Whitman Fellow Designs Genomic Tools to Study Horseshoe Crab Eye Development
They may be famous for their striking blue blood, but horseshoe crabs have an award-winning vision system.
In the 1930s, Haldan Keffer Hartline produced the first single-cell recording of a photoreceptor from a horseshoe crab's large eyes. The results spawned universal discoveries about vision and earned Hartline a shared Nobel Prize in Physiology or Medicine in 1967, with much research conducted at the СƵ.
Despite their long history as model organisms, scientists understand little about horseshoe crabs, particularly at the molecular level. And “pretty much nothing is known about how their eyes develop,” said, a 2025 Whitman Fellow at the СƵ.
Gainett has bridged this research gap by designing experimental protocols and genomic tools specialized for horseshoe crabs. His techniques target the molecular mechanisms that control eye development in embryos, leading to the first gene-edited horseshoe crab.
“For me, it’s interesting to study how you can invent different ‘cameras’ [in the eye]. What are the basic building blocks for inventing different types of [eyes] and changing one type for another?” Gainett said.
Horseshoe crabs are considered “living fossils,” with an incredibly conserved morphology – yet expansive – genome, Gainett said. Perhaps a deeper understanding of their development can demystify their biology and inform why nature evolved some ways of seeing rather than others.
Optical confusion
Gainett, a postdoctoral scientist at Harvard Medical School and Boston Children’s Hospital, has dedicated his research to sensory systems in arthropods, a group of animals that includes insects, crustaceans, and arachnids.
Nature has found all sorts of solutions to optics, he said, with two distinct paths carved from the arthropod evolutionary tree.
Most insects and crustaceans developed compound eyes: a kaleidoscope of tiny lenses that combine pixels to produce an image.
The second solution evolved millions of years ago in arachnids when they diverged from their arthropod ancestors. Spiders, like humans, have single-lens eyes. These eyes function similar to a camera, with features to focus light on the retina and sharpen images.
But millions of years ago, there was an evolutionary hiccup. While spiders evolved camera eyes with high acuity, horseshoe crabs retained compound eyes, sensing their sandy world through fuzzy shapes and shadowy edges.
They are the only creatures within this group to have conserved this eye type, Gainett said. When it comes to evolving vision, he asked: “How do you go from one solution to another?”
To piece together this evolutionary puzzle, Gainett needed to develop molecular techniques to trace the “building blocks” of eye development in horseshoe crabs.
Needling the genome
Horseshoe crab embryos are two-millimeter balloons of rubbery membrane. They’ve got a thick outer layer acting as the animals’ only defense against beach-dwelling predators and a relentless sea. As a result, they’re resilient and impermeable to outside forces – including injection needles used to modify the genetic material.
“How do you get a needle inside a balloon without the balloon exploding?” Gainett asked. “And then how do you remove the needle without the balloon withering?”
By designing refined tools to break through biology.
With collaborator Adair Oesterle at the СƵ, Gainett developed a specialized needle thin enough to sink into the embryo. This advancement made the horseshoe crab genome accessible for targeted modification for the first time.
Gainett used the new needle to precisely prick the embryo and inject CRISPR-Cas9 into the animal’s genome, editing some genes that control eye development.
“Promising results”
As a 2024 Grass Fellow, Gainett isolated a gene responsible for pigmentation. This gene is not essential for development, but if tweaked, it can visibly show researchers something useful about eye formation.
Gainett used CRISPR-Cas9 to modify this pigmentation gene. Successful gene editing would not only change the genome, but also alter the crab’s appearance, bleaching the eyes of their typical blackness.
Gene sequencing analyses revealed cleavages in the DNA right at the sites of Cas9 injection, indicating a modified genome. And the resulting phenotype matched the genotype: The gene-edited embryos developed clear, milky eyes.
From genotype to phenotype, these early results suggest that Gainett fully disrupted the intended eye-color protein in the genome. “These are very, very promising results. I am excited to perfect the method this summer and use it to learn more about the evolution of their eyes,” he said.