Structure and Dynamics of the Hexaploid Wheat Genome
|
|
|
- Jeremy Tyler
- 6 years ago
- Views:
Transcription
1 TGAC 2016 March 30 th Structure and Dynamics of the Hexaploid Wheat Genome Frédéric CHOULET Genetics Diversity Ecophysiology of Cereals INRA U. Clermont-Ferrand, France
2
3 Structure, evolution of wheat genome Recombination Paleogenomics Grain composition Response to abiotic stress Resistanceto pathogens Diversity, selection q Resources Objectives Sequencing the wheat genome Markers Bioinformatics q Research Structure / Expression / Evolution TEs Gene space Duplications Structural variations Epigenome
4 q Why wheat? Important crop Complex genome
5 A Gb AABBDD 85% TEs B D
6 A Launched in 2005 Goal Ø Produce a high quality ref seq of the bread wheat genome Strategy Ø Reduce the complexity B D sorted chromosomes BACs Reference Sequence
7 A B D WGS Brenchley et al. Nature 2012 Ling et al. Nature 2013 Jia et al. Nature 2013 Chapman et al. Genom Biol 2015 sorted chromosomes Chr. Survey Seq (=CSS) IWGSC Science 2014 Physical maps MTPseq 3B Choulet et al. Science 2014 Daron et al. Genom Biol 2015 Pingault et al. Genom Biol 2015 Glover et al. Genome Biol 2015
8 q Chr Survey Seq (2014) q Resources 1 draft seq / chromosome arm 10 Gb - 10 M contigs (N50: 2.4 kb) 99,000 genes ~60% genes "zipped" q Main Results Gene loss-- SSD++ Dominance--
9 q 3B pseudomolecule (3BSEQ project) 774 Mb protein coding genes (pseudogenes: 27%) transposable elements 7, ,879 (86%)
10 1 Recombination LD 0 % 5 centromeric retrotransposons 0 pericentromere 68 Mb 122 Mb 59 Mb 774 Mb
11 (# conditions) 15 8 Expression (%) TE density (/10 Mb) 200 Gene density Mb Choulet et al. Science 2014
12 FPKM Organs & dev. stages Grain Leaf Pingault et al. Genom Biol 2015
13 q Chromosome partitioning: 3B-specific?? 15 Expression breadth 10 3A D barley 6 maize
14 q Accelerated evolution in the Triticeae Wheat 3B 27% nonsyntenic genes Brachy-2 Rice-1 ~10% Sorghum-3 Ø inter-chromosomal gene duplications Ø intra-chromosomal - o o More duplicated genes in the chr. extremties Enriched in adaptation functions Glover et al. Genom Biol 2015
15 q TEs Annotation challenge Impact on genome biology Daron et al. Genom Biol 2015
16 q New tools: CLARITE and ClariTeRep 3B à TEs Copia CACTA Gypsy
17 q Insertion dynamics Fatima 6x 4x A-B-D divergence Myrs Myrs Copia silenced until polyploidization but shared betwa-b-d Gypsy
18 q Evolutionary forces driving TE distribution # copies 0-1 MYA 1-2 MYA 2-3 MYA >3 MYA # copies
19 % nonsyntenic genes syntenic genes 0 % 15 Copia 0-20 kb 0 10 CACTA +20 kb Gypsy 0 0
20 Structural Variations o CNVs o PAVs
21 q Structural Variations (SVs) Small indels Inversions, translocations Duplications & Deletions --> CNVs & PAVs Reference accession#1 accession#2 PAV CNV Main questions: Extent of SVs among the Triticeae, hexaploid wheat acc.? Impact of polyploidization? Relationships betw SVs and chr. organization? Impact on phenotypes?
22 q Structural Variations (SVs) Detection Aligning orthologous sequenced loci ACT view Using resequencing data (short read-based) not properly mapped paired-reads split reads depth of coverage à Limitations in polyploid TE-rich genomes
23 q Resequencing data Chinese Spring ref genome A B D WGS reads Accession#1 A B D limitations: homeologs and paralogs (repeated genes)
24 q Resequencing data Chinese Spring ref genome A B D WGS reads Accession#1 A B D sorted 3B reads Accession#1 3B advantage: diploid context limitations: 3B DNA amplified before seq.
25 q Resequencing data Chinese Spring ref genome A B D sorted 3B reads 45 accessions 22 hexaploids: T. aestivum 6 hexaploids: T. macha, spelta 17 tetraploids: T. durum, dicoccoides, dicoccum, carthlicum Illumina 2x100bp Depth: ~40x
26 o TEs (85%) o Genes (2%)
27 q SVs in genes Methodology BWA & samtools Chinese Spring 3B sorted 3B reads 44 accessions 3B PAVs <10% of the gene length covered by reads CNVs depth of coveragebased approach Normalization: GC% sequencing depth gene length log 2 (cov acc /cov Chinese Sp )
28 q SVs in genes Results PAVs XX% genes deleted in 1+ accessions [XX..XX] CNVs down CNVs : X% of the 3B genes (on average per acc.) up CNVs : X% " XXXX (XX%) genes with no variation among 45 accessions 80% non-variable genes 0%
29 q SVs in genes Results T. aestivum (AABBDD) Nanking_NO25 20% 0 20% T. dicoccoides (AABB) acc_ % 0 20%
30 q SVs in genes Methodology Chinese Spring ref genome A B D WGS reads Accession#1 A B D => develop a fine-tuned strategy? in progress
31 q SVs in TEs Methodology TE junction-based approach (PAVs only) +/-75 bp 101 bp reads
32 q SVs in TEs Results B è ~500k loci to study TE-PAVs along chr3b Ø Polymorphic loci among 45 accessions: XX% Ø Average per accession: XX% [XX%.. XX%] 21
33 q SVs in TEs Results acc Nanking_NO25 22
34 q Conclusions Gene PAVs limited (on 3B) CNVs: XX% of the 3B genes (versus ~10% in barley [Munoz-Amatriain et al. 2013] 14 wild+cultiv. genotypes) High level of TE-related SVs Importance of chr. extremities in the diversity of Triticeae (also observed in barley) q Next Validate the approach/thresholds used for CNV calling SVs at the whole genome level ->use 3B-vs-3B results as QC ->increase sample size through exon capture GO term enrichment Relationships betw TE SVs / gene expression Unmapped reads (pangenome)
35 Wheat genome seq initiatives in 2016: - MTPseq 1A, 1B, 6B, 7A, 7B, 7D - IWGSC Whole Genome Assembly (NRGene) - TGAC WGS (several varieties) - U Maryland WGS Pacbio+Ill - UC Davis Ae. tauschii WGS+MTPseq - BGI T. urartu WGS+MTPseq - Wild Emmer Wheat (NRGene)
36 chr-by-chr approach, status in 2015 A ü ü ü ü ü ü B ü D
37 o IWGSC-Whole Genome Assembly Partners: Strategy: N. Stein C. Pozniak WGS Illumina 180x - 3 MP lib J. Poland A. Diestelfeld A. Scharpe G. Ronen Timeline: Aug > start Sept Oct M. Thompson Nov -> Sequencing done K. Eversole, J. Rogers F. Choulet Dec -> Assembly v0.1 QC (M. Mascher, F. Choulet) Jan > Assembly v0.2
38 o IWGSC-Whole Genome Assembly N Jul 2015-Dec T.ur Ae.t CS CS(3B) Synth WEW CS BGI BGI IWGSC GDEC/CNS IPK/JGI NRGene IWGSC T.ura-BGI Ae.ta-BGI CSS 3B-pseudo Syn-JGI WEW-NRGene IWGSC-WGA 64 kb / scaff 58 kb / scaff 2 kb / >1M scaff 892 kb / 296 scaff 21 kb / scaff 7000 kb / 414 scaff 7394 kb / 547 scaff
39 o IWGSC-Whole Genome Assembly QC :: Completeness? exons: 98.7% match with 100%id-100%ov ISBPs (4.2M): 97.7% match with 100%id-100%ov WGPtags-4B (0.9M): 96.2% match with 100%id-100%ov è Completeness+++
40 o IWGSC-Whole Genome Assembly QC :: Chimeras? :-)) :-) :-( alignment to CSS genes and ISBPs alignment to MTPseq (3B, 1B) alignment to genetic map (POPseq, CsRe) alignment to physical map (WGPtags) alignment to HiC map è Chimeric scaffolds found (<200) -> corrected in v0.2/v0.3
41 o IWGSC-Whole Genome Assembly IWGSC-WGA v0.2 metrics: #Scaff 2kb: 37,872 Size: Gb Gaps: 1.8% L50: Mb / 566 scaff L90: Mb / 2,363 scaff max: Mb 21 pseudomolecules constructed with HiC data (IPK) à 14.0 Gb (96%) IWGSC-WGA ordered
42 IWGSC roadmap update A IWGSC-WGA B D sorted chromosomes CSS Physical maps MTPseq
43 q Integration WGA ó MTPseq in progress Strategy based on comparing ISBPs (speed++ specificity++) MTPseq-scaff WGA-scaff
44 207 WGA-scaff joined by 1B-MTP-scaff representing 593 Mb
45 log(n50) 10 Mb 1 Mb T.urartu BAC+WGS Ae.tauschii BAC+WGS WEW-WGS? IWGSC-WGA 3B 100 kb T.urartu WGS Ae.tauschii WGS Kronos Cadenza Ill-Pacbio TGACv1 Synthetic 10 kb CSS 1 kb 5x-bbsrc AA BB DD AABB others AABBDD Chinese Spring
46 Thanks INRA GDEC Etienne Paux Hélène Rimbert Ambre-A. Josselin Romain De Oliveira Jonathan Kitt Benoit Darrier Nicolas Guilhot Philippe Leroy Pierre Sourdille François Balfourier Charles Poncet Josquin Daron Lise Pingault Natasha Glover Sébastien Theil Aurélie Evrard Emeric Dynomant Aurélien Bernard CEA-Génoscope P. Wincker, V. Barbe et al. INRA CNRGV H. Bergès et al. INRA URGI H. Quesneville, M. Alaux et al. IEB J. Dolezel et al. IWGSC K. Eversole, J. Rogers IWGSC-WGA working team IPK, U Sask, KSU, U TelAviv, GIFS, Illumina, NRGene,
47 Frédéric CHOULET
Organization and evolution of transposable elements along the bread wheat chromosome 3B
Daron et al. Genome Biology 2014, 15:546 RESEARCH Open Access Organization and evolution of transposable elements along the bread wheat chromosome 3B Josquin Daron 1,2, Natasha Glover 1,2, Lise Pingault
The IWGSC: Strategies & Activities to Sequence the Bread Wheat Genome Jane Rogers IWGSC Deputy Executive Director
The IWGSC: Strategies & Activities to Sequence the Bread Wheat Genome Jane Rogers IWGSC Deputy Executive Director ACPFG Seminar University of Adelaide 1st May 2014 The International Wheat Genome Sequencing
Utilization of the IWGSC Resources: Application to Wheat Breeding
Utilization of the IWGSC Resources: Application to Wheat Breeding Wheat Breeding: Securing Tomorrow s Profitability. Dr. Curtis J. Pozniak IWGSC Workshop, PAG, Jan 2014 Use and/or distribution of these
Welcome to the Future: Global Wheat Genome Sequencing Efforts
Welcome to the Future: Global Wheat Genome Sequencing Efforts Crop Development Centre Durum Wheat Breeding and Genetics Program Dr. Curtis J. Pozniak Use and/or distribution of these slides is prohibited
The Genome Analysis Centre. Building Excellence in Genomics and Computational Bioscience
Building Excellence in Genomics and Computational Bioscience Wheat genome sequencing: an update from TGAC Sequencing Technology Development now Plant & Microbial Genomics Group Leader Matthew Clark matt.clark@tgac.ac.uk
de novo sequencing of the sunflower genome
de novo sequencing of the sunflower genome Stéphane Muños LIPM INRA Toulouse stephane.munos@toulouse.inra.fr @stephane_munos @SUNRISE_France 39 Sunflower, an important cropfor Europe Million tons of seed
Wheat Chromosome Engineering and Breeding Jianli Chen
Wheat Chromosome Engineering and Breeding Jianli Chen Chromosome Engineering A process to transfer favorable alleles through inter-specific hybridization and interchange of chromatin using aneupolids Aneuploids?
Phenotypic response conferred by the Lr22a leaf rust resistance gene against ten Swiss P. triticina isolates.
Supplementary Figure 1 Phenotypic response conferred by the leaf rust resistance gene against ten Swiss P. triticina isolates. The third leaf of Thatcher (left) and RL6044 (right) is shown ten days after
Integrating and Leveraging Cereal and Grass Genome Resources. David Marshall Information and Computational Sciences Group
Integrating and Leveraging Cereal and Grass Genome Resources David Marshall Information and Computational Sciences Group David.Marshall@hutton.ac.uk What I m going to cover Brief overview of the new barley
Sequencing the genomes of Nicotiana sylvestris and Nicotiana tomentosiformis Nicolas Sierro
Sequencing the genomes of Nicotiana sylvestris and Nicotiana tomentosiformis Nicolas Sierro Philip Morris International R&D, Philip Morris Products S.A., Neuchatel, Switzerland Introduction Nicotiana sylvestris
Genomic resources and gene/qtl discovery in cereals
Genomic resources and gene/qtl discovery in cereals Roberto Tuberosa Dept. of Agroenvironmental Sciences & Technology University of Bologna, Italy The ABDC Congress 1-4 March 2010 Gudalajara, Mexico Outline
Why can GBS be complicated? Tools for filtering, error correction and imputation.
Why can GBS be complicated? Tools for filtering, error correction and imputation. Edward Buckler USDA-ARS Cornell University http://www.maizegenetics.net Many Organisms Are Diverse Humans are at the lower
Toward a better understanding of plant genomes structure: combining NGS and optical mapping technology to improve the sunflower assembly
Toward a better understanding of plant genomes structure: combining NGS and optical mapping technology to improve the sunflower assembly Céline CHANTRY-DARMON 1 CNRGV The French Plant Genomic Center Created
SNP calling and VCF format
SNP calling and VCF format Laurent Falquet, Oct 12 SNP? What is this? A type of genetic variation, among others: Family of Single Nucleotide Aberrations Single Nucleotide Polymorphisms (SNPs) Single Nucleotide
UC Davis UC Davis Previously Published Works
UC Davis UC Davis Previously Published Works Title Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome
A barley root mutant collection for NGS-based fast-forward genetics
A barley root mutant collection for NGS-based fast-forward genetics Roberto Tuberosa Dept. of Agricultural Sciences University of Bologna, Italy 2 nd Plant Genomics Congress Kuala Lumpur, 19-20 March,
Variant Detection in Next Generation Sequencing Data. John Osborne Sept 14, 2012
+ Variant Detection in Next Generation Sequencing Data John Osborne Sept 14, 2012 + Overview My Bias Talk slanted towards analyzing whole genomes using Illumina paired end reads with open source tools
Sequence Assembly and Alignment. Jim Noonan Department of Genetics
Sequence Assembly and Alignment Jim Noonan Department of Genetics james.noonan@yale.edu www.yale.edu/noonanlab The assembly problem >>10 9 sequencing reads 36 bp - 1 kb 3 Gb Outline Basic concepts in genome
Assembly of a Complex Genome: Defining Elements of Structure and Function
Assembly of a Complex Genome: Defining Elements of Structure and Function James Breen A Thesis presented for the degree of Doctor of Philosophy Murdoch University, Western Australia September 2009 1 This
Gap Filling for a Human MHC Haplotype Sequence
American Journal of Life Sciences 2016; 4(6): 146-151 http://www.sciencepublishinggroup.com/j/ajls doi: 10.11648/j.ajls.20160406.12 ISSN: 2328-5702 (Print); ISSN: 2328-5737 (Online) Gap Filling for a Human
Bioinformatics in next generation sequencing projects
Bioinformatics in next generation sequencing projects Rickard Sandberg Assistant Professor Department of Cell and Molecular Biology Karolinska Institutet May 2013 Standard sequence library generation Illumina
Wheat Genomic Resources in a post reference sequence era: a road map to establish priorities, timelines and outcomes
Wheat Genomic Resources in a post reference sequence era: a road map to establish priorities, timelines and outcomes Prospects in Wheat Genomics -- what is needed from a research perspective Rudi Appels,
CS273B: Deep Learning in Genomics and Biomedicine. Recitation 1 30/9/2016
CS273B: Deep Learning in Genomics and Biomedicine. Recitation 1 30/9/2016 Topics Genetic variation Population structure Linkage disequilibrium Natural disease variants Genome Wide Association Studies Gene
Structural variation. Marta Puig Institut de Biotecnologia i Biomedicina Universitat Autònoma de Barcelona
Structural variation Marta Puig Institut de Biotecnologia i Biomedicina Universitat Autònoma de Barcelona Genetic variation How much genetic variation is there between individuals? What type of variants
Modern Epigenomics. Histone Code
Modern Epigenomics Histone Code Ting Wang Department of Genetics Center for Genome Sciences and Systems Biology Washington University Dragon Star 2012 Changchun, China July 2, 2012 DNA methylation + Histone
A near perfect de novo assembly of a eukaryotic genome using sequence reads of greater than 10 kilobases generated by the Pacific Biosciences RS II
A near perfect de novo assembly of a eukaryotic genome using sequence reads of greater than 10 kilobases generated by the Pacific Biosciences RS II W. Richard McCombie Disclosures Introduction to the challenge
Analysis of the expression of homoeologous genes in polyploid cereals using fluorescence cdna-sscp
Analysis of the expression of homoeologous genes in polyploid cereals using fluorescence cdna-sscp De Bustos A., Perez R., Jouve N. in Molina-Cano J.L. (ed.), Christou P. (ed.), Graner A. (ed.), Hammer
Genome Sequencing-- Strategies
Genome Sequencing-- Strategies Bio 4342 Spring 04 What is a genome? A genome can be defined as the entire DNA content of each nucleated cell in an organism Each organism has one or more chromosomes that
Genome Annotation Genome annotation What is the function of each part of the genome? Where are the genes? What is the mrna sequence (transcription, splicing) What is the protein sequence? What does
UK Wheat Productivity Research Targets and Needs. Commercial Wheat Breeding Perspective. Dr. Richard Summers RAGT Seeds
UK Wheat Productivity Research Targets and Needs Commercial Wheat Breeding Perspective Dr. Richard Summers RAGT Seeds UK Wheat Productivity Research Targets and Needs Global population growth Increased
Goat genome assembly, Availability of an international 50K SNP chip and RH panel: an update of the International Goat Genome Consortium projects
Goat genome assembly, Availability of an international 50K SNP chip and RH panel: an update of the International Goat Genome Consortium projects Gwenola Tosser-Klopp on behalf of IGGC Outline IGGC presentation
Lecture 2: Biology Basics Continued
Lecture 2: Biology Basics Continued Central Dogma DNA: The Code of Life The structure and the four genomic letters code for all living organisms Adenine, Guanine, Thymine, and Cytosine which pair A-T and
Mate-pair library data improves genome assembly
De Novo Sequencing on the Ion Torrent PGM APPLICATION NOTE Mate-pair library data improves genome assembly Highly accurate PGM data allows for de Novo Sequencing and Assembly For a draft assembly, generate
Single Nucleotide Variant Analysis. H3ABioNet May 14, 2014
Single Nucleotide Variant Analysis H3ABioNet May 14, 2014 Outline What are SNPs and SNVs? How do we identify them? How do we call them? SAMTools GATK VCF File Format Let s call variants! Single Nucleotide
CHAPTER 14 Genetics and Propagation
CHAPTER 14 Genetics and Propagation BASIC GENETIC CONCEPTS IN PLANT SCIENCE The plants we cultivate for our survival and pleasure all originated from wild plants. However, most of our domesticated plants
Analysis of large deletions in human-chimp genomic alignments. Erika Kvikstad BioInformatics I December 14, 2004
Analysis of large deletions in human-chimp genomic alignments Erika Kvikstad BioInformatics I December 14, 2004 Outline Mutations, mutations, mutations Project overview Strategy: finding, classifying indels
Genome Sequence of Medicago sativa: Cultivated Alfalfa at the Diploid Level (CADL)
Genome Sequence of Medicago sativa: Cultivated Alfalfa at the Diploid Level (CADL) Maria J. Monteros, Joann Mudge, Andrew D. Farmer, Nicholas P. Devitt, Diego A. Fajardo, Thiru Ramaraj, Xinbin Dai, Zhaohong
Molecular marker redundancy check and construction of a high density genetic map of tetraploid cotton. Jean-Marc Lacape
Molecular marker redundancy check and construction of a high density genetic map of tetraploid cotton Jean-Marc Lacape Raleigh ICGI, October 10, 2012 Background ICGI/2008 Anyang Numerous marker projects
Sequence assembly. Jose Blanca COMAV institute bioinf.comav.upv.es
Sequence assembly Jose Blanca COMAV institute bioinf.comav.upv.es Sequencing project Unknown sequence { experimental evidence result read 1 read 4 read 2 read 5 read 3 read 6 read 7 Computational requirements
Variation detection based on second generation sequencing data. Xin LIU Department of Science and Technology, BGI
Variation detection based on second generation sequencing data Xin LIU Department of Science and Technology, BGI liuxin@genomics.org.cn 2013.11.21 Outline Summary of sequencing techniques Data quality
BMC Genomics. Sample. doi: /s
BMC Genomics This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Homologues of potato chromosome
Welcome to the NGS webinar series
Welcome to the NGS webinar series Webinar 1 NGS: Introduction to technology, and applications NGS Technology Webinar 2 Targeted NGS for Cancer Research NGS in cancer Webinar 3 NGS: Data analysis for genetic
Wide Hybridization in Plant Breeding
Wide Hybridization in Plant Breeding Wide hybridization - a cross of two individuals belonging to different species (also called interspecific hybridization) - Such a cross can be (rarely) realized in
Unit 1: DNA and the Genome Sub-topic 6: Mutation
Unit 1: DNA and the Genome Sub-topic 6: Mutation Page 1 of 24 On completion of this topic I will be able to state that: mutations are random changes in the genome, causing no protein or an altered protein
A tutorial introduction into the MIPS PlantsDB barley&wheat databases. Manuel Spannagl&Kai Bader transplant user training Poznan June 2013
A tutorial introduction into the MIPS PlantsDB barley&wheat databases Manuel Spannagl&Kai Bader transplant user training Poznan June 2013 MIPS PlantsDB tutorial - some exercises Please go to: http://mips.helmholtz-muenchen.de/plant/genomes.jsp
Title: High-quality genome assembly of channel catfish, Ictalurus punctatus
Author s response to reviews Title: High-quality genome assembly of channel catfish, Ictalurus punctatus Authors: Qiong Shi (shiqiong@genomics.cn) Xiaohui Chen (xhchenffri@hotmail.com) Liqiang Zhong (lqzhongffri@hotmail.com)
Next-Generation Sequencing. Technologies
Next-Generation Next-Generation Sequencing Technologies Sequencing Technologies Nicholas E. Navin, Ph.D. MD Anderson Cancer Center Dept. Genetics Dept. Bioinformatics Introduction to Bioinformatics GS011062
The impact of Ty3-gypsy group LTR retrotransposons Fatima on B-genome specificity of polyploid wheats
BMC Plant Biology This Provisional PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. The impact of Ty3-gypsy
Heritable Epigenetic Variation among Maize Inbreds
Heritable Epigenetic Variation among Maize Inbreds Steve R. Eichten 1., Ruth A. Swanson-Wagner 1., James C. Schnable 2, Amanda J. Waters 1, Peter J. Hermanson 1, Sanzhen Liu 3, Cheng-Ting Yeh 3, Yi Jia
Overview of Human Genetics
Overview of Human Genetics 1 Structure and function of nucleic acids. 2 Structure and composition of the human genome. 3 Mendelian genetics. Lander et al. (Nature, 2001) MAT 394 (ASU) Human Genetics Spring
Linking Genetic Variation to Important Phenotypes
Linking Genetic Variation to Important Phenotypes BMI/CS 776 www.biostat.wisc.edu/bmi776/ Spring 2018 Anthony Gitter gitter@biostat.wisc.edu These slides, excluding third-party material, are licensed under
BST227 Introduction to Statistical Genetics
Introduction to Statistical Genetics BIO 227 Lecture 1 Introduction and Overview of Genetic http BST227 Introduction to Statistical Genetics Lecture 1: Introduction and Overview of Genetic Disease http://aryeelab.org/bst227
Next-Generation Sequencing Services à la carte
Next-Generation Sequencing Services à la carte www.seqme.eu ngs@seqme.eu SEQme 2017 All rights reserved The trademarks and names of other companies and products mentioned in this brochure are the property
BENG 183 Trey Ideker. Genome Assembly and Physical Mapping
BENG 183 Trey Ideker Genome Assembly and Physical Mapping Reasons for sequencing Complete genome sequencing!!! Resequencing (Confirmatory) E.g., short regions containing single nucleotide polymorphisms
What is genetic variation?
enetic Variation Applied Computational enomics, Lecture 05 https://github.com/quinlan-lab/applied-computational-genomics Aaron Quinlan Departments of Human enetics and Biomedical Informatics USTAR Center
Ecole de Bioinforma(que AVIESAN Roscoff 2014 GALAXY INITIATION. A. Lermine U900 Ins(tut Curie, INSERM, Mines ParisTech
GALAXY INITIATION A. Lermine U900 Ins(tut Curie, INSERM, Mines ParisTech How does Next- Gen sequencing work? DNA fragmentation Size selection and clonal amplification Massive parallel sequencing ACCGTTTGCCG
Genome Annotation. What Does Annotation Describe??? Genome duplications Genes Mobile genetic elements Small repeats Genetic diversity
Genome Annotation Genome Sequencing Costliest aspect of sequencing the genome o But Devoid of content Genome must be annotated o Annotation definition Analyzing the raw sequence of a genome and describing
De novo Genome Assembly
De novo Genome Assembly A/Prof Torsten Seemann Winter School in Mathematical & Computational Biology - Brisbane, AU - 3 July 2017 Introduction The human genome has 47 pieces MT (or XY) The shortest piece
MHC Region. MHC expression: Class I: All nucleated cells and platelets Class II: Antigen presenting cells
DNA based HLA typing methods By: Yadollah Shakiba, MD, PhD MHC Region MHC expression: Class I: All nucleated cells and platelets Class II: Antigen presenting cells Nomenclature of HLA Alleles Assigned
Surely Better Target Enrichment from Sample to Sequencer and Analysis
sureselect TARGET ENRIChment solutions Surely Better Target Enrichment from Sample to Sequencer and Analysis Agilent s market leading SureSelect platform provides a complete portfolio of catalog to custom
Molecular Basis of Evolutionary Events That Shaped the Hardness Locus in Diploid and Polyploid Wheat Species (Triticum and Aegilops) W
The Plant Cell, Vol. 17, 1033 1045, April 2005, www.plantcell.org ª 2005 American Society of Plant Biologists RESEARCH ARTICLES Molecular Basis of Evolutionary Events That Shaped the Hardness Locus in
The Agilent Technologies SureSelect Platform for Target Enrichment
The Agilent Technologies SureSelect Platform for Target Enrichment Focus your next-gen sequencing on DNA that matters Kimberly Troutman Field Applications Scientist January 27 th, 2011 Agenda 1 Introduction:
A Genomics (R)evolution: Harnessing the Power of Single Cells
A Genomics (R)evolution: Harnessing the Power of Single Cells Fundamental Question #1 If Transcriptional Heterogeneity ( Noise ) is so great in single cells What s the Point? Single Cells = True Biology
Improving yield and quality traits of durum wheat by introgressing chromosome segments from hexaploid wheat
Improving yield and quality traits of durum wheat by introgressing chromosome segments from hexaploid wheat J. Ma 1,3 *, C.Y. Zhang 2 *, G.J. Yan 2,3 and C.J. Liu 1,2,3 1 Plant Industry, CSIRO, Brisbane,
Genomics and Transcriptomics of Spirodela polyrhiza
Genomics and Transcriptomics of Spirodela polyrhiza Doug Bryant Bioinformatics Core Facility & Todd Mockler Group, Donald Danforth Plant Science Center Desired Outcomes High-quality genomic reference sequence
Targeted Sequencing Reveals Large-Scale Sequence Polymorphism in Maize Candidate Genes for Biomass Production and Composition
RESEARCH ARTICLE Targeted Sequencing Reveals Large-Scale Sequence Polymorphism in Maize Candidate Genes for Biomass Production and Composition Moses M. Muraya 1,2, Thomas Schmutzer 1 *, Chris Ulpinnis
Genome research in eukaryotes
Functional Genomics Genome and EST sequencing can tell us how many POTENTIAL genes are present in the genome Proteomics can tell us about proteins and their interactions The goal of functional genomics
3I03 - Eukaryotic Genetics Repetitive DNA
Repetitive DNA Satellite DNA Minisatellite DNA Microsatellite DNA Transposable elements LINES, SINES and other retrosequences High copy number genes (e.g. ribosomal genes, histone genes) Multifamily member
Oat Genomics at IBERS
Oat Genomics at IBERS Minor crop major genome 17Gb 2n=6x 5.1Gb 2n=2x 13Gb 2n=6x 2n=42 3.3Gb 0.43Gb Major genome minor budget >$100M
Association Mapping in Wheat: Issues and Trends
Association Mapping in Wheat: Issues and Trends Dr. Pawan L. Kulwal Mahatma Phule Agricultural University, Rahuri-413 722 (MS), India Contents Status of AM studies in wheat Comparison with other important
LECTURE 12: INSIGHTS FROM GENOME SEQUENCING
LECTURE 12: INSIGHTS FROM GENOME SEQUENCING Read Chapter 10 (p366-375) DOE s Genomics and its implications (link at course website) STS (p359), SNP, SSR (integrates the following) Linkage, Physical, Sequence
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION doi:10.1038/nature11650 1. Sequence Analysis 1.1 Plant Material The Triticum aestivum landrace Chinese Spring was selected for sequencing as it is widely used for cytogenetic
Multi-omics in biology: integration of omics techniques
31/07/17 Летняя школа по биоинформатике 2017 Multi-omics in biology: integration of omics techniques Konstantin Okonechnikov Division of Pediatric Neurooncology German Cancer Research Center (DKFZ) 2 Short
Ensembl: A Genomic Toolset for pigs, poultry, plants, pests, pathogens and pollinators. Paul Kersey
Ensembl: A Genomic Toolset for pigs, poultry, plants, pests, pathogens and pollinators Paul Kersey A brief history of genome sequencing 1995 Haemophilus influenzae 1.8 Mb 1996 Saccharomyces cerevisiae
B&DA Committee Bioinformatics and Data Analysis. PAG January 2016
B&DA Committee Bioinformatics and Data Analysis PAG January 2016 B&DA progress so far Aim: to define standard bfx pipelines for FAANG data Group has skyped many times We have a Wiki: hosted by EBI Sub-groups
About Strand NGS. Strand Genomics, Inc All rights reserved.
About Strand NGS Strand NGS-formerly known as Avadis NGS, is an integrated platform that provides analysis, management and visualization tools for next-generation sequencing data. It supports extensive
De novo whole genome assembly
De novo whole genome assembly Lecture 1 Qi Sun Bioinformatics Facility Cornell University Data generation Sequencing Platforms Short reads: Illumina Long reads: PacBio; Oxford Nanopore Contiging/Scaffolding
CHAPTER 21 LECTURE SLIDES
CHAPTER 21 LECTURE SLIDES Prepared by Brenda Leady University of Toledo To run the animations you must be in Slideshow View. Use the buttons on the animation to play, pause, and turn audio/text on or off.
High-Resolution Oligonucleotide- Based acgh Analysis of Single Cells in Under 24 Hours
High-Resolution Oligonucleotide- Based acgh Analysis of Single Cells in Under 24 Hours Application Note Authors Paula Costa and Anniek De Witte Agilent Technologies, Inc. Santa Clara, CA USA Abstract As
3. human genomics clone genes associated with genetic disorders. 4. many projects generate ordered clones that cover genome
Lectures 30 and 31 Genome analysis I. Genome analysis A. two general areas 1. structural 2. functional B. genome projects a status report 1. 1 st sequenced: several viral genomes 2. mitochondria and chloroplasts
Reference genomes and common file formats
Reference genomes and common file formats Overview Reference genomes and GRC Fasta and FastQ (unaligned sequences) SAM/BAM (aligned sequences) Summarized genomic features BED (genomic intervals) GFF/GTF
RNA-Seq Software, Tools, and Workflows
RNA-Seq Software, Tools, and Workflows Monica Britton, Ph.D. Sr. Bioinformatics Analyst September 1, 2016 Some mrna-seq Applications Differential gene expression analysis Transcriptional profiling Assumption:
Genomics AGRY Michael Gribskov Hock 331
Genomics AGRY 60000 Michael Gribskov gribskov@purdue.edu Hock 331 Computing Essentials Resources In this course we will assemble and annotate both genomic and transcriptomic sequence assemblies We will
Contact us for more information and a quotation
GenePool Information Sheet #1 Installed Sequencing Technologies in the GenePool The GenePool offers sequencing service on three platforms: Sanger (dideoxy) sequencing on ABI 3730 instruments Illumina SOLEXA
Incorporating Molecular ID Technology. Accel-NGS 2S MID Indexing Kits
Incorporating Molecular ID Technology Accel-NGS 2S MID Indexing Kits Molecular Identifiers (MIDs) MIDs are indices used to label unique library molecules MIDs can assess duplicate molecules in sequencing
Mutations during meiosis and germ line division lead to genetic variation between individuals
Mutations during meiosis and germ line division lead to genetic variation between individuals Types of mutations: point mutations indels (insertion/deletion) copy number variation structural rearrangements
Einführung in die Genetik
Einführung in die Genetik Prof. Dr. Kay Schneitz (EBio Pflanzen) http://plantdev.bio.wzw.tum.de schneitz@wzw.tum.de Prof. Dr. Claus Schwechheimer (PlaSysBiol) http://wzw.tum.de/sysbiol claus.schwechheimer@wzw.tum.de
RNA Sequencing Analyses & Mapping Uncertainty
RNA Sequencing Analyses & Mapping Uncertainty Adam McDermaid 1/26 RNA-seq Pipelines Collection of tools for analyzing raw RNA-seq data Tier 1 Quality Check Data Trimming Tier 2 Read Alignment Assembly
Cancer Genetics Solutions
Cancer Genetics Solutions Cancer Genetics Solutions Pushing the Boundaries in Cancer Genetics Cancer is a formidable foe that presents significant challenges. The complexity of this disease can be daunting
Nature Biotechnology: doi: /nbt Supplementary Figure 1. Number and length distributions of the inferred fosmids.
Supplementary Figure 1 Number and length distributions of the inferred fosmids. Fosmid were inferred by mapping each pool s sequence reads to hg19. We retained only those reads that mapped to within a
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Supplementary Material
Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions Joshua N. Burton 1, Andrew Adey 1, Rupali P. Patwardhan 1, Ruolan Qiu 1, Jacob O. Kitzman 1, Jay Shendure 1 1 Department
DISSECTING THE EVOLUTIONARY FORCES SHAPING SEX CHROMOSOME EVOLUTION IN PAPAYA ROBERT VANBUREN DISSERTATION
DISSECTING THE EVOLUTIONARY FORCES SHAPING SEX CHROMOSOME EVOLUTION IN PAPAYA BY ROBERT VANBUREN DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy
Basic Concepts of Human Genetics
Basic oncepts of Human enetics The genetic information of an individual is contained in 23 pairs of chromosomes. Every human cell contains the 23 pair of chromosomes. ne pair is called sex chromosomes
Physical Mapping and Shotgun Sequencing of Wheat Chromosome 2A
Physical Mapping and Shotgun Sequencing of Wheat Chromosome 2A Kuldeep Singh, Punjab Agril. Univ. Ludhiana India IWGSC, Sept 7 2013 Yokohama Japan Team India Punjab Agricultural University, Ludhiana (Kuldeep
Introduction to Bioinformatics
Introduction to Bioinformatics Richard Corbett Canada s Michael Smith Genome Sciences Centre Vancouver, British Columbia June 28, 2017 Our mandate is to advance knowledge about cancer and other diseases
Outline. General principles of clonal sequencing Analysis principles Applications CNV analysis Genome architecture
The use of new sequencing technologies for genome analysis Chris Mattocks National Genetics Reference Laboratory (Wessex) NGRL (Wessex) 2008 Outline General principles of clonal sequencing Analysis principles
Progress in genomics applications in investigating abiotic stresses influencing perennial forage and biomass grasses
Progress in genomics applications in investigating abiotic stresses influencing perennial forage and biomass grasses Dr. Susanne Barth Teagasc Crops Research Centre Oak Park Carlow Irland Global challenges
Ensembl Tools. EBI is an Outstation of the European Molecular Biology Laboratory.
Ensembl Tools EBI is an Outstation of the European Molecular Biology Laboratory. Questions? We ve muted all the mics Ask questions in the Chat box in the webinar interface I will check the Chat box periodically
Read Mapping and Variant Calling. Johannes Starlinger
Read Mapping and Variant Calling Johannes Starlinger Application Scenario: Personalized Cancer Therapy Different mutations require different therapy Collins, Meredith A., and Marina Pasca di Magliano.