GLASS & IRIGIN projects:
Toward African Rices Variability
C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot
Institut de Rec...
Oryza glaberrima: no currently available reference for
whole genome analysis

C. Monat, Ch. Tranchant, A. Ghesquière, F. S...
Oryza glaberrima: no currently available reference for whole
genome analysis
CG14 sequenced but not complete, limited acce...
Oryza glaberrima: no currently available reference for whole
genome analysis
CG14 sequenced but not complete, limited acce...
Oryza glaberrima: no currently available reference for whole
genome analysis
CG14 sequenced but not complete, limited acce...
Illumina Sequencing 55-60x each
PacBioSequencing 12x each

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

GLASS & IRIGI...
Illumina Sequencing 55-60x each
PacBioSequencing 12x each

Different Assemblies
Still working on

C. Monat, Ch. Tranchant, ...
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. Sabo...
http://bioinfo-prod.mpl.ird.fr/blast/blast.html

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

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

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

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

C. Monat, Ch. Tranchant...
IRIGIN Project
Illumina Depth sequencing 25x
SNP and Structural variants scored
100 Oryza barthii
150 O. glaberrima

C. Mo...
IRIGIN Project
Illumina Depth sequencing 25x
SNP and Structural variants scored
100 Oryza barthii
150 O. glaberrima
All NE...
IRIGIN Project
Illumina Depth sequencing 25x
SNP and Structural variants scored
100 Oryza barthii
150 O. glaberrima
All NE...
Future prospects
Improving assemblies CG14/Tog5681 using PacBio reads

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

G...
Future prospects
Improving assemblies CG14/Tog5681 using PacBio reads
Adding New Annotation layers (genes, CDS, Expression...
Future prospects
Improving assemblies CG14/Tog5681 using PacBio reads
Adding New Annotation layers (genes, CDS, Expression...
Future prospects
Improving assemblies CG14/Tog5681 using PacBio reads
Adding New Annotation layers (genes, CDS, Expression...
Genome & Development of Rices Team, IRD
Alain Ghesquière, Director
François Sabot
Pierre Larmande
Christine Tranchant
Céci...
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

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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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Th1_GLASS & IRIGIN projects: Toward African Rices Variability

  1. 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. 2. Oryza glaberrima: no currently available reference for whole genome analysis C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN
  3. 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. 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. 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. 6. Illumina Sequencing 55-60x each PacBioSequencing 12x each C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN
  7. 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. 8. C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN
  9. 9. More differences (sequences and collinearity) than expected with O. sativa C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN
  10. 10. http://bioinfo-prod.mpl.ird.fr/blast/blast.html C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN
  11. 11. C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN
  12. 12. C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN
  13. 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. 14. C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN
  15. 15. C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN
  16. 16. IRIGIN Project Illumina Depth sequencing 25x C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN
  17. 17. IRIGIN Project Illumina Depth sequencing 25x SNP and Structural variants scored C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN
  18. 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. 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. 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. 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. 22. Future prospects Improving assemblies CG14/Tog5681 using PacBio reads C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN
  23. 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. 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. 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. 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. 27. Thanks you for your attention C. Monat, Ch. Tranchant, A. Ghesquière, F. Sabot GLASS & IRIGIN

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