Relevant bibliographies by topics / Internal Transcribed Spacer (ITS) Genomic regions

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Academic literature on the topic 'Internal Transcribed Spacer (ITS) Genomic regions'

Author: Grafiati
Published: 4 June 2021
Last updated: 17 February 2022

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Journal articles on the topic "Internal Transcribed Spacer (ITS) Genomic regions"

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Long-qian, Xiao, and Zhu Hua. "Intra-genomic polymorphism in the internal transcribed spacer (ITS) regions ofCycas revoluta:evidence of incomplete concerted evolution." Biodiversity Science 17, no. 5 (2009): 476. http://dx.doi.org/10.3724/sp.j.1003.2009.09100.

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Yan, Ji Ming, Xiao Hong Shi, Miao Mei, Hong Bo Dai, and Hua Zhi Ye. "Amplifying and Sequencing Analysis the Internal Transcribed Spacer (ITS) Regions of Olpidium Viciae Kusano’s Ribosomal DNA in Broad Bean." Advanced Materials Research 271-273 (July 2011): 507–13. http://dx.doi.org/10.4028/www.scientific.net/amr.271-273.507.

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Plasmodiophora fire of broad bean is responsible for Olpidium Viciae Kusano, which is a kind of Fungi subdivided into bacteria flagellum amon. We have developed a polymerase chain reaction based method for the rapid identification internal transcribed spacer (ITS) regions of productionally significant fungi Olpidium Viciae Kusano from areas of 2500~3000 metres above sea level. Sequences of the nuclear internal transcribed spacer (ITS) regions ITS1 and ITS4 have been used widely in molecular characteristic studies because of their relatively high variability and facility of amplification. A universal quickly SDS micro-DNA extraction method was used combining a RNaseA pretreatment step to remove PCR interferential RNA. Target sequences in ITS regions genomic were amplified by PCR and sequenced. Using Hanpanchun lesion and healthy bean leaves as template and ITS1, ITS4 as primer to amplify ITS region, the results revealed ITS gene of broad bean genome could be amplified with size of 750bp from healthy leaves, it could be amplified two fragments of 750bp and 500bp from the DNA template extracted from Hanpanchun lesion tissue. The ITS sequence of Olpidium Viciae Kusano is 99% homoeology with Cercospora (grey speck) pathogen. This may lay the foundation for research about classification and analyze evolutionary relationships of Olpidium Viciae Kusano.
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Abdullah, Farah Izana, Lee Suan Chua, Zaidah Rahmat, Azman Abd Samad, and Alina Wagiran. "Plant Genomic DNA Extraction for Selected Herbs and Sequencing their Internal Transcribed Spacer Regions Amplified by Specific Primers." Natural Product Communications 11, no. 10 (2016): 1934578X1601101. http://dx.doi.org/10.1177/1934578x1601101017.

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This study was focused on plant genomic DNA extraction and sequencing from five commonly used medicinal herbs, namely Impatiens balsamina, Ficus deltoidea, Centella asiatica, Andrographis paniculata and Orthosiphon aristatus. This molecular technique is another highly reliable alternative for plant species identification besides phytochemical profiling. Three cetyl hexadecyltrimethylammonium bromide (CTAB) based methods with slight modification on incubation time, salt content and other additives were used for DNA extraction. The CTAB method of Doyle and Doyle produced higher DNA concentration from I. balsamina, most probably due to the presence of ammonium acetate in the washing buffer and longer incubation time (2 h). The CTAB based method was suitable for A. paniculata because a high DNA concentration of acceptable quality was obtained for all the modified methods. However, O. aristatus was likely to have a lower DNA concentration (33–87 μg/g) and quality, probably due to the high concentration of phenolic compounds, particularly rosmarinic acid. The extracted genomic DNA was effectively amplified by a polymerase chain reaction using a universal primer of internal transcribed spacer (ITS), particularly AB101 and AB102 at the optimum annealing temperature of 48°C. The DNA sequences were analyzed by phenetic analysis and it was found that they have high similarity with the nucleotide sequences of ITS regions for similar plant species in the GenBank database of the National Center for Biotechnology Information.
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Redmond, Niamh E., and Grace P. McCormack. "Ribosomal internal transcribed spacer regions are not suitable for intra- or inter-specific phylogeny reconstruction in haplosclerid sponges (Porifera: Demospongiae)." Journal of the Marine Biological Association of the United Kingdom 89, no. 6 (2009): 1251–56. http://dx.doi.org/10.1017/s0025315409000411.

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Sequences of the ribosomal internal transcribed spacer regions 1 and 2 (ITS-1 and ITS-2) were employed to investigate relationships between putatively very closely related species of marine haplosclerids and to investigate the species status of Haliclona cinerea. Results indicate that intra-genomic and intra-specific levels of diversity are equivalent, and sequences from multiple clones from a number of individuals of a single species could not be separated on phylogenetic trees. As a result, the ITS regions are not suitable markers for population level studies in marine haplosclerids. Sequences of these regions were highly species specific, and large differences were found between species. ITS sequences from three Callyspongia and three Haliclona species could not be aligned successfully and therefore this locus could not be used to investigate relationships between these putative close relatives. However, ITS sequences retrieved from one H. cinerea were very different from sequences generated from other H. cinerea individuals indicating that this species comprises more than one taxon.
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Gong, Li, Xiaoyu Kong, Hairong Luo, Shixi Chen, Wei Shi, and Min Yang. "Intra-genomic variability and pseudogenes in ribosomal ITS regions of Paraplagusia blochii (Pleuronectiformes: Cynoglossidae)." Animal Biology 70, no. 2 (2020): 145–58. http://dx.doi.org/10.1163/15707563-20191141.

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Abstract Eukaryotic nuclear ribosomal DNA (rDNA) typically evolves in a concerted manner, in which hundreds of rDNA sequences within species show little or no variations, whereas the sequences of different species diverge. There are few studies of the internal transcribed spacer regions (ITS1-5.8S-ITS2) in teleostean fishes and only one report on flatfishes. Here, we reported the discovery of two types of highly divergent ITS1-5.8S-ITS2 rDNA sequences (Type A and B) in the genome of the Bloch’s tonguesole, Paraplagusia blochii. These sequences mainly differ in sequence length, secondary structure, and minimum free energy. According to the potential features of pseudogenes, Type B sequences are speculated to be putative pseudogenic ITS regions. Cluster analyses also supported two major clades that corresponded to the sequence type. To the best of our knowledge, this is the first report of the ITS regions of tonguefish, and may therefore provide useful information for future studies of the rDNA of flatfishes as well as the patterns of rDNA evolution in teleostean fishes.
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Polanco, Carlos, Ana I. González, Álvaro de la Fuente, and Gabriel A. Dover. "Multigene Family of Ribosomal DNA in Drosophila melanogaster Reveals Contrasting Patterns of Homogenization for IGS and ITS Spacer Regions: A Possible Mechanism to Resolve This Paradox." Genetics 149, no. 1 (1998): 243–56. http://dx.doi.org/10.1093/genetics/149.1.243.

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Abstract The multigene family of rDNA in Drosophila reveals high levels of within-species homogeneity and between-species diversity. This pattern of mutation distribution is known as concerted evolution and is considered to be due to a variety of genomic mechanisms of turnover (e.g., unequal crossing over and gene conversion) that underpin the process of molecular drive. The dynamics of spread of mutant repeats through a gene family, and ultimately through a sexual population, depends on the differences in rates of turnover within and between chromosomes. Our extensive molecular analysis of the intergenic spacer (IGS) and internal transcribed spacer (ITS) spacer regions within repetitive rDNA units, drawn from the same individuals in 10 natural populations of Drosophila melanogaster collected along a latitudinal cline on the east coast of Australia, indicates a relatively fast rate of X-Y and X-X interchromosomal exchanges of IGS length variants in agreement with a multilineage model of homogenization. In contrast, an X chromosome-restricted 24-bp deletion in the ITS spacers is indicative of the absence of X-Y chromosome exchanges for this region that is part of the same repetitive rDNA units. Hence, a single lineage model of homogenization, coupled to drift and/or selection, seems to be responsible for ITS concerted evolution. A single-stranded exchange mechanism is proposed to resolve this paradox, based on the role of the IGS region in meiotic pairing between X and Y chromosomes in D. melanogaster.
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Tsakogiannis, Alexandros, Tereza Manousaki, Vasileia Anagnostopoulou, Melanthia Stavroulaki, and Eugenia T. Apostolaki. "The Importance of Genomics for Deciphering the Invasion Success of the Seagrass Halophila stipulacea in the Changing Mediterranean Sea." Diversity 12, no. 7 (2020): 263. http://dx.doi.org/10.3390/d12070263.

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The Mediterranean Sea is subject to pressures from biological invasion due to coastal anthropic activities and global warming, which potentially modify its biogeography. The Red Sea tropical seagrass Halophila stipulacea entered the Eastern Mediterranean over a century ago, and its occurrence is expanding towards the northwest. Here, we highlight the importance of genomics for deciphering the evolutionary and ecological procedures taking place during the invasion process of H. stipulacea and review the relatively sparse genetic information available for the species to date. We report the first draft whole-genome sequencing of a H. stipulacea individual from Greece, based on Illumina Sequencing technology. A comparison of the Internal Transcribed Spacer (ITS) regions revealed a high divergence of the herein sequenced individual compared to Mediterranean populations sequenced two decades ago, rendering further questions on the evolutionary processes taking place during H. stipulacea adaptation in the invaded Mediterranean Sea. Our work sets the baseline for a future analysis of the invasion genomic of the focal species.
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Jackson, Colin J., Richard C. Barton, and E. Glyn V. Evans. "Species Identification and Strain Differentiation of Dermatophyte Fungi by Analysis of Ribosomal-DNA Intergenic Spacer Regions." Journal of Clinical Microbiology 37, no. 4 (1999): 931–36. http://dx.doi.org/10.1128/jcm.37.4.931-936.1999.

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Restriction fragment length polymorphisms (RFLPs) identified in the ribosomal-DNA (rDNA) repeat were used for molecular strain differentiation of the dermatophyte fungus Trichophyton rubrum. The polymorphisms were detected by hybridization ofEcoRI-digested T. rubrum genomic DNAs with a probe amplified from the small-subunit (18S) rDNA and adjacent internal transcribed spacer (ITS) regions. The rDNA RFLPs mapped to the nontranscribed spacer (NTS) region of the rDNA repeat and appeared similar to those caused by short repetitive sequences in the intergenic spacers of other fungi. Fourteen individual RFLP patterns (DNA types A to N) were recognized among 50 random clinical isolates ofT. rubrum. A majority of strains (19 of 50 [38%]) were characterized by one RFLP pattern (DNA type A), and four types (DNA types A to D) accounted for 78% (39 of 50) of all strains. The remaining types (DNA types E to N) were represented by one or two isolates only. A rapid and simple method was also developed for molecular species identification of dermatophyte fungi. The contiguous ITS and 5.8S rDNA regions were amplified from 17 common dermatophyte species by using the universal primers ITS 1 and ITS 4. Digestion of the amplified ITS products with the restriction endonucleaseMvaI produced unique and easily identifiable fragment patterns for a majority of species. However, some closely related taxon pairs, such as T. rubrum-T. soudanense andT. quinkeanum-T. schoenlenii could not be distinguished. We conclude that RFLP analysis of the NTS and ITS intergenic regions of the rDNA repeat is a valuable technique both for molecular strain differentiation of T. rubrum and for species identification of common dermatophyte fungi.
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Pombert, Jean-François, Jinshan Xu, David R. Smith, et al. "Complete Genome Sequences from Three Genetically Distinct Strains Reveal High Intraspecies Genetic Diversity in the Microsporidian Encephalitozoon cuniculi." Eukaryotic Cell 12, no. 4 (2013): 503–11. http://dx.doi.org/10.1128/ec.00312-12.

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ABSTRACTMicrosporidia from the Encephalitozoonidae are obligate intracellular parasites with highly conserved and compacted nuclear genomes: they have few introns, short intergenic regions, and almost identical gene complements and chromosome arrangements. Comparative genomics ofEncephalitozoonand microsporidia in general have focused largely on the genomic diversity between different species, and we know very little about the levels of genetic diversity within species. Polymorphism studies withEncephalitozoonare so far restricted to a small number of genes, and a few genetically distinct strains have been identified; most notably, three genotypes (ECI, ECII, and ECIII) of the model speciesE. cuniculihave been identified based on variable repeats in the rRNA internal transcribed spacer (ITS). To determine ifE. cuniculigenotypes are genetically distinct lineages across the entire genome and at the same time to examine the question of intraspecies genetic diversity in microsporidia in general, we sequencedde novogenomes from each of the three genotypes and analyzed patterns of single nucleotide polymorphisms (SNPs) and insertions/deletions across the genomes. Although the strains have almost identical gene contents, they harbor large numbers of SNPs, including numerous nonsynonymous changes, indicating massive intraspecies variation within the Encephalitozoonidae. Based on this diversity, we conclude that the recognized genotypes are genetically distinct and propose new molecular markers for microsporidian genotyping.
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Chen, Wen, Zeinab Robleh Djama, Michael D. Coffey, et al. "Membrane-Based Oligonucleotide Array Developed from Multiple Markers for the Detection of Many Phytophthora Species." Phytopathology® 103, no. 1 (2013): 43–54. http://dx.doi.org/10.1094/phyto-04-12-0092-r.

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Most Phytophthora spp. are destructive plant pathogens; therefore, effective monitoring and accurate early detection are important means of preventing potential epidemics and outbreaks of diseases. In the current study, a membrane-based oligonucleotide array was developed that can detect Phytophthora spp. reliably using three DNA regions; namely, the internal transcribed spacer (ITS), the 5′ end of cytochrome c oxidase 1 gene (cox1), and the intergenic region between cytochrome c oxidase 2 gene (cox2) and cox1 (cox2-1 spacer). Each sequence data set contained ≈250 sequences representing 98 described and 15 undescribed species of Phytophthora. The array was validated with 143 pure cultures and 35 field samples. Together, nonrejected oligonucleotides from all three markers have the ability to reliably detect 82 described and 8 undescribed Phytophthora spp., including several quarantine or regulated pathogens such as Phytophthora ramorum. Our results showed that a DNA array containing signature oligonucleotides designed from multiple genomic regions provided robustness and redundancy for the detection and differentiation of closely related taxon groups. This array has the potential to be used as a routine diagnostic tool for Phytophthora spp. from complex environmental samples without the need for extensive growth of cultures.
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Dissertations / Theses on the topic "Internal Transcribed Spacer (ITS) Genomic regions"

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Müller, Juceli. "Qualidade fisiológica e associação de Fusarium spp. a sementes de sorgo sacarino." Universidade Federal de Santa Maria, 2017. http://repositorio.ufsm.br/handle/1/11796.

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The present work aims to determine the physiological and sanitary quality of Sweet sorghum (Sorghum bicolor (L.) Moench) seeds, as well as to identify pathogens associated with seed, their transmission to seedlings and the subsequent pathogenicity of isolates obtained, In addition, molecularly identify the fungal species pathogenic to this crop. The experiments were carried out in the Teaching and Seed Research Laboratory (TSRL), of the Plant Engineering Department; In the Elocy Minussi Phytopathology Laboratory, Department of Plant Protection, and at the Biological Institute of São Paulo. Sweet sorghum seeds were used, all without chemical treatment. Sanitary quality was evaluated by sanity test, and physiological characteristics by germination and vigor tests (seedling length, dry mass, emergence, rate of emergence and accelerated aging). It was performed the test of transmission of the pathogens associated to the seeds and the subsequent pathogenicity of the obtained isolates, culminating with the molecular characterization of the identified pathogens, in which were sequenced the Internal Transcribed Spacer (ITS) genomic regions and the Elongation Factor 1 - alpha (TEF1-α) gene. The design used was the completely randomized design, with four cultivars of Sweet sorghum (BRS 506, F19, BRS 511 and BRS 509); For the evaluation of pathogenicity, the factorial scheme is represented by four cultivars and three isolates of Fusarium spp., besides the witness. The seeds of the BRS 509 cultivar were considered to have lower physiological quality than the other cultivars. The DNA sequencing allowed identifying the Fusarium thapsinum species as a pathogenic agent in the sweet sorghum crop, and proven its transmission via seeds.
O presente trabalho teve como objetivo determinar a qualidade fisiológica e sanitária de sementes de cultivares de sorgo sacarino (Sorghum bicolor (L.) Moench), bem como identificar os patógenos associados à semente, sua transmissão às plântulas e a posterior patogenicidade de isolados obtidos, além disso, identificar molecularmente as espécies fúngicas patogênicas a esta cultura. Os experimentos foram realizados no Laboratório Didático e de Pesquisas em Sementes (LDPS), do Departamento de Fitotecnia; no Laboratório de Fitopatologia Elocy Minussi, do Departamento de Defesa Fitossanitária e, no Instituto Biológico de São Paulo. Foram utilizadas sementes de sorgo sacarino, todas sem tratamento químico. A qualidade sanitária foi avaliada pelo teste de sanidade, e as características fisiológicas por meio dos testes de germinação e de vigor (comprimento de plântulas, massa seca, emergência, índice de velocidade de emergência e envelhecimento acelerado). Foi realizado o teste de transmissão dos patógenos associados à semente e a posterior patogenicidade dos isolados fúngicos obtidos, culminando com a caracterização molecular dos patógenos identificados, na qual foram sequenciadas as regiões genômicas Internal Transcribed Spacer (ITS) e o gene do fator de elongação 1-α (TEF1α). O delineamento utilizado foi o inteiramente casualizado com quatro cultivares de sorgo sacarino (BRS 506, Fepagro 19, BRS 511 e BRS 509); já para a avaliação da patogenicidade, o esquema fatorial foi representado pelas quatro cultivares e três isolados de Fusarium sp., além da testemunha. As sementes da cultivar BRS 509 foram consideradas de qualidade fisiológica inferior as demais cultivares. O sequenciamento de DNA permitiu identificar a espécie Fusarium thapsinum como agente patogênico na cultura do sorgo sacarino, sendo comprovada sua transmissão via sementes.
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Conference papers on the topic "Internal Transcribed Spacer (ITS) Genomic regions"

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Rosa, Marcos P., Jose V. C. Vargas, Vanessa M. Kava, et al. "Hydrogen and Compounds With Biological Activity From Microalgae." In ASME 2019 13th International Conference on Energy Sustainability collocated with the ASME 2019 Heat Transfer Summer Conference. American Society of Mechanical Engineers, 2019. http://dx.doi.org/10.1115/es2019-3965.

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Abstract Microalgae have a high biotechnological potential as a source of biofuels (biodiesel, biohydrogen) and other high-added value products (e.g., pharmaceuticals, proteins, pigments). However, for microalgae cultivation to be economically competitive with other fuel sources, it is necessary to apply the concept of biorefinery. This seems to be the most ambitious strategy to achieve viability. Therefore, the objectives of this study were to isolate and identify the main microalgae line used to produce biofuels at Federal University of Parana, Brazil, using the rDNA sequence and micromorphological analysis, and to evaluate the potential of this lineage in the production of hydrogen and co-products with biological activity. For the purification of the lineage (LGMM0001), an aliquot was seeded into solid CHU culture medium and an isolated colony was selected. The genomic DNA was purified using a commercial kit (Macherey-Nagel, Düren, Germany) for molecular identification, the ITS region (ITS1, 5.8S and ITS2) (Internal Transcribed Spacer) was amplified and sequenced using primers LS266 and V9G. Morphological characterization was performed as described by Hemschemeier et al. [1]. Finally, for biological activity research, secondary metabolites were extracted by fractionation and evaluated against bacteria of clinical interest. Through microscopic analysis, general characteristics shared by the genus Tetradesmus were observed. The plasticity of the morphological characteristics of this genus reinforces the need for further studies to classify correctly the species in this group, using DNA sequencing. ITS sequence analysis of LGMM0001 showed 100% homology with sequences from the Tetradesmus obliquus species, so, the lineage was classified as belonging to this species. The evaluated microalgae strain was able to produce hydrogen, showing positive results for gas formation. Biological activity was observed with the extract obtained from the residual culture carried out with alternative medium used in the photobioreactors (PBR), against the Staphylococcus aureus pathogenic lineage. In conclusion, the microalgae strain used in this work was identified as Tetradesmus obliquus (= Acutodesmus obliquus), and was able to produce a compound with economic potential in association with the existing biofuel production process.
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Peck, Kayla, Robert Stedtfeld, Jordan RoseFigura, et al. "Abstract 1484: Microbial sequencing using a single-pool target enrichment of multiple variable regions of the 16S rRNA gene, the nuclear ribosomal internal transcribed spacer (ITS) region, and antimicrobial resistance genes." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-1484.

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Peck, Kayla, Robert Stedtfeld, Jordan RoseFigura, et al. "Abstract 1484: Microbial sequencing using a single-pool target enrichment of multiple variable regions of the 16S rRNA gene, the nuclear ribosomal internal transcribed spacer (ITS) region, and antimicrobial resistance genes." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-1484.

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