a unified expression platform that makes tomato suitable model for exploring plant-environment...

PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017

An unified expression platform that makes tomato a suitable model for exploring plant-environment interactions

Mohamed Zouine (GBF, UMR990 INRA/INPT)

Toulouse, France


Tomato RNA-Seq Data Search

SRA30 projects, 222 conditions, 755 samples (.fastq sequence files)

Plant and fruit Development, Tomato mutants, Hormones treatments , Biotic interactions…

Issues:✓ Different software and parameters for RNA sequences

mapping ✓ Different statistical methods for data normalization

Need for an unified pipeline


TomExpress pipeline

Fastq(FTP)

Public data

(ENA)

Projects/Samples (Annotation download)

Quality Control(fastQC)

Projects/Samples (Manual curation)

Alignment(TopHat/Bowtie)

Counting(HTSeq-count)

Normalization

Database integration(SQL)

Private data

(Apache, HTML, perl, PHP, R)


Depth and mapping statistics

Million of reads

755 illumina RNA-seq sequence files (.fastq)

~ 90% mapped on the reference genome~ 80% mapped on the iTAG gene models

16


TomExpress, a unified ressource to:

• Store the Normalized expression data of the 34,727 tomato genes in 222 conditions.

• Visualize expression profile of a gene in chosen conditions

• Compare expressions between genes

• Create Heat maps of Hierarchical clustering of expression values

• Identify Co-expressions for correlation networks study

TomExpress web portal


The web portal


RIN

Fruit specific expression : RIN


In planta expression data vizualisation


Solyc05g012020: MADS-box transcription factor RIN


Reference genes for Q-PCR

Ubi


Ubi and Actin expression profiles

Actin

Ubi


Good candidate for Q-PCR in fruit development

Solyc04g008380: GAGA-binding transcriptional activator


Hierarchical clustering heatmap


Heatmap of correlation values

Co-expression networks

Co-expressions identification


Web site Access

http://gbf.toulouse.inra.fr/tomexpress


Acknowledgments

GBF, INRA/INPT, Toulouse France:

• Elie Maza

• Anis Djar

• Pierre Frasse

• Mondher Bouzayen

• Mohamed Zouine

a unified expression platform that makes tomato suitable model for exploring plant-environment...

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