RNA-Seq Transcriptome Profiling Reveals Differentially Expressed Genes Involved in Sex Expression in Melon

Melon (Cucumis melo. L.) is an economically important vegetable crop and a model species for the study of sex determination. Although two master genes, G (for gynoecy) and A (andromonoecy) have been cloned, the process of sex expression in melon is complex, and the associated mechanisms and gene network are not well understood. In this study, RNA sequencing was conducted among bulk segregants of four melon plant sex types, namely monoecious (AAGG), gynoecious (AAgg), hermaphrodite (aagg), and andromonoecious (aaGG). About 105 million reads were generated from the melon transcriptome using Illumina HiSeq 2000 sequencing. In total, 76,260 unigenes were generated and mapped to 11,805 annotated proteins in the assembled melon genome. Most of the genes encode proteins related to plant hormone metabolism. Others are related to flora development, including tasselseeds and male sterility genes, which were detected in the phytohormone pathway. Comparisons of paired segregants (AAGG: AAgg, AAGG: aaGG, aagg: AAgg and aaGG: aagg) revealed different gene expression profiles (745, 1342, 858, and 571 genes, respectively). The most highly represented was the serine/threonine protein kinase pathway. In this pathway, ethylene, abscisic acid (ABA), auxin/indole-3-acetic acid (IAA), and aminocyclopropanecarboxylate (ACC) oxidase were involved in different sex type expressions, suggesting that they might have important roles in melon sex determination. Fifteen selected genes were validated via reverse transcription quantitative real-time polymerase chain reaction, and their expression patterns were similar for the two methods. Overall, the melon transcriptome sequences revealed novel gene expression profiles and offer important clues for further study of the molecular mechanism of sex differentiation.