Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments. However, the molecular underpinnings of this unique trait remain unclear. An multinational team of researchers investigated the origin of this innovation by developing the little skate (Leucoraja erinacea) as a genomically enabled model. Their analysis of a high-quality chromosome-scale genome sequence for the little skate shows that it preserves many ancestral jawed vertebrate features compared with other sequenced genomes, including numerous ancient microchromosomes.
The cartilage of the little skate (Leucoraja erinacea) is stained with Alcian blue, the bones with Alizarin red. Image credit: David Gold, Lynn Kee & Meghan Morrissey / MBL Embryology Course.
“We know that animals with a backbone and a skeleton — known as vertebrates — including fish, possess myriad body shapes, but we understand little about the underlying processes controlled by genes,” said Dr. Tetsuya Nakamura, a researcher at Rutgers, the State University of New Jersey.
“In this research, we have identified the genetic mechanisms that create the unique characteristics of the skate body.”
Little skates are an Atlantic Ocean species of skate that are about 40-51 cm (16- 20 inches) long.
Their flat bodies feature enlarged, wing-like pectoral fins that allow the fish to thrive in sea-floor environments.
Their unique shape creates power for rapid forward propulsion.
They also use their flat fins to scoop and flip sand over them to hide from predators, covering everything but their eyes.
“We wondered how this unique body evolved during their evolution,” Dr. Nakamura said.
“If we came to understand how a skate evolved, perhaps it might give us clues to how other vertebrates developed their shapes.”
In conducting their analysis, Dr. Nakamura and colleagues connected the skates’ genotype — their unique sequence of DNA, with their phenotype — their physical properties, from body shape to biochemistry.
They also compared the little skate genome with various shark genomes, including that of the bamboo shark, with whom it shares a common ancestor.
The researchers found similarities between the genomes and gene orders of the little skate and the bamboo sharks, which retain ancestral characters of chromosomes, the essential structures compactly packing DNA in the nucleus of every cell.
In the region of the little skate genome that controls for fin development, they found extensive rearrangements in the order of genes, akin to a shuffling of cards.
This gene shuffling occurred in the region of fin formation genes in skates when compared to sharks.
They also identified a fin-specific enhancer that interacts with several Hox genes, which have been identified in other research to be involved in patterning an animal’s body from head to tail.
In vertebrates, Hox genes determine the position of segmentation for areas of the body including the head.
In the case of the little skate, the team found Hox genes were indispensable for the evolution of its wide fins.
“This extensive conservation of chromosomal identity and gene order, despite 300 million years of divergence, indicates that most cartilaginous fish like skates, rays and sharks likely share this genetic organization,” Dr. Nakamura said.
“Overall, we found that genetic recombination and genome sequence changes are critical for skate-wide fin evolution.”
The results were published in the journal Nature.
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F. Marlétaz et al. The little skate genome and the evolutionary emergence of wing-like fins. Nature, published online April 12, 2023; doi: 10.1038/s41586-023-05868-1
