scholarly journals rDNA Variability Assessed in PCR Reactions of Selected Accessions of Acer

2011 ◽  
Vol 39 (1) ◽  
pp. 260 ◽  
Author(s):  
Milosz SMOLIK ◽  
Marcelina KRUPA-MAŁKIEWICZ ◽  
Beata SMOLIK ◽  
Justyna WIECZOREK ◽  
Katarzyna PREDYGIER
Keyword(s):  
Genetic Similarity ◽  
Its Region ◽  
Universal Primers ◽  
Its Sequence ◽  
Genotypic Variability ◽  
Botanical Variety ◽  
Rdna Sequences ◽  
Pcr Products ◽  
Genetic Profiles ◽  
Rdna Variability

The region of rDNA (SSU, 5.8S, LSU and ITS1, ITS2 spacer sequences) of fourteen Acer accessions was tested in order to determine the possibility to identify genotypic variability within a rDNA sequence. The tests were performed using the PCR technique and a set of combination of several pairs of ‘universal’ primers designed to amplify rDNA sequences. ‘Universal’ primers were selected in such a way as to make the rDNA regions flanking possible in cases where a smaller or larger scope of variability was expected. Thus, within SSU or LSU sequences, monomorphic PCR products were amplified for the tested Acer accessions. Within the ITS sequence, a greater scope of variability was found. This was manifested by the presence of several additional PCR products in the genetic profiles of the tested Acer accessions. The range of their length relative to the ITS region or ITS1, ITS2 or 5.8S corresponded separately to that described in the literature. The analysis of the topology of the constructed tree revealed the presence of two similar groups, ‘a’ and ‘b’. Cultivated varieties and one botanical variety of the Japanese maple were included respectively in these groups and the genetic similarity between the analyzed accessions ranged from 63 to 98%.

Comparison of the ITS Sequences of 5 Common Potentilla Species in Jilin Province of China

2012 ◽  
Vol 554-556 ◽  
pp. 1690-1693 ◽  
Author(s):  
Shao Xuan Zhang ◽  
Xin Rui Liu ◽  
Bo Chuan Wang ◽  
Yun Hui Ling ◽  
De Jun Sun ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Scientific Data ◽  
Jilin Province ◽  
Its Sequences ◽  
Universal Primers ◽  
Its Sequence ◽  
Its Sequence Analysis ◽  
Pcr Products

To find the differences in the internal transcribed spacer(ITS) sequences and provide scientific data for the authentication of Potentilla chinensis and its related species, we extracted the genome DNA from the leaves of 5 common Potetilla species in Jilin Province, amplified the ITS region using ITS universal primers of angiosperm, and sequenced the purified PCR products directly. Polymorphism of ITS sequences was found within P. chinensis and the sequence data suggested that our samples of this species might be related to hybridization. Other 4 species showed intraspecies-stability in ITS sequence. The ITS sequences of these 5 Potentilla species are significantly different. So ITS sequence analysis and other methods derived from it can be used in authentication of Potentilla.

A New Method to Identify Pulsatilla chinesis(Bge) Regel, from Potentilla chinesis Ser. Based on ITS Sequences

2014 ◽  
Vol 1033-1034 ◽  
pp. 179-182
Author(s):  
Shao Xuan Zhang ◽  
Guang Zhu Lin ◽  
Bo Chuan Wang ◽  
Yan Shi
Keyword(s):  
Its Region ◽  
Jilin Province ◽  
Its Sequences ◽  
New Method ◽  
Universal Primers ◽  
Reliable Identification ◽  
Identification Method ◽  
Restriction Sites ◽  
Pcr Products

To establish a reliable identification method of Pulsatilla chinesis (Bge) Regel., from its counterfeits, Potentilla chinesis Ser., we extracted the genome DNA from the leaves of these two plants collected in Jilin Province, amplified the ITS region using ITS universal primers of angiosperm, and sequenced the purified PCR products directly. The obtained sequences were edited by Genetyx and compared. Based on ITS sequences, we used primer PREMIER 5.0 to search the restriction sites of the two ITS sequences and found BtgI can be used to identify them.

scholarly journals An Epidemic of Almond Witches'-broom in Lebanon: Classification and Phylogenetic Relationships of the Associated Phytoplasma

Plant Disease ◽  
2002 ◽  
Vol 86 (5) ◽  
pp. 477-484 ◽  
Author(s):  
Yusuf Abou-Jawdah ◽  
Armig Karakashian ◽  
Hana Sobh ◽  
Marta Martini ◽  
Ing-Ming Lee
Keyword(s):  
Rflp Analysis ◽  
Pigeon Pea ◽  
Universal Primers ◽  
Rrna Gene ◽  
Nested Polymerase Chain Reaction ◽  
Main Trunk ◽  
Stunted Growth ◽  
Rdna Sequences ◽  
Pcr Products ◽  
Almond Trees

An epidemic of almond witches'-broom has devastated almond production in Lebanon. Thousands of almond trees have died over the past 10 years due to the rapid spread of the disease. The symptoms, which include early flowering, stunted growth, leaf rosetting, dieback, off-season growth, proliferation of slender shoots, and witches'-brooms arising mainly from the main trunk and roots, resemble those caused by phytoplasmal infections. For the detection of the putative causal agent, nested polymerase chain reaction (PCR) was performed using universal primers (P1/P7, R16mF2/R16mR1, and R16F2n/R16R2) commonly used for the specific diagnosis of plant pathogenic phytoplasmas. Phytoplasmas were readily detected from infected trees with witches'-broom symptoms collected from three major almond growing regions in Lebanon. Restriction fragment length polymorphism (RFLP) analysis of PCR products amplified by the primer pair R16F2n/R16R2 revealed that the phytoplasma associated with infected almonds is similar to, but distinct from, members of the pigeon pea witches'-broom phytoplasma group (16SrIX). A new subgroup, 16SrIX-B, was designated. Sequencing of the amplified products of the phytoplasma 16S rRNA gene indicated that almond witches'-broom (AlmWB) phytoplasma is most closely related to members of the pigeon pea witches'-broom phytoplasma group (with sequence homology ranging from 98.4 to 99.0%). Phylogenetic analysis of 16S rDNA sequences from AlmWB phytoplasma and from representative phytoplasmas from GenBank showed that the AlmWB phytoplasma represents a distinct lineage within the pigeon pea witches'-broom subclade. The same phytoplasma appears also to infect peach and nectarine seedlings.

Variations in ribosomal DNA sequences and phylogeny of Globodera parasitising solanaceous plants

Nematology ◽  
2000 ◽  
Vol 2 (6) ◽  
pp. 591-604 ◽  
Author(s):  
Sergei Subbotin ◽  
Roland Perry ◽  
Andrew Warry ◽  
Paul Halford
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Its Region ◽  
Globodera Rostochiensis ◽  
Its2 Region ◽  
Restriction Patterns ◽  
Rdna Sequences ◽  
Pcr Products ◽  
Solanaceous Plants ◽  
Its Pcr

AbstractThe D3 expansion region of the 28S gene and the ITS1-5.8S-ITS2 region of rDNA sequences from Globodera rostochiensis, G. pallida, G. tabacum tabacum, G. tabacum virginiae and G. tabacum solanacearum have been aligned and compared. There are no nucleotide differences in the D3 region sequences between G. rostochiensis and G. pallida. Sequence analysis and RFLPs of ITS-PCR products showed that several haplotypes are present in the genomes of G. rostochiensis and G. pallida populations. Restriction patterns of PCR products for eight enzymes for differentiation of these two species are given. Phylogenetic analysis of 41 ITS region sequences obtained from populations and species of the subfamily Punctoderinae revealed four distinct main clades within Globodera parasitising solanaceous plants: G. rostochiensis, G. tabacum, G. pallida and an undescribed Globodera sp. from South America. The utility of RFLP profiles and sequences of the rDNA are discussed for diagnostics and phylogeny of Globodera . Variabilité dans les séquences de l'ADN ribosomal et phylogénie des Globodera parasitant les Solanacées - La région d'expansion D3 du gène 28S et la région ITS1-5.8S-ITS2 des séquences d'ADNr de Globodera rostochiensis, G. pallida, G. tabacum tabacum, G. tabacum virginiae et G. tabacum solanacearum ont été alignées et comparées. Il n'y a pas de différence dans les nucléotides de la séquence de la région D3 entre G.rostochiensis et G.pallida. L'analyse séquentielle et les RFLP des produits du ITS-PCR montrent que plusieurs haplotypes sont présents dans les génomes des populations de G. rostochiensis et G. pallida. Les profils de restriction des produits du PCR de huit enzymes choisies pour la différenciation de ces deux espèces sont donnés. L'analyse phylogénique séquentielle de 41 regions ITS de populations et espèces appartenant à la sous-famille des Punctonerinae a révélé l'existence de quatre clades chez les Globodera parasitant les Solanacées: G. rostochiensis, G. tabacum, G. pallida et une espèce non décrite provenant d'Amérique du Sud. L'utilité pour le diagnostic et la phylogénie des Globodera des profils de RFLP et des séquences d'ADNr est discutée.

scholarly journals Polymorphism in Random Amplified and Nuclear rDNA Sequences Assessed in Certain Apple (Malus × domestica Borkh.) Cultivars

2011 ◽  
Vol 39 (2) ◽  
pp. 264
Author(s):  
Milosz SMOLIK ◽  
Katarzyna MALINOWSKA ◽  
Beata SMOLIK ◽  
Krzysztof PACEWICZ
Keyword(s):  
Rapd Markers ◽  
Rapd Analysis ◽  
Its Region ◽  
Mantel Test ◽  
Rrna Genes ◽  
P Value ◽  
Molecular Tools ◽  
Nuclear Rdna ◽  
Rdna Sequences ◽  
Genetic Profiles

Eigth apple (Malus × domestica Borkh.) cultivars: ‘Delikates’, ‘Cortland’, ‘James Grieve’, ‘Lired’, ‘Jonathan’, ‘Golden Delicious’, ‘Jonagold’ and ‘Idared’ were characterized by two different molecular tools. These included analysis of the distribution of RAPD markers and length variability of the SSU, 5.8S, LSU and ITS region of the nuclear rRNA genes assessed in PCR reactions with different combinations of ‘universal’ primers. RAPD analysis was performed with 17 out of 24 RAPD primers tested. Those amplified a total of 183 loci (872 amplicons) out of which 34 (18.5%) were monomorphic, 128 (69.5%) were polymorphic and 22 (12%) cultivar-specific. Cultivar-specific RAPD products were detected for each apple cultivar. Amplification of the rDNA sequences showed variability. Fifty-four amplicons were generated in the experiment including 14 monomorphic, 26 polymorphic, and 14 cultivar-specific products. Altogether 232 amplicons were generated, whose length ranged from 220 to 940 bp. The analysis of dendrograms constructed on the basis of the analysis of RAPD genetic profiles and profiles amplified on rDNA matrices showed their significant correlation (Mantel test: r(AB) = 0.430; p-value (Two-tailed) = 0.024), which proves that the used methods correctly presented variability within the examined cultivars, and the molecular markers identified in the study can be considered appropriate.

ITS Sequences Analysis of Pulsatilla koreana Nakai. and Potentilla chinesis Ser.

2013 ◽  
Vol 749 ◽  
pp. 246-249
Author(s):  
Shao Xuan Zhang ◽  
Feng Liu ◽  
Yun Hui Ling ◽  
Bo Chuan Wang ◽  
De Jun Sun ◽  
...  
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Scientific Data ◽  
Jilin Province ◽  
Its Sequences ◽  
Universal Primers ◽  
Pcr Products ◽  
Sequences Analysis

To provide scientific data of the internal transcribed spacer (ITS) sequences for the authentication of Pulsatilla chinesis (Bge) Regel, we extracted the genome DNA from the leaves of Pulsatilla koreana Nakai. and Potetilla chinesis Ser. collected in Jilin Province, amplified the ITS region using ITS universal primers of angiosperm, and sequenced the purified PCR products directly. Polymorphism of ITS sequences was found within P. chinensis Ser. and the sequence data suggested that our samples of this species might be related to hybridization. The obtained sequences were edited by Genetyx and reported here.

Higher-level relationships among the eucalypts are resolved by ITS-sequence data

2002 ◽  
Vol 15 (1) ◽  
pp. 49 ◽  
Author(s):  
Dorothy A. Steane ◽  
Dean Nicolle ◽  
Gay E. McKinnon ◽  
René E. Vaillancourt ◽  
Brad M. Potts
Keyword(s):  
Internal Transcribed Spacer ◽  
Sequence Data ◽  
Its Region ◽  
Molecular Data ◽  
Nuclear Ribosomal Dna ◽  
Its Sequence ◽  
Phylogenetic Groups ◽  
Single Section ◽  
Western Australian ◽  
Genus Eucalyptus

This expanded survey of ITS sequences represents the largest analysis of molecular data ever attempted on Eucalyptus. Sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA were included in an analysis of 90 species of Eucalyptus s.s. and 28 species representing eight other genera (Allosyncarpia, Angophora, Arillastrum, Corymbia, Eucalyptopsis, Stockwellia, Lophostemon and Metrosideros). The results of the study indicate that Angophora and Corymbia form a well-supported clade that is highly differentiated from Eucalyptus s.s. Corymbia species are divided between two clades, one of which may be the sister to Angophora. Allosyncarpia, Arillastrum, Eucalyptopsis and ‘Stockwellia’ are also highly differentiated from Eucalyptus s.s. If the genus Eucalyptus is to be expanded to include Angophora and Corymbia(sensu Brooker 2000), ITS data suggest that Allosyncarpia, Eucalyptopsis, ‘Stockwellia’ and potentially Arillastrum should also be included in Eucalyptus s.l. The ITS data suggest that subg. Symphyomyrtus is paraphyletic and that subg. Minutifructus should be included within it. Within subg.Symphyomyrtus, only sect. Maidenaria appears to be monophyletic. Sections Adnataria and Dumaria are probably monophyletic; sections Exsertaria and Latoangulatae are very close and probably should be combined in a single section. Section Bisectae is polyphyletic and is divided into two distinct lineages. The phylogenetic groups depicted by ITS data are consistent with the frequency of natural inter-specific hybridisations as well as data from controlled crosses within subgenus Symphyomyrtus. The ITS data illustrate that subg. Idiogenes and western Australian monocalypts are early evolutionary lines relative to E. diversifolia, E. rubiginosa (monotypic subg. Primitiva) and the eastern monocalypts and that subg. Primitiva should be sunk into subg. Eucalyptus. Subgenus Eudesmia may be monophyletic, grouping with subgenera Idiogenes and Eucalyptus. Further work is required to confirm the phylogenetic positions of the monotypic subgenera Alveolata, Cruciformes, Acerosae and Cuboidea.

scholarly journals Molecular Identification of Fungal Communities in a Soil Cultivated with Vegetables and Soil Suppressiveness toRhizoctonia solani

2013 ◽  
Vol 2013 ◽  
pp. 1-7 ◽  
Author(s):  
Silvana Pompéia Val-Moraes ◽  
Eliamar Aparecida Nascimbem Pedrinho ◽  
Eliana Gertrudes Macedo Lemos ◽  
Lucia Maria Carareto-Alves
Keyword(s):  
Biotic Interactions ◽  
Fungal Communities ◽  
Native Forest ◽  
Metagenomic Dna ◽  
Soil Suppressiveness ◽  
Rdna Sequences ◽  
Pcr Products ◽  
Realistic View ◽  
18S Rdna Sequences ◽  
Total Dna

Fungi constitute an important part of the soil ecosystem, playing key roles in decomposition, cycling processes, and biotic interactions. Molecular methods have been used to assess fungal communities giving a more realistic view of their diversity. For this purpose, total DNA was extracted from bulk soils cultivated with tomato (STC), vegetables (SHC), and native forest (SMS) from three sites of the Taquara Branca river basin in Sumaré County, São Paulo State, Brazil. This metagenomic DNA was used as a template to amplify fungal 18S rDNA sequences, and libraries were constructed inEscherichia coliby cloning PCR products. The plasmid inserts were sequenced and compared to known rDNA sequences in the GenBank database. Of the sequenced clones, 22 were obtained from the SMS sample, 18 from the SHC sample, and 6 from the STC sample. Although most of the clone sequences did not match the sequences present in the database, individual amplified sequences matched with Glomeromycota (SMS), Fungi incertae sedis (SMS), and Neocallimastigomycota (SHC). Most of the sequences from the amplified taxa represent uncultured fungi. The molecular analysis of variance (AMOVA) indicated that fluctuations observed of haplotypes in the composition may be related to herbicide application.

scholarly journals WildTermitomycesSpecies Collected from Ondo and Ekiti States Are More Related to African Species as Revealed by ITS Region of rDNA

2012 ◽  
Vol 2012 ◽  
pp. 1-5 ◽  
Author(s):  
Victor Olusegun Oyetayo
Keyword(s):  
Sequence Analysis ◽  
Phylogenetic Tree ◽  
Molecular Identification ◽  
Internal Transcribed Spacer ◽  
Its Region ◽  
Its Sequence ◽  
African Countries ◽  
African Species ◽  
Its Sequence Analysis ◽  
Degree Of Similarity

Molecular identification of eighteenTermitomycesspecies collected from two states, Ondo and Ekiti in Nigeria was carried out using the internal transcribed spacer (ITS) region. The amplicons obtained from rDNA ofTermitomycesspecies were compared with existing sequences in the NCBI GenBank. The results of the ITS sequence analysis discriminated between all theTermitomycesspecies (obtained from Ondo and Ekiti States) andTermitomycessp. sequences obtained from NCBI GenBank. The degree of similarity of T1 to T18 to gene ofTermitomycessp. obtained from NCBI ranges between 82 and 99 percent.Termitomycesspecies from Garbon with ascension number AF321374 was the closest relative of T1 to T18 except T12 that has T. eurhizus and T. striatus as the closet relative. Phylogenetic tree generated with ITS sequences obtained from NCBI GenBank data revealed that T1 to T18 are more related toTermitomycesspecies indigenous to African countries such as Senegal, Congo, and Gabon.

Phylogenetic Relations of Rhizoplaca Zopf. from Anatolia Inferred from ITS Sequence Data

2006 ◽  
Vol 61 (5-6) ◽  
pp. 405-412 ◽  
Author(s):  
Demet Cansaran ◽  
Sümer Aras ◽  
İrfan Kandemir ◽  
Gökhan Halıcı
Keyword(s):  
Genetic Variability ◽  
Phylogenetic Tree ◽  
Sequence Data ◽  
Volcanic Rocks ◽  
Morphological Characteristics ◽  
Its Rdna ◽  
Its Sequence ◽  
Phylogenetic Relations ◽  
Rdna Sequences

Like many lichen-forming fungi, species of the genus Rhizoplaca have wide geographical distributions, but studies of their genetic variability are limited. The information about the ITS rDNA sequences of three species of Rhizoplaca from Anatolia was generated and aligned with other species from other countries and also with the data belonging to Lecanora species. The examined species were collected from the volcanic rocks of Mount Erciyes which is located in the middle of Anatolia (Turkey). The sequence data aligned with eight other samples of Rhizoplaca and six different species of Lecanora were obtained from GenBank. The results support the concept maintained by Arup and Grube (2000) that Rhizoplaca may not be a genus separate from Lecanora. According to the phylogenetic tree, Rhizoplaca melanopthalma from Turkey with two different samples of R. melanopthalma from Arizona (AF159929, AF159934) and a sample from Austria formed a group under the same branch. R. peltata and R. chrysoleuca samples from Anatolia located in two other branches of the tree formed sister groups with the samples of the same species from different countries. Although R. peltata remained on the same branch with other samples of the same species from other countries it was placed in a different branch within the group. When the three species from Anatolia were considered alone, it was noticed that Rhizoplaca melanopthalma and Rhizoplaca peltata are phylogenetically closer to each other than Rhizoplaca chrysoleuca; the morphological characteristics also support this result.

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