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Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens
microorganisms Review Metagenomics Approaches for the Detection and Surveillance of Emerging and Recurrent Plant Pathogens Edoardo Piombo 1,2 , Ahmed Abdelfattah 3,4 , Samir Droby 5, Michael Wisniewski 6,7, Davide Spadaro 1,8,* and Leonardo Schena 9 1 Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, 10095 Grugliasco, Italy; [email protected] 2 Department of Forest Mycology and Plant Pathology, Uppsala Biocenter, Swedish University of Agricultural Sciences, P.O. Box 7026, 75007 Uppsala, Sweden 3 Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria; [email protected] 4 Department of Ecology, Environment and Plant Sciences, University of Stockholm, Svante Arrhenius väg 20A, 11418 Stockholm, Sweden 5 Department of Postharvest Science, Agricultural Research Organization (ARO), The Volcani Center, Rishon LeZion 7505101, Israel; [email protected] 6 U.S. Department of Agriculture—Agricultural Research Service (USDA-ARS), Kearneysville, WV 25430, USA; [email protected] 7 Department of Biological Sciences, Virginia Technical University, Blacksburg, VA 24061, USA 8 AGROINNOVA—Centre of Competence for the Innovation in the Agroenvironmental Sector, University of Torino, 10095 Grugliasco, Italy 9 Department of Agriculture, Università Mediterranea, 89122 Reggio Calabria, Italy; [email protected] * Correspondence: [email protected]; Tel.: +39-0116708942 Abstract: Globalization has a dramatic effect on the trade and movement of seeds, fruits and vegeta- bles, with a corresponding increase in economic losses caused by the introduction of transboundary Citation: Piombo, E.; Abdelfattah, A.; plant pathogens. Current diagnostic techniques provide a useful and precise tool to enact surveillance Droby, S.; Wisniewski, M.; Spadaro, protocols regarding specific organisms, but this approach is strictly targeted, while metabarcoding D.; Schena, L. -
"Paleogenomics" In
Rev. Cell Biol. Mol. Medicine Paleogenomics 243 Paleogenomics Peter D. Heintzman*, André E. R. Soares*, Dan Chang, and Beth Shapiro Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA 1 Reconstructing Paleogenomes 245 1.1 Ancient DNA 245 1.1.1 The Nature of Ancient DNA 245 1.1.2 The Common Effects of DNA Damage 246 1.2 The Recovery and Sequencing of Ancient DNA 246 1.2.1 Ancient DNA Extraction 246 1.2.2 DNA Library Preparation 247 1.2.3 Capture-Based Target Enrichment 248 1.2.4 Quantification of aDNA and Sequencing 249 1.3 Assembly and Analysis of a Paleogenome 250 1.3.1 Initial Data Processing 251 1.3.2 Mapping and Quality Control 252 1.3.3 Paleogenomic Analysis 253 2 Case Studies 253 2.1 Hominin Paleogenomics 253 2.1.1 The Origin of Hominin Paleogenetics 253 2.1.2 Entering the Paleogenomics Era 254 2.1.3 The First Complete Human Paleogenome 255 2.1.4 Human and Neandertal Paleogenomics 255 2.2 The Black Death and Insights into Ancient Plagues 257 2.3 Reconstruction and Selection of Ancient Phenotypes 258 2.4 Epigenetics of Ancient Species 260 3 Conclusions 261 Acknowledgments 261 References 261 ∗These authors contributed equally to this study. © 2015 Wiley-VCH Verlag GmbH & Co. KGaA Vol 1 | No 3 | 2015 244 Paleogenomics Rev. Cell Biol. Mol. Medicine Keywords Paleogenomics The science of reconstructing and analyzing the genomes of organisms that are not alive in the present day. Ancient DNA (aDNA) Ancient DNA is DNA that is extracted and characterized from degraded biological spec- imens, including preserved bones, teeth, hair, seeds, or other tissues. -
Inference of Natural Selection from Ancient DNA
COMMENT AND OPINION doi:10.1002/evl3.165 Inference of natural selection from ancient DNA Marianne Dehasque,1,2,3,4 Marıa´ C. Avila-Arcos,´ 5 David Dıez-del-Molino,´ 1,3 Matteo Fumagalli,6 Katerina Guschanski,7 Eline D. Lorenzen,8 Anna-Sapfo Malaspinas,9,10 Tomas Marques-Bonet,11,12,13,14 Michael D. Martin,15 Gemma G. R. Murray,16 Alexander S. T. Papadopulos,17 Nina Overgaard Therkildsen,18 Daniel Wegmann,19,20 Love Dalen,´ 1,2 and Andrew D. Foote17,21 1Centre for Palaeogenetics 10691, Stockholm, Sweden 2Department of Bioinformatics and Genetics, Swedish Museum of Natural History 10405 Stockholm, Sweden 3Department of Zoology, Stockholm University 10691 Stockholm, Sweden 4E-mail: [email protected] 5International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro 76230, Mexico 6Department of Life Sciences, Silwood Park Campus, Imperial College London, Ascot SL5 7PY, United Kingdom 7Animal Ecology, Department of Ecology and Genetics, Science for Life Laboratory, Uppsala University 75236, Uppsala, Sweden 8Globe Institute, University of Copenhagen DK-1350, Copenhagen, Denmark 9Department of Computational Biology, University of Lausanne 1015, Lausanne, Switzerland 10SIB Swiss Institute of Bioinformatics 1015, Lausanne, Switzerland 11Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), Parc de Recerca Biomedica` de Barcelona, Barcelona, Spain 12National Centre for Genomic Analysis—Centre for Genomic Regulation, Barcelona Institute of Science and Technology 08028, Barcelona, Spain 13Institucio Catalana -
Make Illumina Part of Your DNA. the Most Comprehensive Set of DNA Analysis Tools Available
Make Illumina part of your DNA. The most comprehensive set of DNA analysis tools available. Illumina’s portfolio of DNA analysis products delivers industry-leading data quality at the lowest cost per study. Accelerate discovery by looking at DNA from every angle. 4 SNP genotyping — Achieve significance with the industry’s best genomic coverage and data quality. 4 CNV analysis — Obtain the most comprehensive access to known and novel CNV regions. 4 DNA sequencing — Sequence virtually anything at a fraction of the cost and time. 4 DNA methylation — Get single CpG site resolution with high- multiplex standard or custom methylation panels. 4 ChIP-Seq — Obtain genome-wide maps of DNA-protein interactions with unprecedented resolution, quality and cost. Make us part of your DNA. Join the growing Illumina Community. Find out how to make Illumina part of your DNA: www.illumina.com/dna?gr Random Shear BAC Library Services Got Gaps? Eliminate gaps in genomic libraries with Lucigen’s exclusive Random Shear BAC Library technical expertise. Resulting in: • Complete genome sequence with as low as 5x coverage • Elimination of restriction site bias found in conventional libraries by utilizing random shearing of DNA into BAC-size fragments • Vast reduction of deleted and rearranged sequences by cloning in our Transcription-Free BAC vectors • Greatly reduced finishing costs. Detailed information on the benefits of Random Shear BAC Libraries for genome projects is available on-line: www.lucigen.com/BAC.pdf Closing centromeric gaps with a Random Shear BAC Library 80 M Notl cut Random Shear BAC clones M 60 40 Centromere 1 20 (~9 Mb) kb No. -
Paleogenomics of Animal Domestication
Paleogenomics of Animal Domestication Evan K. Irving-Pease, Hannah Ryan, Alexandra Jamieson, Evangelos A. Dimopoulos, Greger Larson, and Laurent A. F. Frantz Abstract Starting with dogs, over 15,000 years ago, the domestication of animals has been central in the development of modern societies. Because of its importance for a range of disciplines – including archaeology, biology and the humanities – domestication has been studied extensively. This chapter reviews how the field of paleogenomics has revolutionised, and will continue to revolutionise, our under- standing of animal domestication. We discuss how the recovery of ancient DNA from archaeological remains is allowing researchers to overcome inherent shortcom- ings arising from the analysis of modern DNA alone. In particular, we show how DNA, extracted from ancient substrates, has proven to be a crucial source of information to reconstruct the geographic and temporal origin of domestic species. We also discuss how ancient DNA is being used by geneticists and archaeologists to directly observe evolutionary changes linked to artificial and natural selection to generate a richer understanding of this fascinating process. Keywords Ancient DNA · Archaeology · Domestication · Entomology · Evolution · Genomics · Zoology E. K. Irving-Pease (*) · H. Ryan · A. Jamieson · E. A. Dimopoulos · G. Larson The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK e-mail: [email protected] L. A. F. Frantz (*) The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK School of Biological and Chemical Sciences, Queen Mary University of London, London, UK e-mail: [email protected] Charlotte Lindqvist and Om P. -
Short Tandem Repeat Typing on the 454 Platform
SHORT TANDEM REPEAT TYPING ON THE 454 PLATFORM: STRATEGIES AND CONSIDERATIONS FOR TARGETED SEQUENCING OF COMMON FORENSIC MARKERS Melissa Scheible1,2,*, Odile Loreille1,2, Rebecca Just1,2 and Jodi Irwin1,2,3 1American Registry of Pathology 2Armed Forces DNA Identification Laboratory, Armed Forces Medical Examiner System 3Present affiliation: Federal Bureau of Investigation, Quantico The past several years have seen a dramatic advance in the methods, chemistries and detection platforms available for DNA sequence data generation. Next generation sequencing (NGS) technologies, which produce large volumes of sequence data at extremely low cost relative to current platforms, are being broadly applied to various questions in medical genetics, evolutionary biology, molecular anthropology, phylogeny, epidemiology and metagenomics. For many of these applications, NGS is being used to produce sequence data covering thousands of loci, or even entire organismal genomes in a single sequencing run. Given this capacity, it’s not difficult to envision the potential implications of this technology for criminalistics, missing persons and disaster victim identification purposes. Historically, the recovery of large numbers of forensic markers in a single assay has been restricted by both the technical limitations of current, established capillary based sequencing genotyping technologies, as well as the quality and quantity of DNA originating from the damaged and degraded specimens regularly encountered in forensic casework. These limitations don’t apply in quite the same way to NGS, however. As a result, the simultaneous recovery of the standard autosomal DNA, mitochondrial DNA, and X and Y-chromosomal markers regularly assayed in forensic genetics, along with additional markers of interest, may be possible with these new technologies [1]. -
What's in a Neanderthal
WHAT’S IN A NEANDERTHAL: A COMPARATIVE ANALYSIS Taylorlyn Stephan Oberlin College Dept. of Anthropology Advised by Prof. Amy Margaris TABLE OF CONTENTS I. Abstract – pg. 3 II. Introduction – pg. 3-4 III. Historical Background – pg. 4-5 a. Fig. 1 – pg. 5 IV. Methods – pg. 5-8 a. Figs. 2 and 3 – pg. 6 V. Genomic Definitions – pg. 8-9 VI. Site Introduction – pg. 9-10 a. Fig 4 – pg. 10 VII. El Sidron – pg. 10-14 a. Table – pg. 10-12 b. Figs. 5-7 – pg. 12 c. Figs. 8 and 9 – pg. 13 VIII. Mezmaiskaya – pg. 14-18 a. Table – pg. 14-16 b. Figs. 10 and 11 – pg. 16 IX. Shanidar – pg. 18-22 a. Table – pg. 19-20 b. Figs. 12 and 13 – pg.21 X. Vindija – pg. 22-28 a. Table – pg. 23-25 b. Fig. 14 – pg. 25 c. Figs. 15-18 – pg. 26 XI. The Neanderthal Genome Project – pg. 28-32 a. Table – pg. 29 b. Fig. 19 – pg. 29 c. Figs. 20 and 21 – pg. 30 XII. Discussion – pg. 32- 36 XIII. Conclusion – pg. 36-38 XIV. Bibliography – pg. 38-42 2 ABSTRACT In this analysis, I seek to understand how three separate lines of evidence – skeletal morphology, archaeology, and genomics – are used separately and in tandem to produce taxonomic classifications in Neanderthal and paleoanthropological research more generally. To do so, I have selected four sites as case studies: El Sidrón Cave, Mezmaiskaya Cave, Shanidar Cave, and Vindija Cave. El Sidrón, Mezmaiskaya, and Vindija all have detailed archaeological records and have yielded Neanderthal DNA. -
High-Throughput Pyrosequencing (To Use GS 20; Whole Genome Sequencer)
2007 International Meeting of the Microbiological Society of Korea >>> W1-1 High-throughput Pyrosequencing (to use GS 20; whole genome sequencer) Youseak Go Macrogen Corporation Genomic Analysis Division The Genome sequencer FLX system, developed by 454 Life Science Corporation, is an ultra-high-throughput automatic DNA sequencing system capable carrying out and monitoring sequencing reactions in a massively parallel fashion. Hundreds of thousands of simultaneous reactions, in the “well” of a PicoTiterPlate device. The basic chemistry utilize the release of pyrophosphate (PPi) that occurs with each nucleotide addition during DNA-directed DNA synthesis to generate an amount of light commensurate with the amount of PPi released; this light is captured by a charge-coupled device camera and converted into a digital signal. The raw data resulting from a sequencing run consists of a series of digital images captured by the camera, where the images are a representation of the surface of the PicoTiterPlate device over which the sequencing reaction are taking place; and each image corresponding to one reagent flow over that surface, as defined by the Run script. If the sample DNA fragment present in a given PicoTiterPlate well is extended during a nucleotide flow, light is emitted from the well and captured on the image corresponding to that flow. Furthermore, the amount of light emitted is proportional to the number of nucleotide extended. Knowledge of the nucleotide flowed while each image is being captured, of location on the PicoTiterPlate device where light is being emitted during each flow allows the software to identify PicoTiterPlate wells that contain a DNA library fragment and determine the sequence of the DNA fragments present in each well. -
Nested Patch PCR for Highly Multiplexed Amplification of Genomic Loci
Downloaded from http://cshprotocols.cshlp.org/ at WASHINGTON UNIV SCHOFMED on August 30, 2012 - Published by Cold Spring Harbor Laboratory Press Nested Patch PCR for Highly Multiplexed Amplification of Genomic Loci Katherine E. Varley and Robi D. Mitra Cold Spring Harb Protoc 2009; doi: 10.1101/pdb.prot5252 Email Alerting Receive free email alerts when new articles cite this article - click here. Service Subject Browse articles on similar topics from Cold Spring Harbor Protocols. Categories Amplification of DNA by PCR (51 articles) Bioinformatics/Genomics, general (130 articles) DNA Sequencing (52 articles) Genetic Variation (69 articles) Genetics, general (316 articles) Genome Analysis (97 articles) Genomic DNA (70 articles) High-Throughput Analysis, general (94 articles) Molecular Biology, general (977 articles) Polymerase Chain Reaction (PCR) (61 articles) Polymerase Chain Reaction (PCR), general (136 articles) To subscribe to Cold Spring Harbor Protocols go to: http://cshprotocols.cshlp.org/subscriptions Downloaded from http://cshprotocols.cshlp.org/ at WASHINGTON UNIV SCHOFMED on August 30, 2012 - Published by Cold Spring Harbor Laboratory Press Protocol Nested Patch PCR for Highly Multiplexed Amplification of Genomic Loci Katherine E. Varley and Robi D. Mitra1 Department of Genetics, Center for Genome Sciences, Washington University School of Medicine, St. Louis, MO 63108, USA INTRODUCTION Nested Patch polymerase chain reaction (PCR) amplifies a large number (greater than 90) of targeted loci from genomic DNA simultaneously in the same reaction. These amplified loci can then be sequenced on a second-generation sequencing machine to detect single nucleotide polymorphisms (SNPs) and mutations. The reaction is highly specific: 90% of sequencing reads match targeted loci. Nested Patch PCR can be performed on many samples in parallel, and by using sample-specific DNA barcodes, these can be pooled and sequenced in a single reaction. -
Next-Generation Sequencing: Applications Beyond Genomes
British Yeast Group Meeting 2008 1091 Next-generation sequencing: applications beyond genomes Samuel Marguerat1, Brian T. Wilhelm2 and Jurg¨ Bahler¨ 1,3 Cancer Research UK, Fission Yeast Functional Genomics Group, The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, U.K. Abstract The development of DNA sequencing more than 30 years ago has profoundly impacted biological research. In the last couple of years, remarkable technological innovations have emerged that allow the direct and cost-effective sequencing of complex samples at unprecedented scale and speed. These next-generation technologies make it feasible to sequence not only static genomes, but also entire transcriptomes expressed under different conditions. These and other powerful applications of next-generation sequencing are rapidly revolutionizing the way genomic studies are carried out. Below, we provide a snapshot of these exciting new approaches to understanding the properties and functions of genomes. Given that sequencing-based assays may increasingly supersede microarray-based assays, we also compare and contrast data obtained from these distinct approaches. Sequencing as never before or logistically practical before. Next-generation sequencing Just when the era of sequencing seemed to have passed its should also democratize science in the sense that ambitious peak, technological breakthroughs are launching a new dawn sequencing-based projects can now be tackled by individual with huge potential and broad applications that are already laboratories or institutes, whereas before such projects would transforming biological research. Two pioneering papers re- only have been possible in genome centres. porting new sequencing developments in 2005 have provided the first glimpse of things to come [1,2]. -
Paleogenomics Genome-Scale Analysis of Ancient DNA Series: Population Genomics
springer.com Charlotte Lindqvist, Om P. Rajora (Eds.) Paleogenomics Genome-Scale Analysis of Ancient DNA Series: Population Genomics Paleogenomics is the first comprehensive book on paleogenomics, a rapidly evolving and fascinating field that investigates the genomes of ancient organisms and extinct species Chapters in this book are contributed by some of the leaders in the field, covering a wide array of topics This book provides insight into recent developments of concepts, technical advances and challenges, and promise of paleogenomics This book reviews and synthesizes studies applying paleogenomics to a variety of organisms, from pathogens and plants to primates This book analyzes current insights from paleogenomics into past environments, the evolution and adaptation of organisms to changing 1st ed. 2019, XIV, 427 p. 62 illus., 57 environmental conditions over a long peri illus. in color. Advances in genome-scale DNA sequencing technologies have revolutionized genetic research on ancient organisms, extinct species, and past environments. When it is recoverable after Printed book hundreds or thousands of years of unintended preservation, “ancient DNA” (or aDNA) is often Hardcover highly degraded, necessitating specialized handling and analytical approaches. Paleogenomics 159,99 € | £139.99 | $199.99 defines the field of reconstructing and analyzing the genomes of historic or long-dead [1] 171,19 € (D) | 175,99 € (A) | CHF organisms, most often through comparison with modern representatives of the same or similar 189,00 species. The -
Pyrosequencing Technology for Short DNA Sequencing and Whole
生物物理 47(2),129-132(2007) 理論/実験 技術 Pyrosequencing Technology for Short DNA Sequencing and Whole Genome Sequencing Baback Gharizadeh1, Mehran Ghaderi2 and Pål Nyrén3 1Stanford Genome Technology Center, Stanford University 2Clinical Pathology/Cytology, Karolinska University Hospital 3Department of Biotechnology, Royal Institute of Technology 1.Introduction 2.Pyrosequencing chemistry Recent impressive advances in DNA sequencing technolo- Pyrosequencing technique is based on sequencing-by-syn- gies have accelerated the detailed analysis of genomes from thesis principle8), 9) and employs a series of four enzymes to ac- many organisms. We have been observing reports of complete curately detect short nucleic acid sequences during DNA syn- or draft versions of the genome sequence of several well-stud- thesis. In Pyrosequencing10), the sequencing primer is ied, multicellular organisms. Human biology and medicine hybridized to a single-stranded DNA biotin-labeled template are in the midst of a revolution by Human Genome Project1) (post-PCR alkali treated) and mixed with the enzymes; DNA as the main catalyst. polymerase, ATP sulfurylase, luciferase and apyrase, and the The chain termination sequencing method, also known as substrates adenosine 5′ phosphosulfate (APS) and luciferin. Sanger sequencing, developed by Frederick Sanger and col- Fig. 1 illustrates schematically the chemistry of Pyrose- leagues2), has been the most widely used sequencing method quencing method. Cycles of four deoxynucleotide triphos- since its advent in 1977 and still is in use after more than 29 phates (dNTPs) are separately added to the reaction mixture years since its advent. The remarkable advances in chemistry iteratively. After each nucleotide dispensation, DNA poly- and automation to the Sanger sequencing method has made it merase catalyzes the incorporation of complementary dNTP to a simple and elegant technique, central to almost all past into the template strand.