A genome with a delete key
The deep ocean off the coast of California hosts an animal that challenges a basic principle of biology. The Pacific hagfish (Eptatretus stoutii) and its relatives are jawless eel-shaped creatures that belong to an ancient lineage of animals, the cyclostomes, that diverged from jawed vertebrates about 500 million years ago. For decades, scientists held that virtually every cell in a complex animal contains the exact same set of genetic instructions. Hagfish demonstrate a radical exception. During their embryonic development, the cells destined to become most of the hagfish's body—its somatic cells—systematically destroy and discard large portions of their own DNA. This process is called programmed genome rearrangement (PGR).
Only the germline cells, which become eggs or sperm, retain the complete, unabridged genome. The scale of this genetic deletion is significant. In the Japanese hagfish (Eptatretus burgeri), about 21% of the germline DNA is eliminated from somatic cells. Across different hagfish species, the amount of discarded DNA ranges from 20% to as high as 74.5%. The eliminated material consists of entire chromosomes or large chromosomal fragments, which contain many highly repetitive DNA sequences, often called satellite DNA. This process was first discovered through cytogenetic studies that noticed a stark difference in chromosome counts between germline and somatic tissues. For example, E. burgeri has 52 chromosomes in its reproductive cells but only 36 in its body cells.