Tyler future of genomics thurs 0920
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The document discusses oomycete genomics past, present and future. It summarizes that 5 oomycete genome sequences are currently available with several more underway. Next generation sequencing technologies are accelerating the rate of new sequence generation extraordinarily. The rapid accumulation of sequence data means approaches that integrate data like the VBI Microbial Database and miGenome project will be needed. Undergraduate research in oomycete bioinformatics offers benefits to the community and as a learning experience.
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This document summarizes a project that used metabarcoding to analyze Phytophthora species diversity in UK plant nurseries. Key findings include detecting 58 Phytophthora species across nurseries, with some species of concern like P. cinnamomi and P. quercina found on many hosts. Quarantine pathogens like P. ramorum and P. austrocedri were also detected. The project aims to help nurseries improve management practices to reduce Phytophthora spread and will inform the UK's nursery accreditation system. Ongoing work includes detection method development and discussing results with nursery managers and plant health organizations.
Current trends in plant breeding
This document discusses current trends in plant breeding. It begins by defining plant breeding as the genetic improvement of crops using both traditional and modern techniques to select for desired traits. It then provides background on the history of plant breeding, including the Green Revolution. The document outlines various modern breeding technologies like phenomics, proteomics, transcriptomics, genetic modification, and the role of bioinformatics in data analysis. It discusses using these omics approaches and genome sequencing to enable a second Green Revolution with crops that are higher yielding, more nutritious, and tolerant of environmental stresses. The goal is to produce more food to feed a growing global population in a sustainable way.
Tyler presentation
The document discusses past, present, and future work on oomycete genomics. In the past, genome comparisons found conserved gene order and effector genes associated with repeats. The P. sojae genome is being finished using new sequencing methods. In the future, sequencing capacity is rapidly improving which will enable more oomycete genomes to be sequenced cheaply.
Saha UC Davis Plant Pathology seminar Infrastructure for battling the Citrus ...
Rapidly spreading invasive diseases in systems with little or no prior experimental data or resources pose a unique set of challenges for growers, scientists as well as regulators. As a part of a USDA NIFA CAPS project focused on the psyllid, Diaphorina citri, we have released improved genomics resources including high quality genome assemblies and annotation. We have also created an open access web portal for analyses around the Citrus Greening/Huanglongbing disease complex. Citrusgreening.org includes pathosystem-wide resources and bioinformatics tools for multiple Citrus spp. hosts, the Asian citrus psyllid vector (ACP, Diaphorina citri), and multiple pathogens including Candidatus Liberibacter asiaticus (CLas). To the best of our knowledge, this is the first example of a database to use the pathosystem as a holistic framework to understand an insect transmitted plant disease. Users can submit relevant data sets to enable sharing and allow the community to leverage their data within an integrated system. The system includes the metabolic pathway databases CitrusCyc and DiaphorinaCyc with organism specific pathways that can be used to mine metabolomics, transcriptomics and proteomics results to identify pathways and regulatory mechanisms involved in disease response. The Psyllid Expression Network (PEN) contains expression profiles of ACP genes from multiple life stages, tissues, conditions and hosts. The Citrus Expression Network (CEN) contains public expression data from multiple tissues and conditions for various citrus hosts. All tools connect to a central database. The portal also includes electrical penetration graph (EPG) recordings, information about citrus rootstock trials and metabolomics data in addition to traditional omics data types with a goal of combining and mining all information related to the Huanglongbing pathosystem. User-friendly manual curation tools will allow the continuous improvement of knowledge base as more experimental research is published. The portal can be accessed at https://citrusgreening.org/.
Bioinformatics tools for NGS data analysis
Bioinformatics tools are essential for analyzing next-generation sequencing (NGS) data. The summary describes the typical stages of NGS data analysis:
1. Primary analysis involves demultiplexing, base calling and quality control to produce fastq files.
2. Secondary analysis maps reads to a reference genome to produce SAM/BAM files and calls variants to produce VCF files.
3. Tertiary analysis annotates and filters variants to prioritize those relevant to disease.
Psyllid microflora: Implications for liberibacter disease surveillance and pe...
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This research is improving the understanding of the microflora of Australian psyllids, for better biosecurity preparedness and response management.importance of pathogenomics in plant pathology
The document provides an outline for a seminar on pathogenomics for diagnosis and management of plant diseases. It includes sections on pathogenomics in plant pathology, diagnostic tools using next-generation sequencing technologies, host-microbe interaction and genes involved in virulence and resistance. The outline also lists various bioinformatics databases and molecular techniques used for pathogen detection, including PCR-based methods and microarrays. It discusses several examples of pathogenicity genes and host proteins involved in plant-virus interactions.
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Deciphering the genome of Diaphorina citri to develop solutions for the citru...
The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the causal agent for the citrus greening or Huanglongbing disease which threatens citrus industry worldwide. This vector is the primary target of approaches to stop the transmission of the pathogen. Accurate structural and functional annotation of the psyllid’s gene models and understanding its interactions with the pathogenic bacterium, CLas, is required for precise targeting using molecular methods such as RNAi. We opted for manual curation of gene families in the draft genome of D. citri (Diaci v1.1, contig N50 34.4Kb) that have key functional roles in D. citri biology and pathology. The community effort resulted in Official Gene Set v1.0 with more than 500 manually curated gene models across developmental, RNAi regulatory, and immune-related pathways.
Single copy marker analysis of the current genome shows a significant proportion of 3,350 markers conserved in Hemipterans to be missing (25%) with only 74% present in full-length copies. The manual genome annotation also identified a number of misassemblies and missing genes in the current genome. This is, in-part, due to the complexity introduced when assembling a heterogeneous sample containing DNA from multiple psyllids and exacerbated by the use of short reads. This challenge is common with insect genomes due to the size of individuals. To improve quality of genome assembly, we generated 36.2Gb of Pacbio long reads with a coverage of 80X for the 450Mb psyllid genome. The Canu assembler followed by Dovetail Chicago-based scaffolding was used to create an improved assembly (Diaci v2.0) with a contig N50 of 758.7kb and 1906 contigs. The assembly was polished with Pacbio and Illumina paired-end reads to remove indel and SNP errors. We are employing Dovetail Chicago and 10X Illumina libraries generated from a single psyllid in conjunction with Bionano optical maps to achieve long-range scaffolding of the genome. We have also generated full-length cDNA transcripts from diseased and healthy tissue from multiple life stages with the Pacbio IsoSeq technology. This will be the first time all these methods have been applied to resolve a complex insect genome from a highly heterogeneous sample. The new assembly will be available on https://citrusgreening.org/ which is our portal for all omics resources for the citrusgreening disease. We are continuing with the manual curation effort using the improved genome. We will also present how the improved genome and annotation is contributing to the development of molecular interdiction methods to disrupt the vectoring ability of D. citri.
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This is my midterm report presentation. Check also my last publication: low uplicability and network fragility of cancer genes
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Stat2013
The chi-square test is used to determine if an observed distribution of data differs from the distribution expected if the null hypothesis is true. It requires a contingency table of observed and expected frequencies, a probability value, and degrees of freedom. The chi-square test calculates a test statistic to determine if any difference is statistically significant or likely due to chance. Examples show applying the chi-square test to genetics data on tall and dwarf pea plants and to the distribution of sixes rolled in dice.
Presentation2013
This document discusses the development of a new lightweight version of the Eumicrobedb database called Transcriptomicsdb. The new version reduces the database size and dependencies by decreasing the number of tables and views from 329 to 37 and 127 to 18 respectively in Eumicrobedb-Oracle. It also improves query time from 10 seconds to 1.2 seconds and reduces genome upload time from 12-14 hours to 2 hours. The document describes how the new database will help laboratories with limited hosting facilities to store and analyze sequencing data. It notes that the source code will soon be released to allow others to replicate the database without needing an Oracle license and various bioinformatics packages.
Lecture7,8
Pharmacogenetics refers to how genetic differences affect individuals' responses to drugs. It influences different metabolic pathways and is responsible for over 106,000 deaths annually in the US. Certain genetic mutations can determine how effectively drugs are processed in the body. Microarrays are DNA chips that allow researchers to analyze large numbers of genes simultaneously, helping to identify genetic factors influencing drug responses and diseases.
Lecture5,6
Many diseases are caused by genetic mutations. Over 4000 diseases are linked to altered genes, including heart disease, cancer, autoimmune disorders, and diabetes. Specific mutations are associated with certain cancers, such as mutations in the RB1 and BRCA1 genes which can lead to retinoblastoma and breast cancer respectively. Large-scale projects like the Cancer Genome Atlas and ENCODE project aim to catalogue all mutations in cancers and across the human genome. Immunogenetics research examines the genetic links to immune-related disorders. The HapMap and 1000 Genomes projects studied genetic variants and helped map human genetic diversity.
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The document discusses topics to be covered in an IICB course on 8th December 2012, including primer designing, restriction mapping, and gene prediction. It provides information and guidelines on these topics, such as the appropriate length and properties of primers, the four types of restriction enzymes, and methods for gene prediction including patterns, frame consistency, dicodon frequencies, position-specific scoring matrices, and coding potential. Relevant references and websites discussing these techniques are also listed.
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Genome projects, Secondgen and Thirdgen genome sequencing, application of genome sequencing in predicting disease genes
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This document discusses genomics and genome sequencing. It provides an overview of the history of genome sequencing including early organisms sequenced like bacteriophage. It describes how genomes are sequenced through library construction, cloning, and strategies like Sanger sequencing. Applications of genome sequencing are also mentioned such as predicting genes, studying genome organization and evolution, and understanding the genetic basis of disease.
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- 17 countries contain 70% of global biodiversity and are considered "megadiverse."
- The Barcode of Life project uses DNA barcoding to identify species using markers like COI for animals, ITS for fungi, and rbcL and matK for plants.
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Biological databases
The document discusses the history and process of genome sequencing, as well as several important genome projects such as the Human Genome Project. It also examines the role of databases in genomic research, describing different types of biological databases and how they can be used to store, organize, and retrieve genomic data. Finally, it provides examples of popular databases and genome browsers that are widely used by researchers.
Genome sequencingprojects
This document provides an overview of genome sequencing. It discusses the history of genome sequencing, from early sequencing of small viruses in the 1970s to larger genomes like yeast and the human genome. The document outlines different sequencing technologies over time, from Sanger sequencing to newer single-molecule approaches. It also summarizes key genome projects like ENCODE and 1000 Genomes that have provided insights into non-coding regulatory elements and human genetic variation.
Human encodeproject
A consortium of 440 scientists from 32 laboratories characterized functional elements in the human genome as part of the ENCyclopedia Of DNA Elements (ENCODE) project. They found that 80% of the genome is biochemically active, with millions of regulatory elements such as promoters, enhancers, and insulators. Many of these elements interact with genes over long distances to control gene expression. This study significantly changes understanding of how the genome works.
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This document discusses oomycete genomics research that has been funded by the National Science Foundation, USDA CSREES, and USDA NIFA from 2007-2016. Over 120 destructive oomycete pathogen species have been studied, including the genera Phytophthora and Hyaloperonospora. The genomes of several Phytophthora species have been sequenced, with efforts underway to sequence all species through a new initiative with BGI. Comparisons between sequenced oomycete genomes show both conserved and unique genes. Effector genes associated with disease are located in repeat-rich regions of genomes and have expanded through evolution.
Vbi oomycetes2011 final
The document discusses tools from the US DOE Joint Genome Institute (JGI) for eukaryotic genome annotation and analysis of oomycete genomes. It introduces MycoCosm, a database with over 70 annotated fungal and oomycete genomes that allows manual curation of gene models. The automated annotation pipeline and various gene prediction programs used by JGI are described briefly. The document also outlines the manual curation workflow involving validating gene structures, choosing the best model, and annotating genes.
Chibucos annot go_final
This document discusses Gene Ontology (GO) annotation. It describes how GO provides a common language to describe gene products using controlled vocabularies and ontologies. Key points:
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Rnaseq forgenefinding
The document discusses next generation sequencing methods and RNA sequencing. It covers topics like sequencing formats, data analysis workflows including mapping, clustering, assembly programs, finding new genes and correcting existing ones. It discusses input file types, calculating sequencing depth, available tools for alignment, output file formats, assembly programs, splice junction prediction, and applications of RNA sequencing like gene expression analysis and annotation.
6th July 2012
This document discusses various methods for structural annotation and gene prediction, including:
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Rnaseq forgenefinding
1. Next generation sequencing techniques like 454 sequencing and Illumina sequencing have enabled high-throughput sequencing of genomes and transcriptomes. These techniques can generate billions of bases of sequence data per day.
2. RNA-Seq is a technique that uses next generation sequencing to determine the RNA transcripts present in a cell and their expression levels. It has advantages over previous methods as it is highly sensitive, quantitative, and can discover isoforms and lowly expressed genes.
3. Analyzing RNA-Seq data involves aligning the short reads to a reference genome or transcriptome using tools like Bowtie or BWA. This allows discovery of novel transcripts, splicing patterns, and quantification of expression levels. Numerous studies have used RNA-
Tyler functional annotation thurs 1120
This document discusses functional annotation and the Gene Ontology. It describes how functional annotation attaches biological information to sequences through searches of databases for homology, domains, and pathways as well as manual curation. Searches include BLAST for homology, Pfam and InterPro for domains, and KEGG and Reactome for pathways. Assignments include EC numbers for metabolic pathways and Gene Ontology terms from automated and manual annotation. Manual annotation combines all evidence and allows incorporation of experimental data but requires more time.
Tyler phringe fri 1120
The document describes the PHRINGE Synteny tool, which allows users to visualize synteny between oomycete genomes. The tool displays genomic regions from a source species and highlights regions of conserved gene order and orthologs in target species. Users can mouse over genes for more information or click genes to link to detailed records. The tool is useful for tracking genes like virulence effectors that may not be syntenic across species due to genomic rearrangements.
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Syllabus
Chapter-1
Introduction to objective, scope and outcome the subject
Chapter 2
Introduction: Scope and Specialization of Civil Engineering, Role of civil Engineer in Society, Impact of infrastructural development on economy of country.
Chapter 3
Surveying: Object Principles & Types of Surveying; Site Plans, Plans & Maps; Scales & Unit of different Measurements.
Linear Measurements: Instruments used. Linear Measurement by Tape, Ranging out Survey Lines and overcoming Obstructions; Measurements on sloping ground; Tape corrections, conventional symbols. Angular Measurements: Instruments used; Introduction to Compass Surveying, Bearings and Longitude & Latitude of a Line, Introduction to total station.
Levelling: Instrument used Object of levelling, Methods of levelling in brief, and Contour maps.
Chapter 4
Buildings: Selection of site for Buildings, Layout of Building Plan, Types of buildings, Plinth area, carpet area, floor space index, Introduction to building byelaws, concept of sun light & ventilation. Components of Buildings & their functions, Basic concept of R.C.C., Introduction to types of foundation
Chapter 5
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Chapter 6
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Water Pollution: Water Quality standards, Introduction to Treatment & Disposal of Waste Water. Reuse and Saving of Water, Rain Water Harvesting. Solid Waste Management: Classification of Solid Waste, Collection, Transportation and Disposal of Solid. Recycling of Solid Waste: Energy Recovery, Sanitary Landfill, On-Site Sanitation. Air & Noise Pollution: Primary and Secondary air pollutants, Harmful effects of Air Pollution, Control of Air Pollution. . Noise Pollution Harmful Effects of noise pollution, control of noise pollution, Global warming & Climate Change, Ozone depletion, Greenhouse effect
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1. Palancharmy, Basic Civil Engineering, McGraw Hill publishers.
2. Satheesh Gopi, Basic Civil Engineering, Pearson Publishers.
3. Ketki Rangwala Dalal, Essentials of Civil Engineering, Charotar Publishing House.
4. BCP, Surveying volume 1
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Tyler future of genomics thurs 0920
- 1. Oomycete Genomics, Past, Present and Future Brett Tyler Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University
- 2. Systems Biology of Host-Pathogen Interactions A single genetic network encompasses host and pathogen
- 3. Host-pathogen interactions are influenced by higher scale network connections to... … microbial communities
- 4. Estuarine Ecosystem. www.centralcoastbc.com … and macroecosystems
- 10. Albugo candida Lagenidium giganteum Hyaloperonospora arabidopsidis Bremia lactucae Phytophthora parasitica Peronospora tabacina Phytophthora sojae* *** Peronosporomycetidae Phytophthora capsici Phytophthora ramorum Plasmopara viticola Peronosporales Aphanomyces astaci Pythium ultimum** Phytophthora phaseoli Phytophthora ipomoae Phytophthora andina Phytophthora mirabilis Phytophthora infestans* ** Saprolegniomycetidae Pythiales/Lagenidiales Saprolegnia parasitica Saprolegnia diclina Aphanomyces euteiches high quality assembly short read survey genome funding sought Oomycete Genome Sequencing Summary ESTs * *** strains sequenced
- 11. Sequencing of P. sojae genotypes P7064 P7074 P7076 P6497
- 13. How RXLR effectors enter plant cells pathogen (fungus or oomycete) host plant cell P endocytosis Avr1b lipid rafts P P P P P PI-3-P binding protein Avr1b + PEPP1 Avr1b + 1,3 IP2 P P Inositol-1,3- diphosphate
- 21. New paradigm in undergraduate research VBI, Virginia Tech Year-round mentoring Summer Training Workshops Undergraduate consortium in oomycete bioinformatics Lafayette College Manuel Ospina-Giraldo 3 undergraduates Bowling Green State U Paul Morris; Karen Sirum 5 undergraduates College of Wooster, OH Bill Morgan funded by NSF/USDA microbial sequencing program Franklin & Marshall College Jaime Blair Nova Southeastern College Aurelian Tartar