According to new research, butterfly wing patterns have a basic structure that non-coding regulatory DNA manipulates to produce the variety of wings seen in different species.
The study, “Deep cis-regulatory homology of the butterfly wing pattern ground plan,” which appears as the cover story in the Oct. 21 issue of Science, explains how “junk” DNA, or non-coding regulatory DNA, which sits between genes, accommodates a basic plan conserved over tens to hundreds of millions of years while at the same time allowing wing patterns to evolve very quickly.
The results support the idea that there is an ancient blueprint for color patterns in the genome and that non-coding regulatory DNA acts as switches to turn on some patterns and turn off others.
Anyi Mazo-Vargas, Ph.D. ’20, the study’s first author and a former graduate student in the lab of senior author Robert Reed, professor of ecology and evolutionary biology in the College of Agriculture and Life Sciences, said, “We are interested in knowing how the same gene can build these very different looking butterflies.” At George Washington University, Mazo-Vargas is a postdoctoral researcher at the moment.
Mazo-Vargas says, “We see that there is a very stable group of switches [non-coding DNA] that are active in different places and are driving the gene.”
Key color pattern genes have been discovered in Reed’s lab before, including one called WntA that regulates stripes and another called Optix that regulates color and iridescence in butterfly wing patterns. When the Optix gene was turned off, the wings turned black, and when the WntA gene was taken away, the stripes went away.
The impact of non-coding DNA on the WntA gene was the main topic of this investigation. In particular, 46 of these non-coding parts were looked at in five species of nymphalid butterflies, which are the largest family of butterflies.
When tightly wound coils of DNA unwind, it means that a regulatory element is working with a gene to turn it on or, in some cases, off. This is how non-coding regulatory elements control genes.
In the study, the areas of the genome where this unwinding is taking place were found using a technique called ATAC-seq. In order to pinpoint the genomic areas involved in the formation of butterfly wing patterns, Mazo-Vargas examined ATAC-seq profiles from the wings of five different butterfly species. They were shocked to see that several regulatory regions were shared by a wide variety of butterfly species.
Then, using CRISPR-Cas gene editing technology, Mazo-Vargas and colleagues disabled 46 regulatory elements one at a time to observe how the disruption of each of these non-coding DNA sequences affected wing patterns. When each non-coding part was taken away, it changed a part of the butterflies’ wing patterns.
The fact that these non-coding elements had similar functions to the WntA gene in four different species—the buckeye (Junonia coenia), the painted lady (Vanessa cardui), the hawk moth (Heliconius himera), and the gulf fritillary (Agraulis vanillae)—showed how old they were and that they hadn’t changed much over time. This suggests that they probably came from a long-ago common ancestor.
They also found that D. plexippus, which is the monarch butterfly, used different regulatory parts from the other four species to control its WntA gene. This may be because it lost genetic information as it evolved and needed a new regulatory system to make its unique color patterns.
The majority of evolution, according to Reed, is thought to be caused by mutations in these non-coding areas. “I hope that our paper will serve as a case study that demonstrates how individuals can use this pairing of ATAC-seq and CRISPR to start interrogating these fascinating regions in their own study systems, whether they work on birds, flies, or worms,” the author says.
The National Science Foundation provided funding for the research (NSF).
Theodore Morgan, a program director at the NSF, called the study “a breakthrough for our understanding of the genetic control of complex features, and not only in butterflies.” “The study found new evidence for how regulatory DNA segments can have both positive and negative effects on features like color and shape. It also showed that butterfly color patterns have changed very little over time.”
