RT Journal Article SR Electronic T1 Karyotype stability and unbiased fractionation in the paleo-allotetraploid Cucurbita genomes JF bioRxiv FD Cold Spring Harbor Laboratory SP 150755 DO 10.1101/150755 A1 Honghe Sun A1 Shan Wu A1 Guoyu Zhang A1 Chen Jiao A1 Shaogui Guo A1 Yi Ren A1 Jie Zhang A1 Haiying Zhang A1 Guoyi Gong A1 Zhangcai Jia A1 Fan Zhang A1 Jiaxing Tian A1 William J. Lucas A1 Jeff J. Doyle A1 Haizhen Li A1 Zhangjun Fei A1 Yong Xu YR 2017 UL http://biorxiv.org/content/early/2017/06/15/150755.abstract AB The Cucurbita genus contains several economically important species in the Cucurbitaceae family. Interspecific hybrids between C. maxima and C. moschata are widely used as rootstocks for other cucurbit crops. We report high-quality genome sequences of C. maxima and C. moschata and provide evidence supporting an allotetraploidization event in Cucurbita. 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, when C. maxima and C. moschata diverged. 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 the C. maxima × C. moschata interspecific F1 hybrid and the two parents indicates the predominance of trans-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.