Pumpkin genomes sequenced, revealing uncommon evolutionary history

For some, pumpkins conjure carved Halloween decorations, but for many people around the world, these gourds provide nutrition. Scientists at Boyce Thompson Institute (BTI) and the National Engineering Research Center for Vegetables in Beijing have sequenced the genomes of two important pumpkin species, Cucurbita maxima and Cucurbita moschata. 

"Pumpkins are used as a staple food in many developing countries and are cultivated all over the world for their culinary and ornamental uses," said Zhangjun Fei, associate professor at BTI, Cornell adjunct associate professor of plant pathology and a senior author of the paper. Over two-thirds of the world's pumpkins, squash and gourds are produced in Asia alone.

The researchers sequenced the two different pumpkin species to better understand their contrasting desirable traits: Cucurbita moschata is known for its resistance to disease and other stresses, such as extreme temperatures, while C. maxima is better known for its fruit quality and nutrition.

"The high-quality pumpkin genome sequences will lead to more efficient dissection of the genetics underlying important agronomic traits, thus accelerating the breeding process for pumpkin improvement," said Fei.

Although the pumpkin is considered a diploid today, meaning that it has only two copies of each chromosome, the genome sequence analysis revealed that between 3-20 million years ago, two different ancestral species combined their genomes to create an allotetraploid.

The ancient Cucurbita allotetraploid lost its duplicated genes randomly from both of the contributing diploids. Furthermore, the ancestral chromosome remained largely intact, leaving the modern pumpkin with two subgenomes representing the ancient species that contributed to the paleotetraploid.