Excerpted from EurekAlert!:
“Mockaitis, a biochemist-turned-genomicist, joined the project in early 2009, and quickly set to work with her collaborators to tackle the challenge of sequencing and accurately pasting together the approximately 400 million base pairs of the tree’s genome. Mockaitis’ Cacao Genome Group partners at the U.S. Department of Agriculture’s Subtropical Horticulture Research Station in Miami sent samples to Bloomington, and these were prepared and sequenced in a redundant manner by her sequencing team in the CGB genomics laboratory. Sequence of some of the same material was generated using additional methods in laboratories of the USDA Agricultural Research Service (USDA-ARS) and at the National Center for Genome Resources in Santa Fe, N.M.Raw data were then sent to HudsonAlpha Biotechnology Institute, a partner of the U.S. Department of Energy-funded Joint Genome Institute, for assembly. Other important datasets generated by Mockaitis’ group were not the sequences of the DNA itself, but of the RNA, or transcripts produced in different tissues of the tree. Transcript sequences reveal which genes are expressed (turned on).”