Researchers have discovered that little skate's unique cape-like fins evolved through changes in the non-coding regions of its genome and the three-dimensional structures called 'topologically associated domains' (TADs). This breakthrough highlights the importance of 3D genomic structures in driving
The cartilage of the skate is stained with Alcian blue, the bones with Alizarin red. One of the few places in the world that collects Leucoraja erinacea and breeds it for research, including for the present study, is the Marine Resources Center at the Marine Biology Laboratory in Woods Hole. Credit: David Gold Lynn Kee and Meghan Morrissey, MBL Embryology Course
Scientists at Max Delbrück Center in Berlin, the Andalusian Center for Developmental Biology in Seville and other labs in the United States have discovered how the skate evolved these cape-like fins by peering into their. They found that the key to the evolution of the skate fins lies not in the coding regions of its genome, but rather in the non-coding bits and the three-dimensional complexes that it folds into. These 3D structures are called “topologically associated domains” .
More than 450 million years ago, the genome of a primitive fish — the ancestor of all vertebrate animals — duplicated twice. The expansion in genetic material drove the rapid evolution of more than 60,000are little skates , which belong to a lineage of cartilaginous fishes that includes sharks and rays. These distant cousins are ideal organisms to learn about the evolution of traits that made us human, such as paired appendages. “Skates are cartilaginous fishes called Chondrichthyans.
To overcome this difficulty, the scientists used long-read sequencing technology, together with Hi-C data, to assemble the pieces of the DNA like a puzzle and assign the unordered sequences to skate chromosomes. With the new reference, assembling the 3D structure of the TADs using Hi-C became trivial.
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