Karyotype stability and unbiased fractionation in the paleo-allotetraploidCucurbitagenomes
AbstractTheCucurbitagenus contains several economically important species in the Cucurbitaceae family. Interspecific hybrids betweenC. maximaandC. moschataare widely used as rootstocks for other cucurbit crops. We report high-quality genome sequences ofC. maximaandC. moschataand provide evidence supporting an allotetraploidization event inCucurbita. We are able to partition the genome into two homoeologous subgenomes based on different genetic distances to melon, cucumber and watermelon in the Benincaseae tribe. We estimate that the two diploid progenitors successively diverged from Benincaseae around 31 and 26 million years ago (Mya), and the allotetraploidization happened earlier than 3 Mya, whenC. maximaandC. moschatadiverged. The subgenomes have largely maintained the chromosome structures of their diploid progenitors. Such long-term karyotype stability after polyploidization is uncommon in plant polyploids. The two subgenomes have retained similar numbers of genes, and neither subgenome is globally dominant in gene expression. Allele-specific expression analysis in theC. maxima×C. moschatainterspecific F1hybrid and the two parents indicates the predominance oftrans-regulatory effects underlying expression divergence of the parents, and detects transgressive gene expression changes in the hybrid correlated with heterosis in important agronomic traits. Our study provides insights into plant genome evolution and valuable resources for genetic improvement of cucurbit crops.