The title of the longest genome of any animal on Earth belongs to a surprising contender: the lungfish an ancient freshwater vertebrate that straddles the evolutionary line between aquatic life and land-dwelling creatures. These unique animals, capable of breathing both air and water, and possessing limb-like fins, are thought to share a common ancestor with all tetrapods—four-limbed vertebrates that eventually evolved to walk on land.
A recent breakthrough by scientists has led to the sequencing of the largest lungfish genome, that of the South American lungfish (Lepidosiren paradoxa). With over 90 gigabases, or 90 billion DNA bases, this genome is the largest ever recorded for any animal, dwarfing even the previous record-holder, the Australian lungfish. To put it in perspective, the South American lungfish’s genome is 30 times the length of the human genome, with 18 of its 19 chromosomes each individually larger than the entire human genome.
Unraveling the Lungfish Genome
Despite its enormous size, the lungfish genome contains around 20,000 protein-coding sequences, a number comparable to that of humans. This leaves a vast amount of DNA, whose purpose researchers are still striving to understand.
The sequencing of the South American lungfish genome follows similar work on the Australian lungfish, Neoceratodus forsteri, and the African lungfish, Protopterus annectens. Together, these sequences offer new insights into how these ancient fish have diversified and evolved over the past 100 million years.
Lungfish are named for their ability to breathe air through lungs, a trait that was crucial for the transition to life on land. The three remaining lungfish lineages African, South American, and Australian are considered living fossils, and studying the differences among them can provide valuable information about the evolution of tetrapods, which emerged around 390 million years ago.
One of the key reasons for the lungfish’s colossal genome is the presence of a large number of ‘jumping genes,’ or transposable elements. These rogue DNA sequences can copy themselves and move around the genome, sometimes leading to rapid genetic changes. In the case of the lungfish, these transposons have caused the genome to grow by the size of the human genome every 10 million years for the past 100 million years.
Interestingly, the researchers found that the lungfish has low levels of piRNA, a type of RNA that usually suppresses transposon activity. This has allowed the lungfish genome to continue expanding unchecked.
Despite its enormous size and ongoing expansion, the lungfish genome is surprisingly stable. The arrangement of genes is conservative, allowing researchers to reverse-engineer the chromosome architecture of ancestral lobe-finned fish. This research has confirmed the ancestry of these lungfish, providing a clearer understanding of the evolutionary path leading to tetrapods and, ultimately, to humans.
Comparing the genomes of the three lungfish species has also revealed fascinating differences in their evolution. For example, the Australian lungfish retains limb-like fins and can still use its gills, while the African and South American lungfish have lost their gills and evolved filamentous fins. This limb reversion is linked to changes in a signaling pathway known as Shh, which guides embryonic development.
The genomes of all three lungfish lineages hold crucial information for understanding how molecular and developmental processes contributed to the evolution of tetrapods and the conquest of land. The research, published in Nature, provides a valuable resource for future studies aimed at uncovering the secrets of vertebrate evolution. By studying these ancient genomes, scientists hope to gain a deeper understanding of one of the most significant transitions in the history of life on Earth.
