Cassava (Manihot esculenta) is grown throughout tropical Africa, Asia and the Americas for its starchy storage roots, and feeds an estimated 750 million people each day. Farmers choose it for its high productivity and its ability to withstand a variety of environmental conditions (including significant water stress) in which other crops fail. However, it has very low protein content, and is susceptible to a range of biotic stresses. Despite these problems, the crop production potential for cassava is enormous, and its capacity to grow in a variety of environmental conditions makes it the plant of the future for emerging tropical nations. Cassava is also an excellent energy source - its roots contain 20-40% starch that costs 15-30% less to produce per hectare than starch from corn, making it an attractive and strategic source of renewable energy.

The goals of the Cassava Genome Project are to generate a draft sequence of the cassava genome, and because of the humanitarian importance of the crop, to make that sequence available to all - freely and rapidly. Much of the utility of the genome sequence will come from the development of breeding tools, and as such a perfect reference genome sequence is not needed. Our sequencing strategies have been selected accordingly. The project has built upon a pilot initiated through the DOE-JGI Community Sequencing Program (CSP) by a 14-member consortium led by Claude Fauquet, Joe Tohme and Pablo Rabinowicz. This pilot project produced a little under 1x coverage from over 700,000 Sanger shotgun reads using plasmid and fosmid libraries, and it provided insights into the overall characteristics of the cassava genome, and a valuable source of Sanger paired-end sequences to be used later.

The main phase of the project, led by Steve Rounsley, Dan Rokhsar, Chinnappa Kodira, and Tim Harkins began in Spring 2009 when 454 Life Sciences, a Roche company partnered with DOE-JGI to provide the resources for a whole genome shotgun sequencing of cassava using the 454 GS FLX Titanium platform. Nearly 61 million 454 reads (single and paired-end) were generated and combined with the Sanger data from the pilot project as input for genome assembly. The resulting assembly and its annotation is available through Phytozome and has also been deposited in GenBank in accordance with our commitment to early access and the Fort Lauderdale genome data release policy.

The niversity of Arizona has recently been awarded a 3-year $1.3 million grant by the Bill & Melinda Gates Foundation to expand and improUve upon the initial cassava genome sequence. With its partners, DOE-JGI, 454 Life Sciences and University of Maryland, Baltimore, the newly funded project seeks targeted improvement of the genome assembly and SNP discovery via resequencing of many varieties of cassava. The SNP resource will also be accessible through Phytozome.

The Cassava genome project principal investigators include Claude Fauquet, Joe Tohme, Pablo Rabinowicz, Steve Rounsley, Dan Rokhsar, Chinnappa Kodira, and Tim Harkins.