Th1_GLASS & IRIGIN projects: Toward African Rices Variability

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3rd Africa Rice Congress presentation Theme 1: climate resilient rice Mini symposium: making greater use of Africa' indigenous genetic diversity Author: F. Sabot

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GLASS & IRIGIN projects:
Toward African Rices Variability
C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot
Institut de Recherche pour le Développement - francois.sabot@ird.fr

October 21, 2013

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

Oryza glaberrima: no currently available reference for
whole genome analysis

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

Oryza glaberrima: no currently available reference for whole
genome analysis
CG14 sequenced but not complete, limited access and
based on Oryza sativa

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

Illumina Sequencing 55-60x each
PacBioSequencing 12x each

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

Illumina Sequencing 55-60x each
PacBioSequencing 12x each

Diﬀerent Assemblies
Still working on

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

More diﬀerences (sequences and collinearity)
than expected with O. sativa

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

http://bioinfo-prod.mpl.ird.fr/blast/blast.html

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

http://bioinfo-prod.mpl.ird.fr/cgi-bin/gb2/gbrowse/Tog5681
For TOG5681 only by now

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

IRIGIN Project
Illumina Depth sequencing 25x

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

IRIGIN Project
Illumina Depth sequencing 25x
SNP and Structural variants scored

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

IRIGIN Project
Illumina Depth sequencing 25x
SNP and Structural variants scored
100 Oryza barthii

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

IRIGIN Project
Illumina Depth sequencing 25x
SNP and Structural variants scored
100 Oryza barthii
150 O. glaberrima

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

IRIGIN Project
Illumina Depth sequencing 25x
SNP and Structural variants scored
100 Oryza barthii
150 O. glaberrima
All NERICA families and parents

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

Future prospects
Improving assemblies CG14/Tog5681 using PacBio reads

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

Future prospects
Improving assemblies CG14/Tog5681 using PacBio reads
Adding New Annotation layers (genes, CDS, Expression
level, transposable elements,...)

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

Genome & Development of Rices Team, IRD
Alain Ghesquière, Director
François Sabot
Pierre Larmande
Christine Tranchant
Cécile Monat, PhD student

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

Thanks you for your attention

C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot

GLASS & IRIGIN

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Th1_GLASS & IRIGIN projects: Toward African Rices Variability

1. GLASS & IRIGIN projects: Toward African Rices Variability C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot Institut de Recherche pour le Développement - francois.sabot@ird.fr October 21, 2013 C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

2. Oryza glaberrima: no currently available reference for whole genome analysis C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

3. Oryza glaberrima: no currently available reference for whole genome analysis CG14 sequenced but not complete, limited access and based on Oryza sativa C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

4. Oryza glaberrima: no currently available reference for whole genome analysis CG14 sequenced but not complete, limited access and based on Oryza sativa AfricaRice - IRD joint eﬀort C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

5. Oryza glaberrima: no currently available reference for whole genome analysis CG14 sequenced but not complete, limited access and based on Oryza sativa AfricaRice - IRD joint eﬀort → Sequencing CG14 and TOG5681 C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

6. Illumina Sequencing 55-60x each PacBioSequencing 12x each C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

7. Illumina Sequencing 55-60x each PacBioSequencing 12x each Diﬀerent Assemblies Still working on C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

8. C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

9. More diﬀerences (sequences and collinearity) than expected with O. sativa C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

10. http://bioinfo-prod.mpl.ird.fr/blast/blast.html C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

11. C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

12. C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

13. http://bioinfo-prod.mpl.ird.fr/cgi-bin/gb2/gbrowse/Tog5681 For TOG5681 only by now C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

14. C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

15. C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

16. IRIGIN Project Illumina Depth sequencing 25x C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

17. IRIGIN Project Illumina Depth sequencing 25x SNP and Structural variants scored C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

18. IRIGIN Project Illumina Depth sequencing 25x SNP and Structural variants scored 100 Oryza barthii C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

19. IRIGIN Project Illumina Depth sequencing 25x SNP and Structural variants scored 100 Oryza barthii 150 O. glaberrima C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

20. IRIGIN Project Illumina Depth sequencing 25x SNP and Structural variants scored 100 Oryza barthii 150 O. glaberrima All NERICA families and parents C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

21. IRIGIN Project Illumina Depth sequencing 25x SNP and Structural variants scored 100 Oryza barthii 150 O. glaberrima All NERICA families and parents O. sativa of interest for partners C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

22. Future prospects Improving assemblies CG14/Tog5681 using PacBio reads C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

23. Future prospects Improving assemblies CG14/Tog5681 using PacBio reads Adding New Annotation layers (genes, CDS, Expression level, transposable elements,...) C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

24. Future prospects Improving assemblies CG14/Tog5681 using PacBio reads Adding New Annotation layers (genes, CDS, Expression level, transposable elements,...) Adding Variant Information from IRIGIN, SNP/InDel, SV C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

25. Future prospects Improving assemblies CG14/Tog5681 using PacBio reads Adding New Annotation layers (genes, CDS, Expression level, transposable elements,...) Adding Variant Information from IRIGIN, SNP/InDel, SV Forming AfricaRice and NARs Partners to bioinformatics using these data C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

26. Genome & Development of Rices Team, IRD Alain Ghesquière, Director François Sabot Pierre Larmande Christine Tranchant Cécile Monat, PhD student C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

27. Thanks you for your attention C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

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