The Role of Fluorescence in situ hybridization (FISH)

Slides:

Advertisements

Similar presentations

The Build-up of the Red Sequence at z

Advertisements

The Role of Fluorescence in situ hybridization (FISH) in Sequencing the Tomato Genome.

Progress on the sequencing of the euchromatic gene rich space of chromosome 6 of Solanum lycopersicum cv. Heinz 1706 Sander Peters Cologne Oct 2008.

US Tomato sequencing project update January 14, 2007.

9 Genomics and Beyond Brief Chapter Outline

Fluorescence in situ Hybridization

Automatic Analysis of BrdU Incorporation for Replication Timing Assays Intern: Albert F. Cervantes Advisors: York Marahrens Moira Regelson Silvia Diaz-Perez.

Sequencing Tomato Chr9 Tomato Sequencing Meeting PAG XV 2007 San Diego, 14 January 2007 Antonio Granell IBMCP, Valencia.

Expanding the Tool Kit for BAC Extension Summary of completion criteria developed for NSF Tomato Sequencing Workshop January 14, 2007.

Use of FISH in sequencing tomato chromosome 6 René Klein Lankhorst Hans de Jong Korea meeting 2007.

Genome sequencing. Vocabulary Bac: Bacterial Artificial Chromosome: cloning vector for yeast Pac, cosmid, fosmid, plasmid: cloning vectors for E. coli.

EU-SOL 2008 November 13-16, Toulouse, FRANCE CHROMOSOME 7 SEQUENCING Current status and perspective TG216 TG438 T1112 T1355 T1328 T1428 T1962 T1414 T1497.

Presentation on genome sequencing. Genome: the complete set of gene of an organism Genome annotation: the process by which the genes, control sequences.

SOL Genomics Network Formed in 2003 to answer two questions: – How can a common set of genes give rise to such a wide range of morphologically and ecologically.

PHYSICAL MAPPING AND POSITIONAL CLONING. Linkage mapping – Flanking markers identified – 1cM, for example Probably ~ 1 MB or more in humans Need very.

Chromosome 8 Sequencing: Current Status and Future Prospects toward Finishing Shusei Sato, Erika Asamizu, Takakazu Kaneko, Hiroyuki Fukuoka, Satoshi Tabata.

Update tomato chr. 6 Roeland van Ham Centre for BioSystems Genomics The Netherlands.

SOL 2008 October 12-16, Cologne, Germany CHROMOSOME 7 THE FRENCH CONTRIBUTION TG216 TG438 T1112 T1355 T1328 T1428 T1962 T1414 T1497 T0676 TM18 CT54 T0966.

Tomato Overgo Project and Seed BAC Selection Cornell Team Ying Eileen Wang, 2005 PAG.

BrGSP: the Brassica 'A' genome sequencing project Genetic map anchoring of sequenced BACs (Dec 2008) A01 JWF3 A01 VCS3MDH.

These images illustrate results of in situ hybridization with eight tomato BACs. Putative locations for the BACs are included in the captions. All of these.

Chapter 11: An Introduction to Human Genome.  A linear polynucleotide consisting of four types of monomeric nucleotides  Each nucleotide contains: 

©2000 Timothy G. Standish John 15:4 4Abide in me, and I in you. As the branch cannot bear fruit of itself, except it abide in the vine; no more can ye,

Copyright © 2009 Pearson Education, Inc. Art and Photos in PowerPoint ® Concepts of Genetics Ninth Edition Klug, Cummings, Spencer, Palladino Chapter 12.

Solanum lycopersicum Chromosome 4 Sequencing Update UK-SOL– Dec 2008 Wellcome Trust Medical Photographic Library.

Current Sequencing Status of Tomato Chromosome 2 PLANT GENOME RESEARCH CENTER, KRIBB, KOREA Sanghyeob Lee Sung-Hwan Jo Dal-Hoe Koo Chul-Goo Hur Hong-Seok.

4th Solanaceae Genome Workshop 2007, September 09th- 13th, Jeju Island, Korea THE FRENCH CONTRIBUTION TO THE INTERNATIONAL TOMATO GENOME SEQUENCING PROGRAM.

FINISHING WORKSHOP APRIL 2008 CHROMOSOME 7 THE FRENCH CONTRIBUTION TG216 TG438 T1112 T1355 T1328 T1428 T1962 T1414 T1497 T0676 TM18 CT54 T0966 T0731 TM15.

Chromosomes and chromatin

Restriction Fragments and Mapping Restriction Fragment Analysis – System used to compare the genes and DNA sequences between individuals in a population.

Chromosome 2 Doil Choi, Sunghwan Jo KOREA. Cytological architecture of chromosome kb/µm DAPI (4’-6-diamidino-2-phenylindole) stained pachytene chromosome.

Progress tomato chromosome 6 René Klein Lankhorst.

INDIAN INITIATIVE FOR TOMATO GENOME SEQUENCING Nagendra Singh National Research Centre on Plant Biotechnology Indian Agricultural Research Institute New.

HeterochromatinEuchromatin Relative chromosome length Relative bivalent diameter X 1.23 X 1.00 Relative area Relative optical density.

Solanum lycopersicum Chromosome 4 Mapping and Finishing Update SRC-UK and Wellcome Trust Sanger Institute SOL Korea – September 2007 Wellcome Trust Medical.

Lindsay A. Shearer1, Lorinda K

16 th April 2007 Christine Nicholson, Mapping Core Group Wellcome Trust Sanger Institute Tomato Chromosome 4 Mapping & Use of FPC Copyright Wellcome Trust.

US Contribution to the International Tomato Genome Sequencing Effort Current structure of contributions Ongoing activity summary Funding issues.

Karyotype Lab. Homologous pairs Sex linked inheritance Karyotype--A key to the study of Sex Linked Inheritance Karyotype--A key to the study of Sex Linked.

Physical Mapping of the ASGR-Carrier Chromosome Reveals Collinearity to Chromosome 2 of Sorghum and Foxtail Millet Outside the ASGR Sirjan K. Sapkota,

Restriction Fragments and Mapping

BrGSP: the Brassica 'A' genome sequencing project

Tomato Sequencing Project Meeting at SOL 2008, Oct. 15, 2008

Fig. 1. Genomic analysis. (A) Array CGH analysis of chromosome 12 performed on DNA from blood lymphocytes. Log 2 ratio data are presented according to.

Fluorescence in situ hybridization (FISH). Figs

Olympic medal count (top 15 countries) (rank by Gold)

The Most Visited Countries

DNA Organization in Chromosomes

BAC-Based Physical Map of the Rice Genome.

Genome structures.

Plant & Animal Genome Conference

Development of genome sequencing infrastructure and progress toward sequencing of chromosomes 1, 10 and 11 Steve Tanksley, Cornell U Steve Stack, Colorado.

Sequencing Chromosome 2

GDP (Nominal, in trillions) 2017 World Bank

Status of the US contribution to the international

Clustered 11q23 and 22q11 Breakpoints and 3:1 Meiotic Malsegregation in Multiple Unrelated t(11;22) Families Tamim H. Shaikh, Marcia L. Budarf, Livija.

TG216 TG438 T1112 T1355 T1328 T1428 T1962 T1414 T1497 T0676 TM18 CT54 T0966 T0731 TM15 T1347 T1257 T0848 THE FRENCH CONTRIBUTION TO THE INTERNATIONAL.

Sequencing update of tomato chromosome 3 Chinese Academy of Sciences

Volume 53, Issue 6, Pages (March 2014)

Volume 138, Issue 5, Pages (September 2009)

Integrated Cytogenetic Map of Chromosome Arm 4S of A. thaliana

1 Point! 2 Points! 3 Points! 4 Points! 5 Points!!

Tomato FISH Song-Bin Chang Suzanne Royer Lorrie Anderson Steve Stack.

Volume 1, Issue 5, Pages (September 2008)

Kami Ahmad, Steven Henikoff Molecular Cell

Physical mapping Physical localisation on a chromosome

Linkage, crossing over and chromosomal mapping (2).

2006 Rank Adjusted for Purchasing Power

ALK Gene Rearrangements: A New Therapeutic Target in a Molecularly Defined Subset of Non-small Cell Lung Cancer Benjamin Solomon, MBBS, PhD, Marileila.

Presentation transcript:

The Role of Fluorescence in situ hybridization (FISH) in Sequencing the Tomato Genome

77% of the DNA is in heterochromatin 23% of the DNA is in euchromatin

1 10 11 12 9 6 2 3 4 7 5 8 India Japan Spain Italy USA China UK Korea euchromatin heterochromatin AT-rich satellite DNA 1 10 11 12 9 USA China UK Korea France 6 2 3 4 7 The Netherlands 5 8

Mitotic Meiotic DAPI Phase contrast

Hybridization mixture 50-100-fold excess of unlabeled tomato Cot 100 DNA Chromosomal in situ Suppression (CISS) Hybridization

Functions of FISH in Sequencing the Tomato Genome 1. To determine the locations of anchor BACs 2. To determine distances in Mb 3. To define eu-/heterochromatin borders 4. To demonstrate the order of nearby BACs 5. To locate problem BACs and contigs

BAC 116C14, Slide 126, Chromosome 9, Short (p) Arm Spread number % arm length from centromere 126-06 86.2 126-28 81.9 126-29 82.3 126.30 84.3 126.32 85.8 126.33 85.2 126.34 83.9 126.37 87.6 126.38 87.2 Mean 84.9 Std. Dev. 2.0

Functions of FISH in Sequencing the Tomato Genome 1. To determine the locations of anchor BACs 2. To determine distances in Mb 3. To define eu-/heterochromatin borders 4. To demonstrate the order of nearby BACs 5. To locate problem BACs and contigs

Functions of FISH in Sequencing the Tomato Genome 1. To determine the locations of anchor BACs 2. To determine distances in Mb 3. To define eu-/heterochromatin borders 4. To demonstrate the order of nearby BACs 5. To locate problem BACs and contigs

Functions of FISH in Sequencing the Tomato Genome 1. To determine the locations of anchor BACs 2. To determine distances in Mb 3. To define eu-/heterochromatin borders 4. To demonstrate the order of nearby BACs 5. To locate problem BACs and contigs

Functions of FISH in Sequencing the Tomato Genome 1. To determine the locations of anchor BACs 2. To determine distances in Mb 3. To define eu-/heterochromatin borders 4. To demonstrate the order of nearby BACs 5. To locate problem BACs and contigs

234 Total BACs FISHED to date 70 failed to localize (30%) no FISH signal or multiple signals (in spite of CISS) 164 successfully localized (70%) 24 FISHed to wrong chromosomes Of these 24,11 were checked by sequencing. 7 were overgo false positives 1 was due to a picking error 1 was due to a typographical error 2 were due to mapping errors (< 3% of EXPEN 2000 map) 140 FISHed to correct chromosome

Chromosome 11 green BAC 052K14, red BAC 128G07

Chromosome 11 green BAC 052K14, red BAC 128G07

Chromosome 11 green BAC 052K14, red BAC 128G07

Chromosome 11 green BAC 052K14, red BAC 128G07

Chromosome 11 green BAC 052K14, red BAC 128G07