According to new research, butterfly wing patterns have a basic plan, which is manipulated by noncoding regulatory DNA to create the diversity of wings seen in different species.
The study, “Deep cis-regulatory homology of the butterfly wing pattern ground plan,” published as the cover story in the Oct. Scienceexplains how DNA that sits between genes — “junk” DNA or noncoding regulatory DNA — harbors a basic plan conserved over tens to hundreds of millions of years, while at the same time allowing wing patterns to evolve extremely quickly.
The research supports the idea that a floor plan with an ancient color pattern is already encoded in the genome, and that non-coding regulatory DNA acts as switches to boost some patterns and reject others.
“We’re interested in knowing how the same gene can build these very different-looking butterflies,” said Anyi Mazo-Vargas, Ph.D. ’20, the study’s lead author and a former graduate student in the lab of senior author Robert Reed, a professor of ecology and evolutionary biology in the College of Agriculture and Life Sciences. Mazo-Vargas is currently a postdoctoral researcher at George Washington University.
“We see that there is a very conserved group of switches [non-coding DNA] that work in different positions and are activated and drive the gene,” said Mazo-Vargas.
Previous work in Reed’s lab has uncovered key color pattern genes: one (WntA) that controls streaking and another (Optix) that controls color and iridescence in butterfly wings. When the researchers turned off the Optix gene, the wings appeared black, and when the WntA gene was deleted, the stripe patterns disappeared.
This study focused on the effect of non-coding DNA on the WntA gene. Specifically, the researchers conducted experiments with 46 of these non-coding elements in five species of nymphalid moths, the largest butterfly family.
In order for these noncoding regulatory elements to control genes, tightly wound DNA coils are disconnected, a sign that a regulatory element is interacting with a gene to activate it, or in some cases, turn it off.
In the study, the researchers used a technology called ATAC-seq to identify regions in the genome where this unraveling takes place. Mazo-Vargas compared ATAC-seq profiles of the wings of five butterfly species to identify genetic regions involved in wing pattern development. They were surprised to find that a large number of regulatory regions were shared by very different butterfly species.
Mazo-Vargas and colleagues then used CRISPR-Cas gene-editing technology to knock out 46 regulatory elements one by one, to see the effects on wing patterns when each of these noncoding DNA sequences was broken. When removed, each non-coding element changed an aspect of the butterflies’ wing patterns.
The researchers found that in four of the species — Junonia coenia (buckeye), Vanessa cardui (painted lady), Heliconius himera, and Agraulis vanillae (Wave nacre) — each of these noncoding elements had similar functions with regard to the WntA gene, which shows that they were ancient and conserved, probably coming from a distant common ancestor.
They also found that D. plexippus (monarch) used different regulatory elements from the other four species to control its WntA gene, perhaps because it lost some of its genetic information over the course of its history and had to reinvent its own regulatory system. to develop its unique color patterns.
“We’ve gradually come to understand that most of the evolution takes place because of mutations in these noncoding regions,” Reed said. “What I hope is that this article will be a case study showing how people can use this combination of ATAC-seq and CRISPR to start interrogating these regions of interest in their own study systems, whether they’re working on birds, flies or worms. “
The research was funded by the National Science Foundation (NSF).
“This research is a breakthrough in our understanding of the genetic control of complex traits, and not just in butterflies,” said Theodore Morgan, program director at the NSF. “Not only did the study show how the instructions for butterfly color patterns are deeply conserved in evolutionary history, but it also revealed new evidence for how regulatory DNA segments positively and negatively influence traits such as color and shape.”