Relevant bibliographies by topics / DNA nucleotide sequencing

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'DNA nucleotide sequencing'

Author: Grafiati
Published: 10 September 2021
Last updated: 17 July 2025

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Journal articles on the topic "DNA nucleotide sequencing"

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Randhawa, J. S., and A. J. Easton. "Demystified ... DNA nucleotide sequencing." Molecular Pathology 52, no. 3 (1999): 117–24. http://dx.doi.org/10.1136/mp.52.3.117.

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Gromek, Katarzyna, and Tadeusz Kaczorowski. "DNA Sequencing by Indexer Walking." Clinical Chemistry 51, no. 9 (2005): 1612–18. http://dx.doi.org/10.1373/clinchem.2004.046599.

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Abstract Background: There is a need for DNA sequencing methods that are faster, more accurate, and less expensive than existing techniques. Here we present a new method for DNA analysis by means of indexer walking. Methods: For DNA sequencing by indexer walking, we ligated double-stranded synthetic oligonucleotides (indexers) to DNA fragments that were produced by type IIS restriction endonucleases, which generate nonidentical 4-nucleotide 5′ overhangs. The subsequent amplification (30 thermal cycles) of indexed DNA provided a template for automated DNA sequencing with fluorescent dideoxy terminators. The data gathered in the first sequencing reaction permitted further movement into the unknown nucleotide sequence by digestion of analyzed DNA with selected type IIS restriction endonuclease followed by ligation of the next indexer. A library of presynthesized indexers consisting of 256 oligonucleotides was used for bidirectional analysis of DNA molecules and provided universal primers for sequencing. Results: The proposed protocol was successfully applied to sequencing of cryptic plasmids isolated from pathogenic strains of Escherichia coli. The overall error rate for base-calling was 0.5%, with a mean read length of 550 nucleotides. Approximately 1000 nucleotides of high-quality sequence could be obtained per day from a single clone. Conclusions: Indexer walking can be used as a low-cost procedure for nucleotide sequence determination of DNA molecules, such as natural plasmids, cDNA clones, and longer DNA fragments. It can also serve as an alternative method for gap filling at the final stage of genome sequencing projects.
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Lu, Jun-Qiang, and X. G. Zhang. "Nucleotide Capacitance Calculation for DNA Sequencing." Biophysical Journal 95, no. 9 (2008): L60—L62. http://dx.doi.org/10.1529/biophysj.108.140749.

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Kuśmirek, Wiktor. "Estimated Nucleotide Reconstruction Quality Symbols of Basecalling Tools for Oxford Nanopore Sequencing." Sensors 23, no. 15 (2023): 6787. http://dx.doi.org/10.3390/s23156787.

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Currently, one of the fastest-growing DNA sequencing technologies is nanopore sequencing. One of the key stages involved in processing sequencer data is the basecalling process, where the input sequence of currents measured on the nanopores of the sequencer reproduces the DNA sequences, called DNA reads. Many of the applications dedicated to basecalling, together with the DNA sequence, provide the estimated quality of the reconstruction of a given nucleotide (quality symbols are contained on every fourth line of the FASTQ file; each nucleotide in the FASTQ file corresponds to exactly one estimated nucleotide reconstruction quality symbol). Herein, we compare the estimated nucleotide reconstruction quality symbols (signs from every fourth line of the FASTQ file) reported by other basecallers. The conducted experiments consisted of basecalling the same raw datasets from the nanopore device by other basecallers and comparing the provided quality symbols, denoting the estimated quality of the nucleotide reconstruction. The results show that the estimated quality reported by different basecallers may vary, depending on the tool used, particularly in terms of range and distribution. Moreover, we mapped basecalled DNA reads to reference genomes and calculated matched and mismatched rates for groups of nucleotides with the same quality symbol. Finally, the presented paper shows that the estimated nucleotide reconstruction quality reported in the basecalling process is not used in any investigated tool for processing nanopore DNA reads.
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Lizardi, Paul M., Qin Yan, and Narendra Wajapeyee. "DNA Bisulfite Sequencing for Single-Nucleotide-Resolution DNA Methylation Detection." Cold Spring Harbor Protocols 2017, no. 11 (2016): pdb.prot094839. http://dx.doi.org/10.1101/pdb.prot094839.

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Kim, Yong, R. Bruce Donoff, David T. W. Wong, and Randy Todd. "The nucleotide: DNA sequencing and its clinical application." Journal of Oral and Maxillofacial Surgery 60, no. 8 (2002): 924–30. http://dx.doi.org/10.1053/joms.2002.33864.

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Bowling, John M., Kaylon L. Bruner, Joan L. Cmarik, and Clark Tibbetts. "Neighboring nucleotide interactions during DNA sequencing gel electrophoresis." Nucleic Acids Research 19, no. 11 (1991): 3089–97. http://dx.doi.org/10.1093/nar/19.11.3089.

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Murray, Vincent, Megan E. Hardie, and Shweta D. Gautam. "Comparison of Different Methods to Determine the DNA Sequence Preference of Ionising Radiation-Induced DNA Damage." Genes 11, no. 1 (2019): 8. http://dx.doi.org/10.3390/genes11010008.

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Ionising radiation (IR) is known to induce a wide variety of lesions in DNA. In this review, we compared three different techniques that examined the DNA sequence preference of IR-induced DNA damage at nucleotide resolution. These three techniques were: the linear amplification/polymerase stop assay, the end-labelling procedure, and Illumina next-generation genome-wide sequencing. The DNA sequence preference of IR-induced DNA damage was compared in purified DNA sequences including human genomic DNA. It was found that the DNA sequence preference of IR-induced DNA damage identified by the end-labelling procedure (that mainly detected single-strand breaks) and Illumina next-generation genome-wide sequencing (that mainly detected double-strand breaks) was at C nucleotides, while the linear amplification/polymerase stop assay (that mainly detected base damage) was at G nucleotides. A consensus sequence at the IR-induced DNA damage was found to be 5′-AGGC*C for the end-labelling technique, 5′-GGC*MH (where * is the cleavage site, M is A or C, H is any nucleotide except G) for the genome-wide technique, and 5′-GG* for the linear amplification/polymerase stop procedure. These three different approaches are important because they provide a deeper insight into the mechanism of action of IR-induced DNA damage.
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Alanazi, Abdulaziz M., G. Muhiuddin, Doha A. Al-Balawi, and Sovan Samanta. "Different DNA Sequencing Using DNA Graphs: A Study." Applied Sciences 12, no. 11 (2022): 5414. http://dx.doi.org/10.3390/app12115414.

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Natural genetic material may shed light on gene expression mechanisms and aid in the detection of genetic disorders. Single Nucleotide Polymorphism (SNP), small insertions and deletions (indels), and major chromosomal anomalies are all chromosomal abnormality-related disorders. As a result, several methods have been applied to analyze DNA sequences, which constitutes one of the most critical aspects of biological research. Thus, numerous mathematical and algorithmic contributions have been made to DNA analysis and computing. Cost minimization, deployment, and sensitivity analysis to many factors are all components of sequencing platforms built on a quantitative framework and their operating mechanisms. This study aims to investigate the role of DNA sequencing and its representation in the form of graphs in the analysis of different diseases by means of DNA sequencing.
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Grushevskaya, H. V., N. G. Krylova, I. V. Lipnevich, V. P. Egorova, and A. S. Babenka. "Single nucleotide polymorphism genotyping using DNA sequencing on multiwalled carbon nanotubes monolayer by CNT-plasmon resonance." International Journal of Modern Physics B 32, no. 17 (2018): 1840033. http://dx.doi.org/10.1142/s0217979218400337.

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DNA-nanosensor based on multiwalled carbon nanotubes (MWCNTs) decorated by nanocyclic thiophene-pyrrole complexes of octahedral high-spin Fe has been proposed for high-performance sensing of DNA-hybridization utilizing a surface-enhanced spin-dependent CNT-plasmon resonance. This DNA-nanosensor operates on screening and quenching effects at Raman scattering of light in duplexes DNA-probe/DNA-target at complementary pairing of nucleotides in DNA. Single nucleotide polymorphism (SNP) genotyping has been successfully performed for DNA samples from healthy and cancer-suffering donors.
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Dissertations / Theses on the topic "DNA nucleotide sequencing"

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Boufounos, Petros T. 1977. "Signal processing for DNA sequencing." Thesis, Massachusetts Institute of Technology, 2002. http://hdl.handle.net/1721.1/17536.

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Thesis (M.Eng. and S.B.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2002.<br>Includes bibliographical references (p. 83-86).<br>DNA sequencing is the process of determining the sequence of chemical bases in a particular DNA molecule-nature's blueprint of how life works. The advancement of biological science in has created a vast demand for sequencing methods, which needs to be addressed by automated equipment. This thesis tries to address one part of that process, known as base calling: it is the conversion of the electrical signal-the electropherogram--collected by the sequencing equipment to a sequence of letters drawn from ( A,TC,G ) that corresponds to the sequence in the molecule sequenced. This work formulates the problem as a pattern recognition problem, and observes its striking resemblance to the speech recognition problem. We, therefore, propose combining Hidden Markov Models and Artificial Neural Networks to solve it. In the formulation we derive an algorithm for training both models together. Furthermore, we devise a method to create very accurate training data, requiring minimal hand-labeling. We compare our method with the de facto standard, PHRED, and produce comparable results. Finally, we propose alternative HMM topologies that have the potential to significantly improve the performance of the method.<br>by Petros T. Boufounos.<br>M.Eng.and S.B.
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Fritz, Markus Hsi-Yang. "Exploiting high throughput DNA sequencing data for genomic analysis." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610819.

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Kislyuk, Andrey O. "Algorithm development for next generation sequencing-based metagenome analysis." Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/42779.

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We present research on the design, development and application of algorithms for DNA sequence analysis, with a focus on environmental DNA (metagenomes). We present an overview and primer on algorithm development for bioinformatics of metagenomes; work on frameshift detection in DNA sequencing data; work on a computational pipeline for the assembly, feature prediction, annotation and analysis of bacterial genomes; work on unsupervised phylogenetic clustering of metagenomic fragments using Markov Chain Monte Carlo methods; and work on estimation of bacterial genome plasticity and diversity, potential improvements to the measures of core and pan-genomes.
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Musgrave-Brown, Esther. "Development and application of methods for targeted DNA sequencing of pooled samples." Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.648613.

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Andrews, Daniel James. "Statistical models of PCR for quantification of target DNA by sequencing." Thesis, University of Cambridge, 2015. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708581.

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Lin, Cheng-Hsien Kenny. "An ASIC application for DNA sequencing by Smith-Waterman algorithm (DNASSWA) /." [St. Lucia, Qld.], 2004. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe18716.pdf.

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Wang, Yikang. "Synthesis of some novel phospholipids, and nucleotide analogues, as potential chemotherapeutic agents and for DNA sequencing." Thesis, University of Southampton, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.295106.

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Stranneheim, Henrik. "Enabling massive genomic and transcriptomic analysis." Doctoral thesis, KTH, Genteknologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-45957.

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In recent years there have been tremendous advances in our ability to rapidly and cost-effectively sequence DNA. This has revolutionized the fields of genetics and biology, leading to a deeper understanding of the molecular events in life processes. The rapid advances have enormously expanded sequencing opportunities and applications, but also imposed heavy strains on steps prior to sequencing, as well as the subsequent handling and analysis of the massive amounts of sequence data that are generated, in order to exploit the full capacity of these novel platforms. The work presented in this thesis (based on six appended papers) has contributed to balancing the sequencing process by developing techniques to accelerate the rate-limiting steps prior to sequencing, facilitating sequence data analysis and applying the novel techniques to address biological questions.   Papers I and II describe techniques to eliminate expensive and time-consuming preparatory steps through automating library preparation procedures prior to sequencing. The automated procedures were benchmarked against standard manual procedures and were found to substantially increase throughput while maintaining high reproducibility. In Paper III, a novel algorithm for fast classification of sequences in complex datasets is described. The algorithm was first optimized and validated using a synthetic metagenome dataset and then shown to enable faster analysis of an experimental metagenome dataset than conventional long-read aligners, with similar accuracy. Paper IV, presents an investigation of the molecular effects on the p53 gene of exposing human skin to sunlight during the course of a summer holiday. There was evidence of previously accumulated persistent p53 mutations in 14% of all epidermal cells. Most of these mutations are likely to be passenger events, as the affected cell compartments showed no apparent growth advantage. An annual rate of 35,000 novel sun-induced persistent p53 mutations was estimated to occur in sun-exposed skin of a human individual.  Paper V, assesses the effect of using RNA obtained from whole cell extracts (total RNA) or cytoplasmic RNA on quantifying transcripts detected in subsequent analysis. Overall, more differentially detected genes were identified when using the cytoplasmic RNA. The major reason for this is related to the reduced complexity of cytoplasmic RNA, but also apparently due (at least partly) to the nuclear retention of transcripts with long, structured 5’- and 3’-untranslated regions or long protein coding sequences. The last paper, VI, describes whole-genome sequencing of a large, consanguineous family with a history of Leber hereditary optic neuropathy (LHON) on the maternal side. The analysis identified new candidate genes, which could be important in the aetiology of LHON. However, these candidates require further validation before any firm conclusions can be drawn regarding their contribution to the manifestation of LHON.<br>QC 20111115
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Fletcher, Jeremy Charles. "THE USE OF PYROSEQUENCING FOR THE ANALYSIS OF Y CHROMOSOME SINGLE NUCLEOTIDE POLYMORPHISMS." Master's thesis, University of Central Florida, 2004. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/4487.

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The potential value of the Y chromosome for forensic applications has been recognized for some time with the current work dedicated to Short Tandem Repeat analysis and Single Nucleotide Polymorphism (SNP) discovery. This study examined the ability of two different SNP analysis methods to determine if they could be utilized in forensic applications and ultimately be developed into an established system for Y chromosome SNP analysis. This study examined two principle SNP analysis systems: single base extension and Pyrosequencing. Pyrosequencing was determined to be superior to single base extension, due to the wealth of information provided with sequencing and the flexibility of designing primers for analysis. Using Pyrosequencing, 50 Y chromosome loci were examined and the minimum loci required for maximum diversity for the development of a Y chromosome SNP analysis system were chosen. Thirteen loci were selected based on their ability to discriminate 60 different individuals from three different racial groups into 15 different haplogroups. The Y chromosome SNP analysis system developed utilized nested PCR for the amplification of all 13 loci. Then they were sequenced as groups, ranging from one to three loci, in a single reaction. The Y chromosome SNP analysis system developed here has the potential for forensic application since it has shown to be successful in the analysis of blood, buccal swabs, semen, and saliva, works with as little as 5 pg of starting DNA material, and will amplify only male DNA in the presence of male/female mixtures in which the female portion of the sample overwhelmed the male portion 30,000 to 1.<br>M.S.<br>Department of Chemistry<br>Arts and Sciences<br>Chemistry
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Hasmats, Johanna. "Analysis of genetic variations in cancer." Doctoral thesis, KTH, Genteknologi, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-104438.

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The aim of this thesis is to apply recently developed technologies for genomic variation analyses, and to ensure quality of the generated information for use in preclinical cancer research. Faster access to a patients’ full genomic sequence for a lower cost makes it possible for end users such as clinicians and physicians to gain a more complete understanding of the disease status of a patient and adjust treatment accordingly. Correct biological interpretation is important in this context, and can only be provided through fast and simple access to relevant high quality data. Therefore, we here propose and validate new bioinformatic strategies for biomarker selection for prediction of response to cancer therapy. We initially explored the use of bioinformatic tools to select interesting targets for toxicity in carboplatin and paclitaxel on a smaller scale. From our findings we then further extended the analysis to the entire exome to look for biomarkers as targets for adverse effects from carboplatin and gemcitabine. To investigate any bias introduced by the methods used for targeting the exome, we analyzed the mutation profiles in cancer patients by comparing whole genome amplified DNA to unamplified DNA. In addition, we applied RNA-seq to the same patients to further validate the variations obtained by sequencing of DNA. The understanding of the human cancer genome is growing rapidly, thanks to methodological development of analysis tools. The next step is to implement these tools as a part of a chain from diagnosis of patients to genomic research to personalized treatment.<br><p>QC 20121105</p>
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Books on the topic "DNA nucleotide sequencing"

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Roe, Bruce A. DNA isolation and sequencing. John Wiley & Sons, 1996.

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P, Speed T., and Waterman Michael S, eds. Genetic mapping and DNA sequencing. Springer, 1996.

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Munshi, Anjana. DNA sequencing: Methods and applications. InTech, 2012.

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Alphey, Luke. DNA sequencing from experimental methods to bioinformatics. Springer, 1997.

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K, Nunnally Brian, ed. Analytical techniques in DNA sequencing. Taylor & Francis, 2005.

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Jan, Kieleczawa, ed. DNA sequencing III: Dealing with difficult templates. Jones and Bartlett Publishers, 2009.

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E, Soltis Douglas, Soltis Pamela S, and Doyle Jeff J, eds. Molecular systematics of plants II: DNA sequencing. Kluwer Academic Publishers, 1998.

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J, Howe C., and Ward E. S, eds. Nucleic acids sequencing: A practical approach. IRL Press, 1989.

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Petti, Cathy A. Interpretive criteria for identification of bacteria and fungi by DNA target sequencing: Approved guideline. Clinical and Laboratory Standards Institute, 2008.

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Primrose, S. B. Principles of genome analysis: A guideto mapping and sequencing DNA from different organisms. Blackwell Scientific, 1995.

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Book chapters on the topic "DNA nucleotide sequencing"

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Cui, Songkui, Abdelbagi M. A. Ghanim, and Satoko Yoshida. "Identification of Closely Related Polymorphisms with Striga Resistance Using Next Generation Sequencing." In Mutation Breeding and Efficiency Enhancing Technologies for Resistance to Striga in Cereals. Springer Berlin Heidelberg, 2023. http://dx.doi.org/10.1007/978-3-662-68181-7_9.

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AbstractMolecular markers are powerful tools to enhance speed of breeding. Recent advances of sequencing technology allow us to identify most polymorphisms in a genome. Whole genome resequencing of an F2 segregating population can identify those polymorphisms that co-segregate with a mutant phenotype, which theoretically include the gene responsible for Striga resistance gained through mutagenesis. This protocol explains the isolation of high-quality genomic DNA for sequencing and step-by-step procedures for single nucleotide polymorphism (SNP) identification from bulked F2 sequences.
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Kaeser, Gwendolyn E., and Jerold Chun. "Flow Cytometric and Sorting Analyses for Nuclear DNA Content, Nucleotide Sequencing, and Interphase FISH." In Neuromethods. Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7280-7_3.

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Bahonar, Sajedeh, and Hesam Montazeri. "Somatic Single-Nucleotide Variant Calling from Single-Cell DNA Sequencing Data Using SCAN-SNV." In Variant Calling. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2293-3_17.

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Jankowicz-Cieslak, Joanna, Ivan L. Ingelbrecht, and Bradley J. Till. "Mutation Detection in Gamma-Irradiated Banana Using Low Coverage Copy Number Variation." In Efficient Screening Techniques to Identify Mutants with TR4 Resistance in Banana. Springer Berlin Heidelberg, 2022. http://dx.doi.org/10.1007/978-3-662-64915-2_8.

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AbstractMutagenesis of in vitro propagated bananas is an efficient method to introduce novel alleles and broaden genetic diversity. The FAO/IAEA Plant Breeding and Genetics Laboratory previously established efficient methods for mutation induction of in vitro shoot tips in banana using physical and chemical mutagens as well as methods for the efficient discovery of ethyl methanesulphonate (EMS) induced single nucleotide mutations in targeted genes. Officially released mutant banana varieties have been created using gamma rays, a mutagen that can produce large genomic changes such as insertions and deletions (InDels). Such dosage mutations may be particularly important for generating observable phenotypes in polyploids such as banana. Here, we describe a Next Generation Sequencing (NGS) approach in Cavendish (AAA) bananas to identify large genomic InDels. The method is based on low coverage whole genome sequencing (LC-WGS) using an Illumina short-read sequencing platform. We provide details for sonication-mediated library preparation and the installation and use of freely available computer software to identify copy number variation in Cavendish banana. Alternative DNA library construction procedures and bioinformatics tools are briefly described. Example data is provided for the mutant variety Novaria and cv Grande Naine (AAA), but the methodology can be equally applied for triploid bananas with mixed genomes (A and B) and is useful for the characterization of putative Fusarium Wilt TR4 resistant mutant lines described elsewhere in this protocol book.
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Kernaleguen, Magali, Christian Daviaud, Yimin Shen, et al. "Whole-Genome Bisulfite Sequencing for the Analysis of Genome-Wide DNA Methylation and Hydroxymethylation Patterns at Single-Nucleotide Resolution." In Methods in Molecular Biology. Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7774-1_18.

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Derbala, David, Abel Garnier, Eric Bonnet, Jean-François Deleuze, and Jörg Tost. "Whole-Genome Bisulfite Sequencing Protocol for the Analysis of Genome-Wide DNA Methylation and Hydroxymethylation Patterns at Single-Nucleotide Resolution." In Methods in Molecular Biology. Springer US, 2024. http://dx.doi.org/10.1007/978-1-0716-4051-7_18.

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V., Santhy, Nagamani Sandra, Kundapura V. Ravishankar, and Bhavya Chidambara. "Molecular Techniques for Testing Genetic Purity and Seed Health." In Seed Science and Technology. Springer Nature Singapore, 2023. http://dx.doi.org/10.1007/978-981-19-5888-5_15.

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AbstractWith the globalization of seed trade and transgenic variety development, the application of molecular technologies for seed quality gained more significance in both the internal and international markets. Besides germination, genetic purity and seed health are the two most important seed quality parameters that determine the planting value of a seed lot. Compared to the conventional methods of testing, molecular marker technologies are more efficient for quality analysis as these are more accurate, robust, abundant, and faster. Among the various markers, simple sequence repeats (SSRs), due to their genome-wide presence, reproducibility, multi-allelic nature, and co-dominant inheritance, have emerged as the best markers, for establishing varietal distinctness, identity, and variety/hybrid seed purity testing. With the advent of the next-generation sequencing (NGS) technology, single nucleotide polymorphic (SNP) markers also became widely popular, and the closest to being an ideal marker besides SSRs, in seed genetic purity testing. With large-scale GM crop cultivation, testing for the adventitious presence and trait purity are two added components of seed quality testing. The methods of GM seed quality testing include DNA-based (conventional and real-time PCR), protein-based (lateral flow test and ELISA), and bioassay-based technologies. DNA-based methods including PCR/real-time PCR assays have been successfully employed to detect the adventitious presence of transgenic seeds in seed trade especially at international level, as well as in the national gene banks for germplasm conservation. ISTA plays a prominent role in international harmonization and providing universal guidelines on use of different methods to detect GM seeds. The BMT group of UPOV and the Working Group on DNA Methods of the Variety Committee of ISTA, work in tandem to standardize suitable molecular techniques for establishing variety identity and purity testing, respectively. In the area of seed health testing also, molecular detection assays such as, PCR (nested PCR, multiplex PCR, real-time PCR), loop-mediated isothermal amplification (LAMP), and DNA microarray with many advantages over the conventional assays have been proven highly useful. However, there is a need to validate the usefulness of molecular markers through stringent multi-laboratory tests for their reproducibility before recommending them in routine seed purity and health testing.
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Roux, Nicolas, Rachel Chase, Ines van den Houwe, et al. "Somaclonal variation in clonal crops: containing the bad, exploring the good." In Mutation breeding, genetic diversity and crop adaptation to climate change. CABI, 2021. http://dx.doi.org/10.1079/9781789249095.0037.

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Abstract Somaclonal variation describes random cellular changes in plants regenerated through tissue culture. It occurs in certain crops that undergo micropropagation and has been recorded in different explant sources, from leaves and shoots to meristems and embryos. In banana (Musa spp.), a clonal crop conserved in vitro, somaclonal variation has been observed after prolonged periods in tissue culture, resulting from an increase in subcultures performed on a given clone. According to scientific literature, variants, or off-types, often show characteristics such as abnormal growth and flower or fruit defects in frequencies ranging from 1% to 32%. This variation poses a problem for gene bank managers, whose mandate is to maintain the genetic integrity of their collections for research and breeding. In the case of the Bioversity International Musa Germplasm Transit Centre (ITC), stress during the in vitro process is minimized by various techniques and plants are regenerated after 10 years, making it a long and costly process. Identifying somaclonal variation at an early stage would be an ideal solution; however, this requires suitable molecular markers. Recent studies revealed that techniques such as direct DNA sequencing and single nucleotide polymorphisms (SNPs) are able to detect the underlying factors of somaclonal variation and are becoming more accessible. On the other hand, somaclonal variation can be beneficial as it allows the natural development of new varieties and supplies genetic stocks used for future genetic studies. Harnessing the diversity of somaclones is easier, faster and cheaper compared with other methods of crop improvement, although it is also less predictable. So far, variants of crops such as apple, strawberry, potato and banana have been successfully adopted into global markets. In this chapter, we will discuss how to minimize the adverse effects of somaclonal variation while maximizing its benefits for greater crop diversity, with a particular focus on banana.
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Slatter, Tania, and Alison Fitches. "DNA sequencing." In Tools and Techniques in Biomolecular Science. Oxford University Press, 2013. http://dx.doi.org/10.1093/hesc/9780199695560.003.0004.

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This chapter looks at DNA sequencing, a technique used to determine the precise order of the nucleotide bases-adenine, guanine, cytosine, and thymine-in a DNA fragment. The chapter explains the first-generation sequencing methods: the chemical method introduced by Maxam and Gilbert in 1977, the Sanger dideoxy-chain-termination sequencing method, and the chain-termination cycle sequencing method. It also tackles the uses of next-generation sequencing methods which use newer technologies. The chapter gives an overview of the next-generation sequencing procedure and explains the template preparation. It describes the various sequencing platforms, namely, the Roche 454, Illumina system, and SOLiD system. The chapter also lists some bioinformatic tools for the analysis of next-generation sequencing data. Lastly, it discusses the limitations of next-generation sequencing.
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"RNA sequencing." In Nucleic Acids Sequencing, edited by C. J. Howe and Es Ward. Oxford University PressOxford, 1990. http://dx.doi.org/10.1093/oso/9780199630561.003.0006.

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Abstract The first complete nucleotide sequence of a gene was published in 1964 by Robert Holley and associates. (1). This sequence was inferred from the transcript of the gene encoding yeast alanine tRNA. Determination of the 77 nucleotide sequence required 1 g of alanine tRNA, recovered from. 200 g of bulk tRNA, isolated from 140 kg of baker’s yeast and nine years of effort. Holley was awarded the Nobel prize in 1968. This effort compares with the thousand or so nucleotides of sequence now determined from a single high resolution sequencing gel. Recombinant DNA and associated sequencing technology have revolutionized the sequencing of biopolymers and it is now generally far easier to sequence the gene directly than to work with the products of transcription or translation. Yet, from the early sixties to the late seventies the world of nucleic acid sequencing was an RNA world. The history of nucleic acid sequencing technology is largely contained within the history of RNA sequencing. Although the early sequencing technology is cumbersome by contemporary standards, much remains useful in specialized applications. This chapter does not address all of the earlier technology, nor would it be appropriate to do so. Rather, those classical approaches that retain current utility are discussed in detail. Associated but less generally useful techniques are referenced or discussed in passing.
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Conference papers on the topic "DNA nucleotide sequencing"

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Koide, T. "CHARACTERIZATION OF THE GENE FOR HUMAN HISTIDINE-RICH GLYCOPROTEIN." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643599.

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Human histidine-rich glycoprotein (HRG) is a single-chain glycoprotein in plasma which is considered to modulate a coagulation and fibrinolysis system with the ability to bind to heparin, plasminogen, fibrinogen, thrombospondin, etc. Recently we have elucidated the primary structure of HRG by determining the nucleotide sequence of its cDNA, and showed that HRG is composed of several different types of internal repeats, each one of which shows considerable homology with the functional and/or structural domains of other proteins including high molecular weight kininogen, antithrombin III, cystatins, and proline-rich protein and peptide. Thus, the multifunctional property of HRG was suggested to be due to its multi-domain structure. In the present studies, a human genomic DNA library, cloned in the bacteriophage vector Charon 4A, was screened for HRG gene using a full-length cDNA coding for human IMI as a probe. A total of 7 clones were isolated from 6 × 105 phage and each was plaque purified. The entire HRG gene is represented in 3 genomic inserts with overlapping sequences that carry human DNA spanning 30 kb. Overlapping gene fragments were subcloned into pUC9 and characterized by Southern blot hybridization using 5’ and 3’ end probes isolated from human HRG cDNA and by DNA sequencing. These studies have shown that the gene for human HRG spans about 9 kb and consists of at least 5 exons and 4 introns. The putative histidine-rich region consisted of 12 tandemly repeated sequences of a 5 amino acid segment and 2 proline-rich regions contiguous to it are likely to be involved within one exon.
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Ploos van Amstel, J. K., A. L. van der Zanden, E. Bakker, P. H. Reitsma, and R. M. Bertina. "INDEPENDENT ISOLATION OF HUMAN PROTEIN S cDNA AND THE ASSIGNMENT OF THE GENE TO CHROMOSOME 3." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1644638.

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Protein S is a vitamin K-dependent glycoprotein, that serves as a cofactor of activated protein C. A hereditary deficiency in protein S is associated with an increased risk for the development of venous thrombosis. The deficiency is inherited as an autosomal dominant trait. We isolated a cDNA coding for protein S and assigned its gene to chromosome 3.A human liver cDNA library in phage xgtll (complexity 1.2 × 106 , D. Stafford, Chapel Hill) was screened by using immuno-purifiedpolyclonal anti-protein S IgG as a probe. Approximately 1.5 x 10 recombinants of the amplified library were screened. Out of eighteen positive clones one clone was found, after nucleotide sequence analysis, to code for a peptide with a high degree of homology with the carboxy terminal region of the already published bovine protein S. This clone pSP84 (450 bp) was used as a probe to screen a human liver cDNA library in plasmid pUC9. From this library we isolated several positive clones. Clone pSUL5 contained the largest insert (2200 base pairs). Dideoxy sequencing revealed that it codes for 330 amino acids of the carboxy terminal part of protein S. Furthermore, it contained a 1200 base pairs 3' untranslated region. The predicted amino acid sequence did not differ from the published sequence of human protein S, although at the nucleotide level some differences could be detected.Clone pSUL5 was used to localize the protein S gene to its chromosome. The assignment was done by hybridization to Pst I digested DNA from human-hamster c.q. human-mouse somatic cell hybrids. In this way we got strong indication that the protein S gene is located on chromosome 3.
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Antonarakis, E. "The Molecular Genetics of Hemophilia A Stylianos." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643980.

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Hemophilia A is a common X linked hereditary disorder of blood coagulation due to deficiency of factor 8. The gene for factor 8 has been cloned and characterized (Nature 312:326-342, 1984). It is divided into 26 exons and 25 introns and spans 186 kb of DNA. The CGNA is 9 kb and codes for 2351 amino acids. The first 19 amino acids comprise the secretory leader peptide and the mature excreted polypeptide consists of 2332 amino acids. The nucleotide sequence of the exons and the exon-intron junctions is known and the complete amino acid sequence has been deducedSeveral laboratories have used cloned factor 8 DNA sequences as probes to characterized mutations that are responsible for hemophilia A in certain pedigrees. These mutations have been characterized by restriction analysis, oligonucleotide hybridization, cloning and sequencing of DNA from appropriate patientsIn about 500 patients with hemophilia A examined, the molecular defect has been recognized in 39. Both gross alterations (mainly deletions) and point mutations of the factor 8 gene have been found.A total of 19 different deletions have been observed. No two unrelated pedigrees share the same exact deletion.The size of the deleted DNA varies from 1.5 kb to more than 210 kb. All but one of these deletions are associated with severe hemophilia A. A deletion of 6 kb that contains exon 22 only is associated with moderate hemophilia. Some deletions are present in patients with inhibitors to factor 8. No correlation of the size or the position of the deletions can be found with the presence of inhibitors to factor 8.A total of 20 point mutations have been characterized. All are recognized by restriction analysis and involve Taq I sites. All are mutations of CpG dinucleotides and generate nonsense or missence codons. Unrelated pedigrees have the same single nucleotide change because of independent origin of the same mutation. In many instances de novo occurrence of a point mutation has been observed. CpG dinucleotides are hot spots for mutation to TG or CA presumably because of spontaneous deamination of methylcytosine. Some point mutations are present in patients with inhibitors but no correlation of the site of mutation and inhibitor formation has been found. The nonsense mutations are present in patients with severe hemophilia A. A missense mutation (Arg Gin) in exon 26 was found in a patient with mild hemophilia while another Arg Gin mutation in exon 24 has been observed in a patient with severe disease. The creation of a donor splice site in IVS 4 of factor 8 gene has been observed in a patient with mild hemophilia.Few DNA polymorphisms within the factor 8 gene and two other closely linked polymorphisms have been used for carrier detection and prenatal diagnosis of hemophilia A. These DNA markers are useful in more than 90% of families at risk for hemophilia A.The author thanks Drs. Gitschier, Din, Olek, Pirastou, Lawn for communication of their data prior to publication.The hemophilia project at Johns Hopkins was supported by an Institutional grant and NIH grant to S.S.A. and Haig H. Kazazian, Jr.
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Imamovic, Alma, Saud H. AlDubayan, Nathanael Moore, Celine G. Han, Brendan Reardon, and Eliezer M. Van Allen. "Abstract 5296: R2D2: An integrated analysis framework to infer the functional impact of single nucleotide variants (SNVs) using matched germline and tumor DNA and RNA sequencing data." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-5296.

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Sauer, M., J. Arden-Jacob, K. H. Drexhage, et al. "How many labeled mononucleotide molecules can be identified in water on the single-molecule level." In Laser Applications to Chemical and Environmental Analysis. Optica Publishing Group, 1998. http://dx.doi.org/10.1364/lacea.1998.lma.5.

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One of the most popular application of the single-molecule detection (SMD) technique is fast DNA sequencing on the single-molecule level as proposed by Keller and coworkers.1,2 The principle idea of this very elegant method involves the incorporation of fluorescently labeled mononucleotides in a growing DNA strand, attachment of a single labeled DNA to a support (generally latex beads), movement of the supported DNA into a flowing sample stream, microchannel or microcapillary3 and detection of the analyte molecules as they are cleaved from the DNA strand by an exonuclease. The DNA sequence is determined by the order in which differently labeled nucleotides are detected and identified. Although a lot of problems are associated with the enzymatic incorporation of labeled mononucleotides and the selective handling of a single DNA strand different detection and identification strategies have been developed. However, up to now, only two different dyes have been successfully identified on the single-molecule level in aqueous solution due to their different fluorescence lifetimes.4,5 Hence, the critical question in DNA sequencing on the single strand is how many labels can be identified on the single-molecule level in aqueous solvent systems.
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Jett, James H., Lloyd C. Davis, Jong Hoon Hahn, et al. "Single Molecule Detection in Flowing Sample Streams As An Approach to DNA Sequencing." In Laser Applications to Chemical Analysis. Optica Publishing Group, 1990. http://dx.doi.org/10.1364/laca.1990.tha3.

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We are exploring a technique which has the potential to sequence large fragments of DNA at a rate of hundreds of bases per second. Our technique is based upon a projected ability to detect single chromophores by laser-induced fluorescence in flowing sample streams.1 The technique involves: (1) labeling the nucleotides with base specific tags suitable for fluorescence detection, (2) selecting a desired fragment of DNA, (3) suspending the single DNA fragment in a flowing sample stream, (4) sequentially cleaving labeled bases from the free end of the DNA fragment using an exonuclease, and (5) detecting and identifying the cleaved, labeled bases as they flow through a focused laser beam.2
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Goodwin, Peter M., Jay A. Schecker, Charles W. Wilkerson, Jr., et al. "DNA sequencing by single molecule detection of labeled nucleotides sequentially cleaved from a single strand of DNA." In OE/LASE'93: Optics, Electro-Optics, & Laser Applications in Science& Engineering, edited by Richard A. Keller. SPIE, 1993. http://dx.doi.org/10.1117/12.146712.

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Taniguchi, Masateru, and Tomoji Kawai. "Development of Gating Nanopores for Next-Generation DNA Sequencing Using Mechanically Controllable Break Junctions." In ASME-JSME-KSME 2011 Joint Fluids Engineering Conference. ASMEDC, 2011. http://dx.doi.org/10.1115/ajk2011-36014.

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We have developed two types of devices—vertical and parallel—for incorporating a microfluidic channel into a gating nanopore. The vertical device consists of a single nanogap electrode with a nanopore perpendicular to the surface of a silicon substrate. The parallel device is similar, except the nanopore is parallel to the surface of the substrate. Furthermore, while the vertical device was fabricated using nanofabrication technologies, the parallel device was fabricated using a mechanically controllable break junction that enables atomic-level control of the electrode gap; hence, measurement of single atoms and molecules is possible. Both devices can identify single gold nanoparticles passing through them by measuring the strength of their electrical signals. The parallel device can also identify the individual nucleotides in a DNA molecule.
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Schecker, Jay A., Peter M. Goodwin, Rhett L. Affleck, et al. "Flow-based continuous DNA sequencing via single molecule detection of enzymatically cleaved fluorescent nucleotides." In Photonics West '95, edited by Gerald E. Cohn, Jeremy M. Lerner, Kevin J. Liddane, Alexander Scheeline, and Steven A. Soper. SPIE, 1995. http://dx.doi.org/10.1117/12.206012.

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Kolhe, Ravindra, Pankaj Ahluwalia, Saleh Heneidi, Sudha Ananth, Vamsi Kota, and Ashis Mondal. "Abstract LB-227: Guideline adherent clinical validation of a comprehensive DNA/RNA panel (523 genes-TruSight Oncology 500) for determination of single nucleotide variants (SNV’s), small insertions or deletions (Indels), copy number variations (CNV’s), splice variations (SV’s), gene fusions (GF’s), tumor mutation burden (TMB) and micro-satellite instability (MSI) on anext-generation sequencing (NGS)platform in a CLIA setting." 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-lb-227.

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Reports on the topic "DNA nucleotide sequencing"

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Steffenson, B. J., I. Mayrose, Gary J. Muehlbauer, and A. Sharon. ing and comparative sequence analysis of powdery mildew and leaf rust resistance gene complements in wild barley. United States-Israel Binational Agricultural Research and Development Fund, 2021. http://dx.doi.org/10.32747/2021.8134173.bard.

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Our overall, long-term goal is to exploit the genetic diversity present in cereal wild relatives for the development of cultivars with durable disease resistance. Our specific objectives for this proposal were to: 1) Utilize Association Genetics Resistance Gene Enrichment Sequencing (AgRenSeq) to identify and clone powdery mildew and leaf rust resistance gene complements in wild barley and 2) Conduct comparative sequence analyses of the cloned resistance genes to elucidate the basis of their specificity and evolution. The deployment of resistant cultivars is the most effective, economically efficient, and environmentally sound means of controlling plant diseases, especially in small grain cereals. The systems selected for study in this proposal are barley (Hordeum vulgare ssp. vulgare, Hvv), its wild progenitor (Hordeum vulgare ssp. spontaneum, Hvs) and the powdery mildew (Blumeria graminis f. sp. hordei, Bgs) and leaf rust (Puccinia hordei, Ph) pathogens. We compiled a diverse panel of Hvs accessions (the Wild Barley Diversity Collection or WBDC; N = 314) from across its native range and evaluated it to 40 isolates of Bgs and 12 isolates of Ph. We obtained genomic DNA sequences enriched for Nucleotide Binding Site-Leucine Rich Repeat (NLR) type resistance genes for 203 WBDC accessions, plus cultivar Morex for which the first reference genome sequence of barley was based. We assembled the 250 bp Illumina sequencing reads into contigs using CLC assembly cell. From this effort, we successfully assembled the sequences of 201 WBDC accessions plus Morex and used NLR Parser to identify contigs containing NLR genes. AgRenSeq was then used to identify k-mers (short oligonucleotide sequences of length k) that were associated with resistance to each isolate of the two pathogens. This analysis was performed individually for all WBDC accessions and each individual pathogen race (9,898 host accession x pathogen race combinations). We visualized the results from these analyses in Manhattan plots and identified 311 and 144 peaks for powdery mildew and leaf rust resistance, respectively. The next step in the analysis was to identify the contigs associated with the peaks in the Manhattan plots. BLAST (Basic Local Alignment Search Tool) searches were employed to identify closely related contigs in other WBDC accessions or in Morex. We identified two candidate R genes that were only present in resistant WBDC accessions. One of these was present in seven WBDC lines and was associated with resistance to four leaf rust isolates. BLAST analysis of this gene revealed that it was Rph15, one of the most widely effective leaf rust resistance genes reported in Hordeum. This gene was cloned and functionally validated in association with our Australian colleagues (Cheng et al., 2021). We are currently in the process of cloning six of other resistance genes: four for powdery mildew and two for leaf rust. As the contigs do not contain much of the promoter sequences, we have employed a genome walking approach to identify 2,500 bp of promoter sequence. To speed up and simplify the cloning of resistance genes from the WBDC, the PI established the International Wild Barley Sequencing Consortium (IWBSC; https://iwbsc.umn.edu/) comprised of over 60 researchers from 14 different countries and raised over $150,000 through crowdfunding to pay for 10X depth sequence coverage. Genome-wide association study (GWAS) of whole genome sequencing (WGS) data identified extremely strong and clear signals of association for several resistance genes which will facilitate gene cloning in concert with a wild barley pan-genome currently under construction. The cloning of multiple resistance gene can facilitate the development of durably resistant cultivars by inserting, through transgenesis, cassettes of multiple resistance genes.
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Levisohn, Sharon, Maricarmen Garcia, David Yogev, and Stanley Kleven. Targeted Molecular Typing of Pathogenic Avian Mycoplasmas. United States Department of Agriculture, 2006. http://dx.doi.org/10.32747/2006.7695853.bard.

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Intraspecies identification (DNA "fingerprinting") of pathogenic avian mycoplasmas is a powerful tool for epidemiological studies and monitoring strain identity. However the only widely method available for Mycoplasma gallisepticum (MG) and M. synoviae (MS)wasrandom amplified polymorphic DNA (RAPD). This project aimed to develop alternative and supplementary typing methods that will overcome the major constraints of RAPD, such as the need for isolation of the organism in pure culture and the lack of reproducibility intrinsic in the method. Our strategy focussed on recognition of molecular markers enabling identification of MG and MS vaccine strains and, by extension, pathogenic potential of field isolates. Our first aim was to develop PCR-based systems which will allow amplification of specific targeted genes directly from clinical material. For this purpose we evaluated the degree of intraspecies heterogeneity in genes encoding variable surface antigens uniquely found in MG all of which are putative pathogenicity factors. Phylogenic analysis of targeted sequences of selected genes (pvpA, gapA, mgc2, and lp) was employed to determine the relationship among MG strains.. This method, designated gene targeted sequencing (GTS), was successfully employed to identify strains and to establish epidemiologically-linked strain clusters. Diagnostic PCR tests were designed and validated for each of the target genes, allowing amplification of specific nucleotide sequences from clinical samples. An mgc2-PCR-RFLP test was designed for rapid differential diagnosis of MG vaccine strains in Israel. Addressing other project goals, we used transposon mutagenesis and in vivo and in vitro models for pathogenicity to correlated specific changes in target genes with biological properties that may impact the course of infection. An innovative method for specific detection and typing of MS strains was based on the hemagglutinin-encoding gene vlhA, uniquely found in this species. In parallel, we evaluated the application of amplified fragment length polymorphism (AFLP) in avian mycoplasmas. AFLP is a highly discriminatory method that scans the entire genome using infrequent restriction site PCR. As a first step the method was found to be highly correlated with other DNA typing methods for MG species and strain differentiation. The method is highly reproducible and relatively rapid, although it is necessary to isolate the strain to be tested. Both AFLP and GTS are readily to amenable to computer-assisted analysis of similarity and construction of a data-base resource. The availability of improved and diverse tools will help realize the full potential of molecular typing of avian mycoplasmas as an integral and essential part of mycoplasma control programs.
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Joel, Daniel M., Steven J. Knapp, and Yaakov Tadmor. Genomic Approaches for Understanding Virulence and Resistance in the Sunflower-Orobanche Host-Parasite Interaction. United States Department of Agriculture, 2011. http://dx.doi.org/10.32747/2011.7592655.bard.

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Oroginal Objectives: (i) identify DNA markers linked to the avirulence (Avr) locus and locate the Avr locus through genetic mapping with an inter-race Orobanche cumana population; (ii) develop high-throughput fingerprint DNA markers for genotypingO. cumana races; (iii) identify nucleotide binding domain leucine rich repeat (NB-LRR) genes encoding R proteins conferring resistance to O. cumana in sunflower; (iv) increase the resolution of the chromosomal segment harboring Or₅ and related R genes through genetic and physical mapping in previously and newly developed mapping populations of sunflower; and (v) develop high-throughput DNA markers for rapidly and efficiently identifying and transferring sunflower R genes through marker-assisted selection. Revisions made during the course of project: Following changes in O. cumana race distribution in Israel, the newly arrived virulent race H was chosen for further analysis. HA412-HO, which was primarily chosen as a susceptible sunflower cultivar, was more resistant to the new parasite populations than var. Shemesh, thus we shifted sunflower research into analyzing the resistance of HA412-HO. We exceeded the deliverables for Objectives #3-5 by securing funding for complete physical and high-density genetic mapping of the sunflower genome, in addition to producing a complete draft sequence of the sunflower genome. We discovered limited diversity between the parents of the O. cumana population developed for the mapping study. Hence, the developed DNA marker resources were insufficient to support genetic map construction. This objective was beyond the scale and scope of the funding. This objective is challenging enough to be the entire focus of follow up studies. Background to the topic: O. cumana, an obligate parasitic weed, is one of the most economically important and damaging diseases of sunflower, causes significant yield losses in susceptible genotypes, and threatens production in Israel and many other countries. Breeding for resistance has been crucial for protecting sunflower from O. cumana, and problematic because new races of the pathogen continually emerge, necessitating discovery and deployment of new R genes. The process is challenging because of the uncertainty in identifying races in a genetically diverse parasite. Major conclusions, solutions, achievements: We developed a small collection of SSR markers for genetic mapping in O. cumana and completed a diversity study to lay the ground for objective #1. Because DNA sequencing and SNPgenotyping technology dramatically advanced during the course of the study, we recommend shifting future work to SNP discovery and mapping using array-based approaches, instead of SSR markers. We completed a pilot study using a 96-SNP array, but it was not large enough to support genetic mapping in O.cumana. The development of further SNPs was beyond the scope of the grant. However, the collection of SSR markers was ideal for genetic diversity analysis, which indicated that O. cumanapopulations in Israel considerably differ frompopulations in other Mediterranean countries. We supplied physical and genetic mapping resources for identifying R-genes in sunflower responsible for resistance to O. cumana. Several thousand mapped SNP markers and a complete draft of the sunflower genome sequence are powerful tools for identifying additional candidate genes and understanding the genomic architecture of O. cumana-resistanceanddisease-resistance genes. Implications: The OrobancheSSR markers have utility in sunflower breeding and genetics programs, as well as a tool for understanding the heterogeneity of races in the field and for geographically mapping of pathotypes.The segregating populations of both Orobanche and sunflower hybrids are now available for QTL analyses.
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