2 September 2022

A bitter mystery: Sequencing the world’s oldest plant genome

Kew scientists and partners have sequenced the oldest plant genome using 6,000-year-old seeds from a watermelon relative

By Dr Oscar Alejandro Pérez Escobar and Chelsea Snell

With their sweet, red and juicy flesh, watermelons (Citrullus lanatus subsp. vulgaris) are a popular summer fruit.

For scientists, they are a crop with a mysterious history.

It’s generally accepted by the scientific community that watermelons originated in Africa, but exactly where they were domesticated from a bitter-tasting wild fruit into a sweet-tasting one is hotly debated.

Evidence gathered from DNA suggests that the closest relative is the Kordofan melon (C. lanatus subsp. cordophanus) and ancient tomb paintings show that Egyptians were consuming watermelon in the Nile Valley in 4360 BP.

However, with the discovery of ancient watermelon seeds at an archaeological site in the Sahara Desert in Libya, we are now reconsidering its origin.

Three slices of yellow fleshed watermelon laid out on white paper. A small knife with a red handle is laid next to the slices. — Yellow watermelon has a sweet pulp but contains less lycopene, hence its yellow colour © Oscar Pérez-Escobar/RBG Kew.

Puzzling discovery

Discovering ancient watermelon seeds that had been collected from Libya and Sudan and radiocarbon dated (C-14) to more than 6,000 and 3,000 years ago was perplexing given that the current evidence didn’t support Libya as a place of watermelon domestication.

Working with our partners from the UK, Germany and US we were able to obtain genome sequences using the seeds in addition to watermelon specimens held in Kew’s Herbarium, some of which date back to the early 19th century.

As far as we are aware, the genome sequences generated from the seeds are among the oldest ever attained from plant remains whose age have been verified using radiocarbon dating techniques.

A computer scan of four ancient watermelon seeds labelled a to d. Each one has marks on the surface. — Ancient watermelon seeds found in Libya with teeth marks © Aldona Mueller-Bieniek.

Egusi melon

Our results showed that the seeds came from a watermelon relative known as the egusi watermelon or egusi gourd (Citrullus mucosospermus), from West Africa. The raw fruits are bitter and inedible, due to the chemical cucurbitacin in their flesh and are instead grown for their seeds, which are similar in size and flavour to pumpkin seeds.

Surprisingly, we found human teeth marks on the ancient seeds which supports our theory that Neolithic Libyans collected, and even cultivated, the watermelon relative to eat its seeds and not its flesh.

Guillaume Chomicki and Susanne Renner smiling and holding a herbarium specimen of a Citrullus specimen — Guillaume Chomicki and Susanne Renner with a herbarium specimen of Citrullus © Susanne R. Renner.

The research also yielded many genetic insights into the domestication history of the sweet watermelon whereby genes have been exchanged over generations. This is particularly useful for watermelon crop improvement breeding programmes as we can identify useful genes, such as those for pest and disease resistance.

Finally, our study is a great example of how plant collections, representing thousands of years of evolutionary and cultural history, can be used in different ways in multidisciplinary research.