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Consortium Using 454, Illumina Sequencers to Decode Cacao Genome

SAN DIEGO (GenomeWeb News) — A consortium of researchers is using sequencers made by Roche 454 and Illumina, and possibly also Sanger sequencing and other methods, to decode the cacao genome, according to a US Department of Agriculture-Agriculture Research Service researcher.

Brian Scheffler, a computational molecular biologist and director of the USDA-ARS Mid-South Area Genomics Laboratory, described the plan to sequence the 400-megabase genome during a workshop at this year's at the Plant and Animal Genome conference, held here Jan. 10-14.

"Everyone says America runs on oil," Scheffler said during the session. In fact, "America runs on coffee and chocolate."

Last June, the USDA-ARS, along with IBM and candy maker Mars, announced that they were embarking on a five-year study to sequence the cacao genome. At yesterday's session, several individuals involved in the collaboration shed additional light on the project.

Describing the project's decision to use a combination of 454 and Illumina sequencers, Scheffler emphasized the need to balance quality, speed, and cost. He said the team is using several complementary approaches to perform whole-genome shotgun sequencing of the cacao genome, including long- and short-read, high-throughput sequencing.

The researchers plan to use long random-sheared and paired-end reads generated by Roche 454 sequencing, along with short paired-end reads generated using Illumina technology. The team will likely also use Sanger sequencing, BAC-end sequencing, and fosmid sequencing to fill in remaining gaps, Scheffler said.

A bioinformatics group at IBM will carry out quality assurance for the project, while researchers at the Department of Energy's Joint Genome Institute will bring their own methods to help assemble and annotate the genome, Scheffler said.

He said the cacao consortium also aims to make data accessible to other research groups and work with cacao breeders and end-users.

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