IWGSC sequence repository : how to facilitate pseudomolecule assembly?

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HAL Id: hal-02741662

https://hal.inrae.fr/hal-02741662

Submitted on 3 Jun 2020

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IWGSC sequence repository : how to facilitate

pseudomolecule assembly?

Michael Alaux, Frédéric Choulet, Loïc Couderc, Françoise Alfama-Depauw,

Veronique Jamilloux, Thomas Letellier, Raphaël-Gauthier Flores, Claire

Guerche, Mikaël Loaec, Etienne Paux, et al.

To cite this version:

Michael Alaux, Frédéric Choulet, Loïc Couderc, Françoise Alfama-Depauw, Veronique Jamilloux, et

al.. IWGSC sequence repository : how to facilitate pseudomolecule assembly?. PAG XXIII - Plant

and Animal Genome Conference, Jan 2015, San Diego, United States. �hal-02741662�

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Michael Alaux

IWGSC Sequence Repository:

How to facilitate pseudomolecule assembly ?

Michael Alaux

IWGSC S&P, San Diego, 13 January 2015

Michael Alaux

Wheat@URGI website

Michael Alaux

Wheat@URGI

http://wheat-urgi.versailles.inra.fr

Michael Alaux

Wheat@URGI

http://wheat-urgi.versailles.inra.fr Google-like

Quick Links to data Intermine

Look at Wheat3BMine (Letellier et al.) - computer demo 3 session, January

the 13th at 11AM - poster P0654 Search wheat data into GnpIS

Michael Alaux http://wheat-urgi.versailles.inra.fr

Wheat@URGI

Michael Alaux http://wheat-urgi.versailles.inra.fr

Wheat@URGI

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Michael Alaux

Wheat@URGI

http://wheat-urgi.versailles.inra.fr http://wheat-urgi.versailles.inra.fr Michael Alaux

Wheat@URGI

Michael Alaux

Sequence Repository

Michael Alaux

http://wheat-urgi.versailles.inra.fr/Seq-Repository

Sequence Repository

Click on a chromosome to access the

survey sequence chromosome arm

assembly for:

BLAST (

Public

)

Download (

Public

)

Browsers:



Physical maps



Annotated reference sequence

3B (Public)



Annotated survey sequence

(Public)

Michael Alaux

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http://wheat-urgi.versailles.inra.fr/Seq-Repository

Sequence Repository

Michael Alaux

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Sequence Repository

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Michael Alaux

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Sequence Repository

Michael Alaux

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Sequence Repository

Michael Alaux

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Sequence Repository

Michael Alaux

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Sequence Repository

Michael Alaux

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Sequence Repository

Michael Alaux

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Sequence Repository

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Michael Alaux

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Sequence Repository

Michael Alaux

Sequence Repository: 3B example

Michael Alaux

BLAST

Michael Alaux

BLAST

https://urgi.versailles.inra.fr/blast/

• Public BLAST

https://urgi.versailles.inra.fr/blast/

• More than 250 000 BLAST searches the past 2 years !

Michael Alaux

BLAST

https://urgi.versailles.inra.fr/blast/ Michael Alaux

BLAST

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Michael Alaux

BLAST

https://urgi.versailles.inra.fr/blast/ Michael Alaux

Physical maps

Michael Alaux

Physical maps

https://urgi.versailles.inra.fr/gb2/gbrowse/wheat_phys_pub/ Michael Alaux

Physical contig Deletion bin BACs Markers

Physical maps

https://urgi.versailles.inra.fr/gb2/gbrowse/wheat_phys_pub/ Michael Alaux https://urgi.versailles.inra.fr/gb2/gbrowse/wheat_phys_pub/

Physical maps

Michael Alaux type genetic maps chr cM. QTL Primers MetaQTL

Physical maps

https://urgi.versailles.inra.fr/gb2/gbrowse/wheat_phys_pub/

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Michael Alaux

Physical maps

https://urgi.versailles.inra.fr/gb2/gbrowse/wheat_phys_pub/ Michael Alaux

3B reference sequence annotation

Michael Alaux

3B annotation

https://urgi.versailles.inra.fr/gb2/gbrowse/wheat_annot_3B Michael Alaux

3B annotation

Scaffolds BACs Gaps Pseudomolecule https://urgi.versailles.inra.fr/gb2/gbrowse/wheat_annot_3B Michael Alaux

3B annotation: Scaffold

Michael Alaux

3B annotation: BAC

https://urgi.versailles.inra.fr/gb2/gbrowse/wheat_annot_3B

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Michael Alaux

3B annotation

Markers Genes

TE

3B annotation: Marker

Michael Alaux

3B annotation: Gene

3B annotation: TE

DNA Transposon Superfamily (DTX)

Michael Alaux

Survey sequence browser

Michael Alaux

Survey sequence

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Michael Alaux

Survey sequence

https://urgi.versailles.inra.fr/gb2/gbrowse/wheat_survey_sequence_annotation Michael Alaux

Support to assembly and

data submission

Michael Alaux

BAC sequence assembly

 3B MTP BAC sequencing

 3B physical map

 Assembly and scaffolding

 Ordering scaffolds

 Perform the Annotation

 Bioinformatic tools

Michael Alaux

BAC sequence assembly

What are the needs ?

i.e. distribute the bioinformatics softwares

Michael Alaux

Data submission

Michael Alaux

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Michael Alaux Annotation browser o 3B ref o Survey seq GBrowse / JBrowse Physical maps browser GBrowse Genetic maps, Markers, QTLs, MetaQTLs GnpIS SNPs GnpIS Germplasm GnpIS Wheat@URGI website Sequence repository

Wheat dataflow overview

Data Tools Google-like search Intermine Blast Download Browsers BLAST o 3B ref o Survey seq Phenotyping GnpIS Genotyping GnpIS Association GnpIS Michael Alaux