Development of "Melonet-DB" Gene Expression Database for Functional Genomics Research of Muskmelon

Melon (Cucumis melo) is an important Cucurbitaceae crop widely produced in the world. It exhibits a broad range of genetic variation including both climacteric and non-climacteric fruit types. The climacteric type cultivar “Earl’s favorite Harukei-3” is known for its sweetness and rich aroma, and hence used for breeding of high-grade muskmelon in Japan. To promote functional genomics research and breeding in muskmelon, we are developing induced mutant library as well as genome editing methodology in ‘Harukei-3’. However, in reverse genetics approaches, it is often difficult to select target gene(s) due to the presence of multiple candidates (homologues) in the melon genome. Because transcriptome information is useful to distinguish gene functions among homologues, we conducted RNA-seq analysis in 30 developmental tissues in ‘Harukei-3’. These tissues included root, stems, leaves, flowers tissues, and callus in addition to the peels and fleshes of developing fruits. After separating microbial contamination reads, expression profiles of around 20,700 melon genes were obtained by Tophat-Cufflinks pipeline using ‘DHL92’ as a reference (>1 [max]FPKM). Organ types were clearly distinguished according to the global expression profile in principal component analysis. In addition, weighted genome-wide correlation network analysis classified these genes into 44 co-expression groups according to the expression patterns. Expression of some co-expression groups was prominent in specific sink organs. Finally, to explore these datasets efficiently, we developed web-based application tools, ‘Gene expression viewer’ and ‘Coexpression viewer’, in our web site ‘Melonet-DB (http://melonet-db.agbi.tsukuba.ac.jp/)’. In this presentation, we’d like to introduce some features of these tools.