The Atlas blue butterfly (Polyommatus atlantica) is found in the mountain ranges of Morocco and northeastern Algeria. This peculiar and elusive insect was suspected of containing a genome with a high number of chromosomes. Now, a team from the Institute of Evolutionary Biology (IBE), a joint center of the Spanish National Research Council (CSIC) and Pompeu Fabra University (UPF), and the Wellcome Sanger Institute has confirmed that it is the multicellular animal genome with the most chromosomes sequenced to date, with exactly 229 chromosome pairs. By comparison, the human genome has 23 pairs of chromosomes.

The study reveals that the chromosomes, rather than duplicating, would have fragmented over three million years, starting from an ancestral genome of 24 chromosomes, typical of many butterflies in this group. This mechanism has also been observed in human cancer cells, so its study could have implications for medicine.

For the first time, the team has sequenced the high-quality reference genome for the Atlas blue butterfly. This allows for comparison with that of other butterflies and moths to better understand how species form and change over time, shedding light on their evolution.

Knowing the genetic history of a species also allows us to predict how its next stage might develop. For example, how a species might respond to rising global temperatures and whether it possesses genes or mechanisms that protect it. This could guide conservation efforts for this threatened species.

Revealed the animal genome with the most chromosomes

Changes in chromosome number are thought to contribute to the formation of new species and help them adapt to their environment. In fact, the group to which the Atlas blue belongs includes many closely related species that evolved in a short period of time.

In this new research, the team discovered that this butterfly's chromosomes had fragmented at points where the DNA is less compacted. This means that the amount of genetic information is roughly the same, but it's packed into smaller sections.

All chromosomes except the sex chromosomes fragmented, and researchers estimate that this caused the chromosome number to increase from 24 to 229 in about three million years, a relatively short period by evolutionary standards.

Atlas blue butterfly (Polyommatus atlantica). Credit to Roger Vila.

“Generating the reference genome sequence of this butterfly has allowed us to clarify just how exceptional its genome is, having suffered hundreds of breaks and generated tiny, functional chromosomes. Even more surprising was the discovery of a possible mechanism for this phenomenon that would involve telomeric repeats, which normally protect the ends of chromosomes,” comments Roger Vila, principal investigator at the Institute of Evolutionary Biology (IBE), who participated in the study.

Investigating the reasons behind the Atlas blue butterfly genome fragmentation

This type of extreme chromosomal change is generally assumed to be negative; however, the Atlas blue butterfly has evolved and survived for millions of years using this strategy. It is only now, due to climate change and human impacts on the environment, that its populations are threatened. The destruction of cedar forests and overgrazing could lead to the collapse of Polyommatus atlantica populations.

“I've been researching this butterfly for many years, and I'm one of the few people who've been able to observe it in the wild. Unfortunately, the P. atlantica is seriously threatened by the destruction of its habitat. Breeding this species in captivity and sequencing its genome while it was still possible has been key to understanding its evolution,” explains Vila.

The discovery of this chromosome fragmentation raises multiple questions that could be addressed in the future. Chromosome breakage could contribute to greater genetic diversity by allowing more frequent reshuffling of genome fragments, or it could have other benefits. While this mechanism could help butterflies adapt quickly, species with many chromosomes may also face challenges due to the added complexity of this process, which could make them more vulnerable to extinction over time.

Further research and comparisons with other butterflies could reveal whether specific genes have been lost or preserved, giving us more insight into butterfly biology and a deeper understanding of their past and future evolution.

Habitat: The Atlas cedar forests of the mountainous areas of Morocco and Algeria are the habitat of the Polyommatus atlantica butterfly. Unfortunately, these ecosystems are threatened by indiscriminate logging and overgrazing.

A new window for future studies on evolution, conservation, and human health

Chromosomal rearrangements also occur in human cancers, so studying these processes in the Atlas Blue’s DNA could lead to new advances in human health and highlight possible ways to reduce or halt this phenomenon in cancer cells.

Dr. Charlotte Wright, first author of the study and a researcher at the Wellcome Sanger Institute, comments: “When we set out to understand butterfly evolution, we knew we had to sequence the Atlas Blue butterfly, the most extreme and, in some ways, mysterious butterfly. Thanks to Roger Vila, who had previously worked with colleagues to find and identify this elusive butterfly, we were able to sequence this species, which highlights the collaborative nature of science.”

Dr. Roger Vila, author from the Institute of Evolutionary Biology, says: “Chromosome breakage has been observed in other butterfly species, but not at this level, suggesting that there are important reasons for this process, which we can now begin to explore. Furthermore, since chromosomes hold all the secrets of a species, investigating whether these changes affect a butterfly’s behavior could help us better understand how and why new species arise.”

Professor Mark Blaxter, lead author from the Wellcome Sanger Institute, notes: “Genomes hold the key to a species’ origin, but also to its possible future. To tell the story of our planet, we need to know the history of each species and see where they overlap and interact. This also allows us to apply knowledge from one genome to another. For example, chromosome rearrangement is also seen in human cancer cells, and understanding this process in the Atlas Girl could help us find ways to limit or halt it in cancer cells in the future.”

Referenced article:

C. J. Wright, D. Absolon, M. Gascoigne-Pees, et al. (2025) ‘Constraints on chromosome evolution revealed by the 229 chromosome pairs of the Atlas blue butterfly’. Current Biology. DOI: 10.1016/j.cub.2025.08.032