Research Sheds New Light on Stability of Gene Order in Chromosomes Across Animal Kingdom

Professor Daniel Martínez talks in class with a student holding a laptop computer.

Imagine four decks of cards, each with the same number of cards in identical order. Now visualize those card decks being shuffled continuously for 48 straight hours. What are the odds that at the end of the shuffling process, the cards in each deck would still be in exactly the same order?

A new paper published today in Science Advances reveals that, hard as it is to imagine, this is exactly what researchers are finding in the order of genes on chromosomes across the animal kingdom. Animal chromosomes have been shuffling for at least 700 million years, explains Daniel E. Martínez, professor of biology at Pomona College and one of the paper’s authors. “But when you look at them today, you find the same order of genes in the chromosomes. The same genes appear on the same groups of genes in chromosomes in all animals. Why are the genes not being shuffled?” That, he notes, is what the paper examines in sponges, hydra, scallops, jellyfish and a chordate (a close relative to vertebrates).

“It’s an absolutely surprising finding,” Martínez says. “Chromosomes break all the time. They rearrange, and two can get together and form another chromosome.” Yet upon closer examination, regardless of the type of animal, the approximate order of the genes remains the same. “I think we expected there would be a lot more freedom for gene order to change,” he says. “It’s pretty amazing that animals have maintained gene order in chromosomes in such a neat way.”

Using the card analogy again, Martínez notes that “You have to suspect something is gluing the cards together” to retain their order. He gives two potential reasons that genes have retained their order in chromosomes over millions of years. One is the location of the genes. “You might not be able to move it without disrupting how the gene functions,” he suggests, but adds that there is evidence against this hypothesis.

“A second one is more feasible,” Martínez continues. “When cells divide to make gametes, similar chromosomes find each other. In order to find each other, they need to have a very similar order of genes. If you scramble that, they wouldn’t be able to match up during cell division.”

The number of chromosomes varies throughout the animal kingdom. Humans have 23 pairs of chromosomes, while fruit flies have only four. Yet in 700 million years, animal evolution has been unable to shuffle the chromosomes in a way that causes genes to change their place in the sequence. Hydras—the long-time focus of Martínez’ research—have the same gene order as humans.

Martínez became involved in this area of inquiry during a 2021 sabbatical at the University of Vienna, where he worked with the paper’s first author, Oleg Simakov. “I never could have imagined five years ago that I’d be involved in a study that would do this,” he says, because five years ago scientists could not sequence entire chromosomes.

“That’s the exciting part of being a scientist,” Martínez says. “You never know what you’re going to discover next.”