Melon (Cucumis melo L.) is an important Cucurbitaceae crop produced world-wide, exhibiting wide genetic variations and comprising both climacteric and non-climacteric fruit types. The muskmelon cultivar "Earl's favorite Harukei-3 (Harukei-3)" known for its sweetness and rich aroma is used for breeding of high-grade muskmelon in Japan. We conducted RNA-seq transcriptome studies in 30 different tissues of the 'Harukei-3' melon. These included root, stems, leaves, flowers, regenerating callus, and ovaries, in addition to the flesh and peel sampled at 7 stages of fruit development. The expression patterns of 20,752 genes were determined with FPKM > 1 in at least one tissue. Principal component analysis distinguished 30 melon tissues based on the global gene expression profile, and further, the weighted gene correlation network analysis classified melon genes into 45 distinct co-expression groups. Some co-expression groups exhibited tissue-specific gene expression. Furthermore, we developed and published web-application tools designated "Gene expression map viewer" and "Coexpression viewer" on our website Melonet-DB (http://melonet-db.agbi.tsukuba.ac.jp/) to promote functional genomics research in melon. By using both the tools, we analyzed melon homologs of tomato fruit ripening regulators such as E8, RIPENING-INHIBITOR (RIN) and NON-RIPENING (NOR). The "Coexpression viewer" clearly distinguished fruit ripening-associated melon RIN/NOR/CNR homologs from those expressed in other tissues. In addition, several other MADS-box, NAM/ATAF/CUC (NAC), and homeobox transcription factor genes were identified as fruit ripening-associated genes. Our tools provide useful information not only for research on melon but also on other fleshy fruit plants.
