andrade conilon-2012

The Complete Genome Sequence of Coffea canephora

Alan C. Andrade

alan.embrapa@embrapa.br

The importance of C. canephora:

2n=2x=22

Allogamous species2n=4x=44

Autogamous species

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

http://www.lge.ibi.unicamp.br/cafe/

https://alanine.cenargen.embrapa.br/

Functional Genomics

Functional Genomics

Coffee ESTs

Espécie BP > 20 BP Total Reads

250 BP

Phred≥20

Reads Total Qualidade

(%)

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

Unigene Set

• Contigs: 19.031

• Singlets: 13.928

• Unigene: 33.000

% of Unigene

12%

75%

13%

dbEST Brazil-ESTs Common

Coffea sp. : 246,541 ESTs

71.1%

28.9%

no hits found

hits

71.1%No hitsHits

28.9%

Lin et al., 2005Vieira et al., 2006Poncet et al., 2006

Cost:

Service, R.F. Science, 2006

• Gouveia et al. 2005

• Ferreira et al. 2007

• Nunes et al. 2007

• RAPD, AFLP

NGS technologies

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 sequencingtechnologies, there has been a more than a million-fold improvement in the rate ofsequence generation over this time scale.

Stratton, MR. Nature, 2009

Stratton, MR. Nature, 2009

Output still increasing!

Pareek et al., 2011

Metzker, ML. Nature, 2010

Cost reduction:

Morrell et al, Nature, Feb. 2012

Crop genome size. Genome size of published crop genomes (green) andunpublished (blue).

Plant genomes

Plant genomes

Plant genomes

Coffee Genomics

International Coffee Genome Network

Founding meeting

Paris – 4 & 5 April 2005

(http://www.coffeegenome.org )

Coffee GenomicsPatrick 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

Coffee Genomics

Genotype: Double-haploid

HD 200-94 - IRD

Genome estimated size: 710 Mb

Coffee GenomicsFinal 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

Coffee Genomics

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

Applied Coffee Genomics

Applied Coffee Genomics

Applied Coffee Genomics

Applied Coffee Genomics

Applied Coffee Genomics

The basics is the same:Comparisons!

Diferences Similarities

Sequences

Phenotype

Phenotyping

Phenotyping...

Germplasm Collection

Experimental field of Embrapa

Real Data from the neighbours...

CBH: circunference at breast height; HG: height growth; WSG: wood specific gravity; PY: Pulp Yield

Eucalyptus grandis

Resende et al., New Phytologist 2012

Real Data from the neighbours...

CBH: circunference at breast height; HG: height growth; WSG: wood specific gravity; PY: Pulp Yield

Resende et al., New Phytologist 2012

Eucalyptus grandis

Real Data from the neighbours...

CBH: circunference at breast height; HG: height growth; WSG: wood specific gravity; PY: Pulp Yield

Resende et al., New Phytologist 2012

Partners:

Thank you!

The new variety “Genoma” is coming…