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Genetic Linkage

The Peaceable Genomes of Pumpkins

“For pottage and puddings and custards and pies
Our pumpkins and parsnips are common supplies,
We have pumpkins at morning and pumpkins at noon,
If it were not for pumpkins we should be undoon."

Pilgrim verse, circa 1633

The pumpkin became a Thanksgiving staple at the second celebration, after the immigrants to the New World had learned about its nutritional value and versatility from the original Americans.

A Brief History of Pumpkins

Pumpkins arose in South America some 30 million years ago as two older species merged. The first Native Americans discovered eclectic uses for the squash, roasting seeds, eating strips of succulent orange flesh, adding flowers to soups and stews, grinding flour from saved seeds, and using the outsides not as lanterns but as archaic Tupperware.

Anyone who’s tossed a pumpkin onto the lawn after Halloween to discover vines snaking along the ground the next summer knows how easy it is to grow. At first Native Americans sprinkled pumpkin seeds along river and stream banks, but once these early farmers began to cultivate corn, they realized that the broad pumpkin leaves spread on the soil surface kept weeds out and moisture in, enabling the maize roots to anchor the towering plants.

The pilgrims devised their own recipes. One favorite was to hollow a pumpkin out and stuff it with eggs, cream, honey, and spices and bury it in hot ashes. Hours later they hauled the blackened squash out and scooped out the delicious innards. The pilgrims also used pumpkin to make beer, and inverted the fruits to guide bowl-like haircuts.

Early explorers brought pumpkin seeds back to Europe and beyond, and today most pumpkins are grown in India and China.

The word “pumpkin” comes from the Greek Pepõn, which means large melon. It’s in genus Cucurbita, and in a “tribe” with muskmelons, cucumbers, and watermelons.

Modern pumpkins are of two species. Cucurbita maxima has nutritious, orange flesh with an appealing texture and flavor. C. moschata is known for its resistance to stress, from insect pests to non-biological threats like extreme temperatures. Crossing the species yields the hardy hybrid Shintosa, which has such terrific resistance to pests and stress that growers graft melons and cucumber stems to its seedlings.

Doubling Genomes

Many modern species can trace their roots to genome doublings. The genomes of some species have even doubled twice, including those of all vertebrates and of pumpkins. An article in the October issue of Molecular Plant unveiled the genome sequences of the two pumpkin species, from researchers at the Cornell-affiliated Boyce Thompson Institute (BTI) and the National Engineering Research Center for Vegetables in Beijing.

The idea of double genome doubling in evolution goes back to a 1970 book, Evolution by Gene Duplication, by geneticist Susumu Ohno, which became known as the 2R hypothesis.

The genomes of the ancestors of all flowering plants doubled about 160 million years ago. The grasses are pros at it: the genomes of corn, rice, wheat, and sugarcane doubled some 70 million years ago, those of corn and sugarcane doubling again.

In most cases of genome doubling, over time, genes that duplicate functions are lost, typically mostly from one ancestral genome. That’s actually what happened to us, with about 5% of our genomes holding remnants of gene partners past, spread over 1 to 14% of each chromosome. Corn, cotton, mustard weed, and some cabbages have also jettisoned most of one ancestral genome.

A Genetic Tale of Two Pumpkins

Sequencing of the two pumpkin genomes enabled researchers to better pinpoint the times of genome duplication, and to flesh out the genetic characteristics and adaptive traits of each.

Both species have 20 chromosomes, which represent two “paleo-subgenomes.” The first genome divergence was about 31 million years ago, and the second happened between 3.04 and 3.84 million years ago. Geneticists can figure this out using genes with known mutation rates coupled with comparisons of chromosome configurations as well as archaeological data.

The pumpkins are unusual. Since about 3 million years ago, the genomes of the two ancestors from the more recent doubling have peacefully co-existed within the same nucleus, unlike the other double-doublers that have selectively lost most of the contributions of one parent species. This makes pumpkins “paleotetraploid.” (“Ploid” refers to one full set of chromosomes, so paleotetraploid means “old four sets.”) Other genomically peaceful paleotetraploids are wheat and the African clawed frog Xenopus laevis, beloved model organism of developmental biologists.

“We were excited to find out that the current two subgenomes in pumpkin largely maintain the chromosome structures of the two progenitors despite sharing the same nucleus for at least 3 million years,” said Shan Wu, first author of the paper and a BTI postdoc.

Drilling down to the details, C. maxima’s genome is about 387 million bases to C. moschata’s 372 million. C. maxima, the tasty one, has 30 disease resistance genes to C. moschata’s 57. And the ultra-resistant hybrid Shintosa is more than the sum of its ancestral parts.

Each pumpkin genome has about 4 dozen genes that show signs of positive selection – persisting because they provide a reproductive or survival advantage. And more than 40% of each genome consists of repeated sequences, holdovers from the most ancient doubling.

Sequencing the genomes of this favorite fruit will have practical repercussions, such as breeding for resistance to powdery mildew and increased carotenoid levels, making the pumpkin mash more nutritious.

Said Zhangjun Fei, associate professor at BTI and senior author of the paper, “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.”

The new insights into the past of pumpkins might also improve the pie that we eat today. Happy Thanksgiving!

This post first appeared at my weekly blog DNA Science for Public Library of Science.

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