Cucurbita Maxima and Cucurbita Moschata Assembly

The Cucurbita genus contains several economically important species in the gourd family (Cucurbitaceae). We report high-quality draft genome sequences of C. maxima and C. moschata and provide evidence supporting an allotetraploidization event in Cucurbita. We partition the genome into two homoeologous subgenomes, marked by different genetic distances to the Benincaseae clade. We estimate that the two diploid progenitors successively diverged from Benincaseae around 30.6-32.5 and 25.9-27.4 Mya. About 70% of the duplicated genes due to the genome merger were retained in two homoeologous copies, most of which exhibit different expression patterns. The subgenomes have presumably maintained the chromosome structures of the diploid progenitors, and have evolved to lose similar numbers of genes with neither subgenome being globally dominant in gene expression. We determined the regulatory mechanisms underlying the expression divergence between C. maxima and C. moschata and detected genes with transgressive expression patterns in the interspecific F1 hybrid, 'Shintosa', correlating with heterosis.