NYU researchers sequence the genome of extinct date palms germinated from 2,000-year-old seeds

One of the date palms that was germinated from a 2,200 year old seed, now growing in Israel. Credit: Marcos Schonholz/The Arava Institute for Environmental Studies

One of the date palms that was germinated from a 2,200 year old seed, now growing in Israel. Credit: Marcos Schonholz/The Arava Institute for Environmental Studies

In the 1993 film Jurassic Park, scientists bring dinosaurs back from extinction using DNA extracted from mosquitoes that were preserved in amber for millions of years. While dinosaur DNA remains elusive in real life, the idea of resurrecting extinct species is gaining traction in plant genome research.

Researchers from NYU Abu Dhabi’s Center for Genomics and Systems Biology have successfully sequenced the genome of previously extinct date palm varieties that lived more than 2,000 years ago using a technique called “resurrection genomics.” The study, published in the Proceedings of the National Academy of Sciences, marks the first time researchers have sequenced the genomes of plants from ancient germinated seeds.

Rather than dinosaur DNA, the researchers used date palm seeds that were recovered from archaeological sites in modern-day Israel and radiocarbon-dated from the 4th century BCE to the 2nd century CE. The seeds were germinated to yield viable, new plants. The researchers conducted whole genome sequencing of these germinated ancient samples and used these data to examine the genetics of these previously extinct Judean date palms.

By examining the genome of a species (Phoenix dactylifera L.) that thrived millennia ago, NYU Biology Professor Michael D. Purugganan and his NYU Abu Dhabi colleagues, along with research partners in Israel and France, were able to see how these plants evolved over a period of time. In this case, they observed that between the 4th century BCE and 2nd century CE, date palms in the eastern Mediterranean started to show increasing levels of genes from another species, Phoenix theophrasti, which today grows in Crete and some other Greek islands, as well as southwestern Turkey, as a result of hybridization between species. They conclude that the increasing level of genes from P. theophrasti over this period shows the increasing influence of the Roman Empire in the eastern Mediterranean.

Resurrection genomics offers an alternative to other approaches to sequencing ancient DNA and is particularly useful for ancient and extinct plant species, the researchers note. Ancient plant DNA can be tricky to study, as it easily degrades without the protection of material like bone, and only small quantities are usually found—but regrowing the whole plant offers new possibilities.

“We are fortunate that date palm seeds can live a long time—in this case, more than 2,000 years—and germinate with minimal DNA damage, in the dry environment of the region,” said Purugganan, who is also affiliated with NYU Abu Dhabi and the Institute for the Study of the Ancient World (ISAW). “This ‘resurrection genomics’ approach is a remarkably effective way to study the genetics and evolution of past and possibly extinct species like Judean date palms. By reviving biological material such as germinating ancient seeds from archaeological and paleontological sites, or historical collections, we can not only study the genomes of lost populations but also, in some instances, rediscover genes that may have gone extinct in modern varieties.”

So, it is likely that scientists will use resurrection genomics to bring dinosaurs back from extinction?

“In principle, resurrection genomics can be used to revive extinct species or populations. There is actually an interest in this area. However, dinosaurs are probably not possible—but certainly plants, if we have seeds, or even bacteria or other microbes are possible,” said Purugganan.