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

<p>A large dataset of replicated transcriptomes was developed to accelerate <em>T</em><em>heobroma cocoa</em> 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.</p><p>Excel or any text editor or spreadsheet program.</p>