A Unified Expression Platform That Makes Tomato Suitable Model For Exploring Plant-Environment Interactions

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Presented at Plant Genomics and Gene Editing Congress: Europe. For more information visit: www.global-engage.com TomExpress platform was developed to provide the tomato community with a browser and integrated web-tools for public RNA-Seq data visualization and data mining. RNA-Seq raw sequence data available in public databases were mapped de novo on a unique tomato reference genome sequence, and post-processed using the same pipeline with accurate parameters.

Sciences

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

PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE,
Amsterdam , 16-17 March 2017
Tomato RNA-Seq Data Search
SRA
30 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

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

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

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

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

PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE,
Amsterdam , 16-17 March 2017
RIN
Fruit specific expression : RIN

PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE,
Amsterdam , 16-17 March 2017
In planta expression data vizualisation

PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE,
Amsterdam , 16-17 March 2017
Solyc05g012020: MADS-box
transcription factor RIN

PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE,
Amsterdam , 16-17 March 2017
Reference genes for Q-PCR
Ubi

PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE,
Amsterdam , 16-17 March 2017
Ubi and Actin expression profiles
Actin
Ubi

PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE,
Amsterdam , 16-17 March 2017
Good candidate for Q-PCR in fruit development
Solyc04g008380: GAGA-binding transcriptional activator

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

PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE,
Amsterdam , 16-17 March 2017
Heatmap of correlation values
Co-expression networks
Co-expressions identification

PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE,
Amsterdam , 16-17 March 2017
Web site Access
http://gbf.toulouse.inra.fr/tomexpress

PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE,
Amsterdam , 16-17 March 2017
Acknowledgments
GBF, INRA/INPT, Toulouse France:
• Elie Maza
• Anis Djar
• Pierre Frasse
• Mondher Bouzayen
• Mohamed Zouine

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A Unified Expression Platform That Makes Tomato Suitable Model For Exploring Plant-Environment Interactions

1. 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

2. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Tomato RNA-Seq Data Search SRA 30 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

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

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

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

6. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 The web portal

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

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

9. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 RIN Fruit specific expression : RIN

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

11. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 In planta expression data vizualisation

12. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Solyc05g012020: MADS-box transcription factor RIN

13. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Reference genes for Q-PCR Ubi

14. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Ubi and Actin expression profiles Actin Ubi

15. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Good candidate for Q-PCR in fruit development Solyc04g008380: GAGA-binding transcriptional activator

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

17. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Hierarchical clustering heatmap

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

19. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Heatmap of correlation values Co-expression networks Co-expressions identification

20. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Web site Access http://gbf.toulouse.inra.fr/tomexpress

21. PLANT GENOMICS & GENE EDITING CONGRESS: EUROPE, Amsterdam , 16-17 March 2017 Acknowledgments GBF, INRA/INPT, Toulouse France: • Elie Maza • Anis Djar • Pierre Frasse • Mondher Bouzayen • Mohamed Zouine

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