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

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