1. The Complete Genome Sequence
of Coffea canephora
Alan C. Andrade
alan.embrapa@embrapa.br

2. The importance of C. canephora:
2n=2x=22 2n=4x=44
Allogamous species Autogamous species

3. Challenges
Growers and Industry
• Climate changes
• Competition with other commodities (Bioenergy)
• Sustainable production systems
• Preservation of natural resources (minerals, water, etc.)
• Quality (Competition with other beverages)
• Socio-economic aspects

4. Functional Genomics
https://alanine.cenargen.embrapa.br/
http://www.lge.ibi.unicamp.br/cafe/

5. Functional Genomics

6. Coffee ESTs
Espécie BP > 20 BP Total Reads Reads Total Qualidade
250 BP (%)
Phred≥20
Coffea arabica 83.368.331 181.429.319 131.718 187.078 71,10
Coffea canephora 8.074.170 14.735.317 12.359 15.322 80,66
Coffea racemosa 8.475.698 14.530.379 12.097 15.546 77,81
Total 99.918.199 210.695.015 156.174 217.946 71,66
% of Unigene Unigene Set
No hits
no hits found
71.1% Hits
hits
• Contigs: 19.031
71.1% dbEST Brazil-ESTs Common
• Singlets: 13.928
13% 12%
• Unigene: 33.000
Lin et al., 2005
28.9%
28.9% Vieira et al., 2006
Poncet et al., 2006
Coffea sp. : 246,541 ESTs 75%

7. Cost:
Service, R.F. Science, 2006

8. NGS
•
•
technologies
Gouveia et al. 2005
Ferreira et al. 2007
• Nunes et al. 2007
• RAPD, AFLP

9. Stratton, MR.
Nature, 2009
Improvements in the rate of DNA sequencing over the past 30 years and into the future.
From slab gels to capillary sequencing and second-generation sequencing
technologies, there has been a more than a million-fold improvement in the rate of
sequence generation over this time scale.

10. Output still increasing!
Stratton, MR. Nature, 2009
Pareek et al., 2011

11. Cost reduction:
Metzker, ML. Nature, 2010

12. Plant genomes
Crop genome size. Genome size of published crop genomes (green) and
unpublished (blue). Morrell et al, Nature, Feb. 2012

13. Plant genomes

14. Plant genomes

15. Coffee Genomics
(http://www.coffeegenome.org )
International Coffee Genome
Network
Founding meeting
Paris – 4 & 5 April 2005

16. Coffee Genomics
Patrick Wincker, Benoit Bertrand, Xavier
Argout, Alexandre de Kochko,
Philippe Lashermes
Ray Ming, Victor A. Albert, Steve Rounsley,
Chifumi Nagai
Alan C. Andrade
Giorgio Graziosi, Giovanni Giuliano
Robert Henry
David Sankoff
Jayarama

17. Coffee Genomics
Genotype: Double-haploid
HD 200-94 - IRD
Genome estimated size: 710 Mb

18. Coffee Genomics
Final status – Sequencing Completed!
Total coverage for assembly: 29 X
- 454: 28.8 X
single end : 14,83 X
long single end: 8,24 X
mate paired reads : 5,8 X (2,2X de 8kb, 3,6X de 20kb)
- Sanger sequencing (BAC ends ): 0.2X
- For assembly correction and gap closure :
Solexa : 69,7 X
- single end : 7,3X
- paired end reads : 62,4X

19. Coffee Genomics
Final Assembly statistics
scaffold statistics:
N50 size= 1260636 number= 108
N80 size= 65268 number= 635
N90 size= 21947 number= 2191
Assembly
size= 568577705 number= 13345
minSize= 1995 maxSize= 9027918
averageSize= 42606

20. Applied Coffee Genomics

21. Applied Coffee Genomics

22. Applied Coffee Genomics

23. Applied Coffee Genomics

24. Applied Coffee Genomics

25. The basics is the same:Comparisons!
Diferences Similarities

26. Sequences
Phenotype

27. Phenotyping

28. Phenotyping...

29. Germplasm Collection

30. Experimental field of Embrapa

31. Real Data from the neighbours...
Eucalyptus grandis
Resende et al.,
New Phytologist 2012
CBH: circunference at breast height; HG: height growth; WSG: wood specific gravity; PY: Pulp Yield

32. Real Data from the neighbours...
Eucalyptus grandis
Resende et al.,
New Phytologist 2012
CBH: circunference at breast height; HG: height growth; WSG: wood specific gravity; PY: Pulp Yield

33. Real Data from the neighbours...
Resende et al.,
New Phytologist 2012
CBH: circunference at breast height; HG: height growth; WSG: wood specific gravity; PY: Pulp Yield

34. Partners:

35. Thank you!
The new variety “Genoma” is coming…