The cacao gene atlas: A transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L

A large dataset of replicated transcriptomes was developed to accelerate
Theobroma cocoa genomics research with the long-term goal of progressing
breeding towards developing high-yielding elite varieties of cacao. RNAs
were extracted and transcriptomes were sequenced from 123 different
tissues and stages of development representing major organs and
developmental stages of the cacao lifecycle. In addition, several
experimental treatments and time courses were performed to measure gene
expression in tissues responding to biotic and abiotic stressors. Samples
were collected in replicates (3-5) to enable statistical analysis of gene
expression levels for a total of 390 transcriptomes.  We describe
the creation of the atlas,and its global characterization and define sets
of genes co-regulated in highly organ- and temporally-specific manners. To
promote wider use of these data, all raw sequencing data, expression read
mapping matrices, scripts, and other information used to create the
resource are freely available online. A gene expression browser with a
graphical user interface was developed to display gene expression patterns
and to provide easy access of raw data and statistical analyses.