). Our findings pave the way for further and more specific investigations of local Pompia germplasm resources that may help the preservation and valorisation of this valuable citrus fruit tree.

scholarly journals Reconstruction of molecular phylogeny of closely related Amorphophallus species of India using plastid DNA marker and fingerprinting approaches

2016 ◽  
Vol 23 (1) ◽  
pp. 155-167 ◽  
Author(s):  
Avinash R. Gholave ◽  
Kiran D. Pawar ◽  
Shrirang R. Yadav ◽  
Vishwas A. Bapat ◽  
Jyoti P. Jadhav
Keyword(s):  
Molecular Phylogeny ◽  
Dna Marker ◽  
Plastid Dna

scholarly journals The solution to the cytological paradox of isomorphy.

1987 ◽  
Vol 104 (3) ◽  
pp. 739-748 ◽  
Author(s):  
L J Goff ◽  
A W Coleman
Keyword(s):  
Cell Size ◽  
Dna Content ◽  
Nuclear Dna ◽  
Nuclear Dna Content ◽  
Plastid Dna ◽  
Diploid Cell ◽  
Red Alga ◽  
Haploid Nucleus ◽  
Two Generations ◽  
A Cell

Cells with polyploid nuclei are generally larger than cells of the same organism or species with nonpolyploid nuclei. However, no such change of cell size with ploidy level is observed in those red algae which alternate isomorphic haploid with diploid generations. The results of this investigation reveal the explanation. Nuclear DNA content and other parameters were measured in cells of the filamentous red alga Griffithsia pacifica. Nuclei of the diploid generation contain twice the DNA content of those of the haploid generation. However, all cells except newly formed reproductive cells are multinucleate. The nuclei are arranged in a nearly perfect hexagonal array just beneath the cell surface. When homologous cells of the two generations are compared, although the cell size is nearly identical, each nucleus of the diploid cell is surrounded by a region of cytoplasm (a "domain") nearly twice that surrounding a haploid nucleus. Cytoplasmic domains associated with a diploid nucleus contain twice the number of plastids, and consequently twice the amount of plastid DNA, than is associated with the domain of a haploid nucleus. Thus, doubling of ploidy is reflected in doubling of the size and organelle content of the domain associated with each nucleus. However, cell size does not differ between homologous cells of the two generations, because total nuclear DNA (sum of the DNA in all nuclei in a cell) per cell does not differ. This is the solution to the cytological paradox of isomorphy.

A minisatellite DNA marker for discriminating between European and North American Atlantic salmon (Salmo salar)

1995 ◽  
Vol 52 (11) ◽  
pp. 2305-2311 ◽  
Author(s):  
John B. Taggart ◽  
Eric Verspoor ◽  
Paul T. Galvin ◽  
Paloma Morán ◽  
Andrew Ferguson
Keyword(s):  
Atlantic Salmon ◽  
Allele Frequency ◽  
Salmo Salar ◽  
North American ◽  
Nuclear Dna ◽  
Dna Marker ◽  
Low Frequency ◽  
Geographic Range ◽  
Minisatellite Dna ◽  
Atlantic Salmon Salmo Salar

A highly discriminatory and practical nuclear DNA genetic marker that can distinguish between Atlantic salmon (Salmo salar) of European and North American origin is described. Screening of 2847 European and 247 North American Atlantic salmon from much of its geographic range for variability at a minisatellite locus, Ssa-A45/2/2, revealed the continental stocks to be almost fixed for two different-sized, easily discernable alleles. Virtually all European Atlantic salmon were homozygous for a 3.00-kb allele (frequency > 0.999), while a smaller 2.77-kb allele (frequency = 0.946) predominated in all North American populations. Whereas the 2.77-kb allele was found exclusively in North American salmon, an allele indistinguishable in size from the 3.00-kb European diagnostic allele was also observed at low frequency (0.036) in North American fish. Eight other continent-specific rare alleles (highest frequency = 0.006) were also observed. The results suggest that little, if any, natural gene flow occurs between the two continental groups of Atlantic salmon.

Taxonomic revision of Bromeliaceae subfam. Tillandsioideae based on a multi-locus DNA sequence phylogeny and morphology

Phytotaxa ◽  
2016 ◽  
Vol 279 (1) ◽  
pp. 1 ◽  
Author(s):  
MICHAEL H.J. BARFUSS ◽  
WALTER TILL ◽  
ELTON M.C. LEME ◽  
JUAN P. PINZÓN ◽  
JOSÉ M. MANZANARES ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Nuclear Dna ◽  
Taxonomic Revision ◽  
Plastid Dna ◽  
Morphological Characters ◽  
Seed Morphology ◽  
Identification Key ◽  
New Genera ◽  
Stigma Morphology

A taxonomic revision of Bromeliaceae subfam. Tillandsioideae is presented based on a multi-locus DNA sequence phylogeny (viz., plastid DNA loci rpoB-trnC-petN, trnK-matK-trnK, and ycf1, and the nuclear DNA gene PHYC) and new or re-evaluated morphology (e.g., leaf, inflorescence, sepal, petal, ovary, stigma, stamen, pollen, ovule, and seed morphology). This enables the circumscription of monophyletic units using synapomorphic combinations of diagnostic morphological characters. Stigma morphology has proven to be indicative for super-specific taxa in Tillandsioideae. One new stigma type and several subtypes of previously described stigmas were found. The four tribes proposed earlier are mostly confirmed, but Catopsideae replaces the formerly used name Pogospermeae for the monotypic tribe of Catopsis. In addition, the two new subtribes Cipuropsidinae and Vrieseinae are proposed within tribe Vrieseeae. Several new genera are established to render taxonomic units monophyletic and morphologically well circumscribed. They represent segregates of either Mezobromelia (Gregbrownia: 4 spp.), Tillandsia (viz., Barfussia: 3 spp., Josemania: 5 spp., Lemeltonia: 7 spp., Pseudalcantarea: 3 spp., and Wallisia: 4 spp. and 1 hybrid), or Vriesea (viz., Goudaea: 2 spp., Jagrantia: 1 sp., Lutheria: 4 spp., Stigmatodon: 18 spp., and Zizkaea: 1 spp.). The new subgenera Tillandsia subg. Pseudovriesea and T. subg. Viridantha are established, and T. subg. Aerobia is resurrected. An identification key to all accepted genera of Bromeliaceae subfam. Tillandsioideae is provided. Furthermore, to clarify nomenclatural uncertainties, typifications are proposed for Catopsis subg. Tridynandra, Thecophyllum [unranked] Biflorae, Tillandsia subg. Aerobia, T. sect. Caricifoliae, T. sect. Conostachys, T. sect. Cyathophora, T. sect. Eriophyllum, T. sect. Macrocyathus, T. sect. Platystachys Baker auct. non al., Tillandsia sect. Strepsia, Vriesea subg. Conostachys Mez auct. non al., T. lindenii K. Koch auct. non al., and T. macropetala.

scholarly journals Proplastid Dna Synthesis at Pachytene in Pollen Mother Cells of Lilium Henryi

1982 ◽  
Vol 56 (1) ◽  
pp. 293-302
Author(s):  
D. R. SMYTH
Keyword(s):  
Dna Synthesis ◽  
Dna Sequences ◽  
Nuclear Dna ◽  
Buoyant Density ◽  
Plastid Dna ◽  
Electron Microscopic ◽  
Pollen Mother Cells ◽  
Specific Hybridization ◽  
Chloroplast Dna Sequences ◽  
Mother Cells

About three-quarters of the DNA synthesis occurring in pachytene pollen mother cells of Lilium henryi takes place in proplastids. Only around 15% can be attributed to mitochondrial labelling and 10% to nuclear DNA synthesis. Label was identified in the proplastid genome by its location in electron microscopic autoradiographs, by its buoyant density (1.698 g/ml), and by its specific hybridization to chloroplast DNA sequences from spinach. Proplastids, while apparently not dividing at pachytene, may be replicating their DNA in readiness for subsequent proliferation in developing microspores. The annealing properties of plastid DNA closely parallel those of labelled pachytene DNA sequences implicated in meiotic exchange events.

scholarly journals Development of PCR-based Fingerprinting Tool in Banana (Musa sp., AAA) and Conversion of Negative to Positive DNA Marker

HortScience ◽  
2002 ◽  
Vol 37 (7) ◽  
pp. 1108-1111 ◽  
Author(s):  
Reynato P. Umali ◽  
Nanako Kameya ◽  
Ikuo Nakamura
Keyword(s):  
Rapd Markers ◽  
Dna Marker ◽  
Plastid Dna ◽  
Base Substitution ◽  
Molecular Tools ◽  
Arbitrary Primers ◽  
Musa Sp ◽  
Phylogenetic Identification ◽  
The Subject ◽  
Potential Use

The banana (Musa sp., AAA) genome is continuously expanding due to the high frequency of somaclonal variation. Because of this increasing diversity, numerical and morphological methods of taxonomic and phylogenetic identification of banana cultivars became laborious, difficult, and often the subject of disagreements. The aim of this study, therefore, is to develop molecular tools for DNA fingerprinting that can discriminate Musa, AAA Cavendish subgroup cultivars. In this paper, we showed that the plastid-subtype identity (PS-ID) sequence of the noncoding region between rpl16 and rpl14 genes of plastid DNA was highly conserved except for single-base substitution and deletion. These differences separated the clones into three groups (G1, G2, and G3) and suggested that clones within groups are closely related maternally. Using arbitrary primer A13, we later identified negative RAPD markers A133.0 and A131.3 specifically for S4 (selection from Giant Cavendish subgroup, AAA) and S11 (`Morado' from `Red' and `Green Red' subgroup, AAA), respectively. Fragments corresponding to the missing bands were sequenced and used as templates to design new primers with overlapping sequences. Two of these primers, Ba3.0A and Ba1.3A, successfully generated positive markers consistently amplified as Ba3.0A0.8 and Ba1.3A0.6 for S4 and S11, respectively. It is proposed that the method just described can be a better alternative over screening more arbitrary primers in generating positive markers in cases when negative ones were already identified. Results of PS-ID subtype analysis likewise suggested potential use in identifying wild maternal progenitor in polyploid bananas.

scholarly journals Identification and Monitoring of Amomi Fructus and its Adulterants Based on DNA Barcoding Analysis and Designed DNA Markers

Molecules ◽  
2019 ◽  
Vol 24 (22) ◽  
pp. 4193 ◽  
Author(s):  
Eui Jeong Doh ◽  
Jung-Hoon Kim ◽  
Guemsan Lee
Keyword(s):  
Dna Barcoding ◽  
Dna Markers ◽  
Dna Marker ◽  
Intergenic Spacer ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Traditional Medicines ◽  
Amomum Villosum ◽  
Reliable Methods ◽  
A New Species

Amomi Fructus is one of the traditional medicines derived from the ripe fruits of the Zingiberaceae family of plants, which include Amomum villosum, A. villosum var. xanthioides, and A. longiligulare. Owing to their highly similar morphological traits, several kinds of adulterants of Amomi Fructus have been reported. Therefore, accurate and reliable methods of identification are necessary in order to ensure drug safety and quality. We performed DNA barcoding using five regions (ITS, matK, rbcL, rpoB, and trnL-F intergenic spacer) of 23 Amomi Fructus samples and 22 adulterants. We designed specific DNA markers for Amomi Fructus based on the single nucleotide polymorphisms (SNPs) in the ITS. Amomi Fructus was well separated from the adulterants and was classified with the species of origin based on the detected SNPs from the DNA barcoding results. The AVF1/ISR DNA marker for A. villosum produced a 270 bases amplified product, while the ALF1/ISF DNA marker produced a 350 bases product specific for A. longiligulare. Using these DNA markers, the monitoring of commercially distributed Amomi Fructus was performed, and the monitoring results were confirmed by ITS analysis. This method identified samples that were from incorrect origins, and a new species of adulterant was also identified. These results confirmed the accuracy and efficiency of the designed DNA markers; this method may be used as an efficient tool for the identification and verification of Amomi Fructus.

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