The genome of the South American lungfish is larger than that of any other animal

A South American lungfish (Lepidosiren paradoxa) is seen in a laboratory at Louisiana State University in Baton Rouge, U.S., on March 18, 2024. | Photo credit: Katherine Segars/LSU

The South American lungfish is an extraordinary creature – in some ways, a living fossil. Inhabiting slow-flowing and stagnant waters in Brazil, Argentina, Peru, Colombia, Venezuela, French Guiana and Paraguay, it is the closest living relative of the first terrestrial vertebrates and closely resembles its primitive ancestors from more than 400 million years ago.

This freshwater species (Lepidosiren paradoxa) also has another feature: the largest genome of any animal on Earth – all the genetic information of an organism. Scientists have now sequenced its genome, revealing that it is about 30 times the size of the human genetic blueprint.

The parameter for the size of the genome was the number of base pairs, the basic units of DNA, in an organism’s cellular nucleus. If stretched out like a ball of yarn, the length of DNA in each cell of this lungfish would be about 60 meters. The human genome stretches only about 2 meters.

“Our analysis showed that the South American lungfish genome has grown enormously during the past 100 million years, leading to an increase equivalent to one human genome every 10 million years,” said Igor Schneider, an evolutionary biologist at Louisiana State University, one of the authors of the study published this week in the journal Biology. Nature,

In fact, 18 of the South American lungfish’s 19 chromosomes — thread-like structures that carry an organism’s genomic information — are each individually larger than the entire human genome, Schneider said.

Even though they are huge, there are plants that have larger genomes. The current record holder is a thorn fern species called Tmesipteris oblanceolata from the French overseas territory of New Caledonia in the Pacific Ocean. Its genome is more than 50 times the size of the human genome.

So far, the largest known animal genome belongs to another lungfish, the Australian lungfish (Neoceratodus forsteri) The South American lungfish had a genome more than twice as large. The world’s four other lungfish species, all living in Africa, also have large genomes.

Lungfish genomes are composed largely of repetitive elements – about 90% of the genome. The researchers said the massive genome expansion recorded in lungfish genomes is likely related to the lack of a mechanism in these species that normally suppresses such genomic duplications.

“Animal genome size varies greatly, but the significance and causes of genome size variation remain unclear. Our study advances our understanding of genome biology and structure by identifying mechanisms that regulate genome size while maintaining chromosomal stability,” Schneider said.

The South American lungfish grows up to about 1.25 meters in length. While other fish rely on gills to breathe, the lungfish also has a pair of lung-like organs. It lives in the oxygen-poor, swampy environments of the Amazon and Parana-Paraguay river basins, and supplements the oxygen it gets from the water by breathing oxygen from the air.

Lungfish first appeared in the Devonian Period. It was during the Devonian Period that one of the most important moments in the history of life on Earth occurred: when fish with lungs and fleshy fins evolved into the first tetrapods, the four-legged land vertebrates that now include amphibians, reptiles, birds, and mammals.

Because the predecessors of today’s lungfish were ancestors of tetrapods, their genomes could provide insights into how long-ago vertebrates evolved features, such as limbs, that made life on land possible.

For example, the researchers showed that the genetic machinery that governs the activity of the so-called sonic hedgehog SHH gene, which controls key events during embryonic development, likely controls the formation of the bone equivalent of fingers in the lungfish fin. Those fingers in the lungfish fin eventually evolved into fingers and toes in tetrapods.

“Tetrapod ancestors conquered land with limbs that evolved from fins, and breathed air through lungs. These features probably predated the colonization of land. Only by studying the biology of living lungfish lineages can we investigate the genomic basis and molecular-developmental mechanisms that facilitated the water-land transition of vertebrates,” Schneider said.