Information System for Information System for Comparative Analysis of Legume Comparative Analysis of Legume

GenomesGenomes Anita Dalwani

Advisors: Dr. Roger Innes,

Dr. Haixu Tang

LAYOUTLAYOUT

• Motivation• Participants• Background• Design• Results/Demo• Future Work

Motivation?Motivation?

MotivationMotivation• Goal of legume genome project

- Investigate the process of genome restructuring following polyploidization in plants (soybean and its relatives in the Glycine genus)

- Try answering questions like :

- Genome evolution on both short(<100,000yrs) and long (>50 million yrs) time scale

- Evolution of disease resistance (R) genes.

MotivationMotivation

• To answer these questions:

- 1 Mbp syntenic genomic regions from six taxa as well as their duplicated regions in the polyploidy members (12 such regions in total) will be sequenced and analyzed.

- These regions contain several important disease resistance (R) genes.

MotivationMotivation

Plant species and accession No. of regions to be analysed

Whole

Genome size (megabases)

G. max cultivar Williams 82 2 1103

G. max PI 96983 2 1103

G. tomentella G1188 (2n=80) 4 2083

G. tomentella race D3 (2n-40) 2 1103

Teramnus labialus 1 < 700

Medicago truncatula 1 466

MotivationMotivation

• Information System

- central repository for the data

- stores and retrieves updated information

- bioinformatics and visualization tools

ParticipantsParticipants

Participants University Roles

Roger Innes

Tom Ashfield

Anita Dalwani

Murali Mohan

Innes Lab

Indiana University, Bloomington.

Principal Investigator

R gene evolution

Database development, Web application.

Database development.

Nevin Young

Steve Cannon

Roxanne Denny

Young Lab,

University of Minnesota

Co-PI

phylogenetic; R genes; comparative genomics.

Lab Manager

Jeff Doyle

Bernard Pfeil

Doyle Lab

Cornell University

Co-PI

phylogenetic and polyploidy

Bruce Roe

Majesta Siegfried

Roe Lab,

Oklahoma University

Co-PI

Bac sequencing

Saghai Maroof

Milind Ratnaparkhe

Jafar Mammado

Maroof Lab,

Virginia Tech

Co-PI

R genes; comparative genomics

R genes; comparative genomics

BackgroundBackground• Procedure

1. Create and make available Bacterial Artificial Chromosome (BAC) libraries of each species.

Indexing available BAC, BAC end sequences, library, probes, vector, gel images

BackgroundBackground

2. Assemble syntenic BAC contigs from each library

i. Strategically chosen soybean clones are used as probes

Probe 53 - ACCCGT

Probe 21 - AATTC

Probe 9 - GTACTT

Probe 26 - AAACT

Probe 1 - CCCC

Probe 3 - AATC

ACCCGT AATTC GTACTT AAACT CCCC AATC

ii. Individual probes are hybridized to high-density BAC filters representing all the target genomes

BackgroundBackground

BackgroundBackground

iii. Integrity of contigs is confirmed by fingerprinting

iv. Set of clones that hybridize to two or more probes are selected

v. BACs representing the tentative minimum tiling path will be end sequenced

Probe53 Probe21 Probe9 Probe26 Probe1 Probe3

Bac1

Bac2 Bac2

Bac3

Bac4Bac4

Bac5

Bac6

Bac7

Bac8Bac8

Probe53 Probe21 Probe9 Probe26 Probe1 Probe3

Bac2 Bac2

Bac3

Bac4Bac4

Bac8Bac8

ACCCGT AATTC GTACTT AAACT CCCC AATC

ACCCGT AAATC

CTTCTT

CCGCAATCT

AATCCCCC

BackgroundBackground

3. DNA sequencing, Assembly , Annotation

4. Compare the content, order and sequence of gene

5. Results available for public

Importance Importance

• Information System- Centrally available data

- User-friendly interface for retrieving the information

- Updated progress information

- Tools for interpreting the results.

Works as an Laboratory Management Information System

DesignDesign

• Steps for designing the Information System.

1. Design the Database

- Data: BAC, BES, Probes, Libraries, vector, library screen hits etc.

DesignDesign

- Visualize the relationship between these large amount of data.

For example, Library table stores detailed information about

each library used rather than having each BAC storing the library information

DesignDesign

- Created tables based on these relationship

Main tables used in the database are:

BAC BES GEL IMAGES GENOMIC SOUTHERNS GENOTYPE LIBRARY LIBRARY SCREENS LIBRARY SCREEN HITS PRIMER PROBE PROBE WITHIN BACS VECTOR

DesignDesign

B A C

P R O B E

L IB R A R Y

H a s

H a s

B E S

H a sP R IM E R

H a s

is a

D e r i ve dfr o m

is a

DesignDesignL ib raryS creen

L ib raryS creen h its

H a s

DesignDesign

2. Populate the database with initial set of data

- Initial set of data was stored in form of MS- Excel.

- Perl script for parsing information.

DesignDesign

• Web Database Application- understanding the needs for the project - Web database interface - displays information about the

project- add and update interface- tools for analyses

DesignDesign

• For determining the tiling path

- Designing a Visualization tool

- displays the locations of the clones with respect to probes

- Probes are strategically chosen from soybean genomes

DesignDesign

- Input : library name

- subset of probes with at least one hit with the library are selected

- BAC clones for the library are generated which have hits with probes

- Probes are arranged in order of their position

- BACs are mapped to these probes.

DesignDesign

• System Specifications

- Database: Oracle 9i

- Languages: PHP, Perl, HTML, JavaScript

- Web Server: Apache 1.3.29

- Platform: Unix (SunOS 5.9)

ResultsResults

Future WorkFuture Work

• Comparative physical Mapping

• Bioinformatics tools

• Public interface

AcknowledgementsAcknowledgements

• Dr. Roger Innes

• Dr. Haixu Tang

• Dr. Sun Kim

• Legume genome project team

ReferencesReferences

• Innes, Roger W. Comparative Analysis of Legume Genome Evolution, Proposal submitted to National Science Foundation.

• Tang, Haixu. Comparative physical mapping: ordering clones by cross species hybridization Dec 2004.

• www.bio.indiana.edu/~nsflegume