Frequently Asked Questions (FAQ)

How were you able to accelerate the preliminary release of the cacao genome so significantly?

Most importantly, we were able to benefit from significant advances in sequencing technology over the past two years. Another key to our success was constant re-calibration and real-time collaboration among all of our very dedicated partners. We had a methodology that was trackable to everyone at all times. This coalition of like-minded scientists worked tirelessly to bring this invaluable resource to fruition and make it available to the research community in a timely manner.

When is the “complete” genome going to be available?

The “preliminary” cacao genome is 90 percent there in terms of helping cacao breeders and farmers with immediately usable information. However, we will be conducting further analysis of the genome to characterize specific traits associated with individual genes. We look forward to releasing a more complete genomic analysis sometime next year.

Why is it important that the preliminary genome sequence be publicly available?

We believe that it is important for all cacao breeders and geneticists to have access to this valuable information so that their research can proceed as quickly as possible and have the maximum benefit for cacao farmers everywhere. The public availability of the data also allows us to integrate molecular biology into traditional breeding programs in such a way that cacao will become the model for breeding of superior tropical, perennial tree crops.  

So where do people go to access the data and how will they be allowed to use it?

Public access to the genome will be available permanently without patent via the Cacao Genome Database. Before viewing the data, users have to agree that they will not seek any intellectual property protection over the data, including gene sequences contained in the database. The Information Access Agreement allows any cacao breeders and other researchers to freely use the genome information to develop new cacao varieties. This allows for a level playing field and a healthy competitive environment that will ultimately benefit the sustainability of cacao production in the long term.

Why is the genome release going to prevent patenting of the cacao genome?

We will continue to analyze and characterize the cacao genome in preparation for a peer-reviewed publication. By making this resource available through a public database now, it should prevent wholesale patenting of the cacao genome and allow anyone to utilize the genome in cacao improvement efforts.


Why do we need a Cacao Genome Database?

The cacao genome sequencing project is generating a large amount of sequence data, transcript data, physical map data, and single-nucleotide polymorphism (SNP) data. These data will be produced by USDA and other scientists and require a website for the deposition, curation, manipulation and distribution of the data. The cacao genome database will contain comprehensive data of the genetically anchored cacao physical map, annotated EST databases of cacao, cacao maps and markers, all publicly available cacao sequences and the raw and assembled output of the ongoing genome sequencing project. Annotations of ESTs and genomic sequence will include contig assembly, putative function, simple sequence repeats, ORFs, Gene Ontology and anchored position to the cacao physical map where applicable. The integrated map viewer will provide a graphical interface to the genetic, transcriptome and physical mapping information. New cacao map data will be added to CMap, a web-based tool that allows users to view comparisons of genetic and physical maps. ESTs, BACs and markers will be queried by various categories and the search result sites will be linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users will be able to compare their sequences with the annotated cacao sequences via a dedicated BLAST sequence similarity server, search their sequences for microsatellites using the SSR server or assemble their ESTs using the CAP3 Server.