Thirty times as large as the human genome: An international team of researchers led by Konstanz evolutionary biologist Axel Meyer and Würzburg biochemist Manfred Schartl has mapped the largest genome of all animals, the lungfish genome. Their data helps explain how the fish ancestors of today’s land vertebrates were able to conquer land.
Join us as we travel back in time! We have arrived at the Devonian period, about 420 to 360 million years ago. In a shallow area near the water’s edge, something happened that would change life on our planet forever: a fish from the lobe-finned class uses its pair of powerful pectoral fins to pull itself out of the shallow water toward land and drag its body over the surface. muddy surface on the coastline. The fish is in no hurry to return to the water. It can breathe air easily because this fish already has lungs, as we terrestrial vertebrates still have today.
This scenario, or one similar to it, could be the first time a vertebrate moved on land, one of the most important events in evolutionary history. Because all later land vertebrates, or tetrapods, can be traced back to a fish. This includes not only amphibians, reptiles and birds, but also mammals, including humans. Yet one mystery remains: why were the fish of this lobe-finned lineage so well prepared to conquer land?
A look at his living relatives
To find the answer to this question after such a long time, the genetic material of the closest living relatives of our Devonian ancestor has now been analyzed, which makes it possible to draw conclusions about its appearance. Only three genera of these close relatives, the lungfish, are still alive: one in Africa, one in South America and one in Australia. It seems that evolution has forgotten them, because these ancient ‘living fossils’ still look very much like their ancestors. Because our genetic material, DNA, consists of nucleobases and the sequence of these nucleobases contains the actual genetic information, a comparative analysis of the genomes of lungfish is only possible with knowledge of their complete sequences.
We already knew that the genomes of lungfish are enormous, but how gigantic they really are and what we can learn from them has not been clear until now. Accordingly, the sequencing of lungfish genomes was very labor-intensive and complicated from both technical and bioinformatic perspectives. However, an international research team led by Konstanz biologist Axel Meyer and Würzburg biochemist Manfred Schartl has now succeeded in completely mapping the genome of the South American lungfish and that of a member of the African lineage. The previously largest genome sequence of the Australian lungfish (Neoceratodus) had already been mapped by the same team. The findings of their latest research have been published in the journal Nature.
Very big, but why?
The genetic material of the South American lungfish in particular breaks all records in terms of size: ‘With more than 90 gigabases (or 90 billion bases), the DNA of the South American species is the largest of all animal genomes and more than twice as large as the DNA from the South American lungfish. large as the genome of the previous record holder, the Australian lungfish, 18 of the 19 chromosomes of the South American lungfish are individually larger than the entire human genome with its almost 3 billion bases,” says Meyer. Autonomous transposons are responsible for the lungfish genome growing to this enormous size over time. These are DNA sequences that ‘replicate’ and then change their position in the genome, causing the genome to grow.
Although this also occurs in other organisms, the research team’s analyzes showed that the growth rate of the South American lungfish’s genome is by far the fastest ever: every 10 million years in the past, its genome has grown by the size of the entire human genome. “And it continues to grow,” reports Meyer. “We found evidence that the transposons responsible are still active.” The researchers identified the mechanism for this massive genome growth: the extreme expansion is at least partly due to the very low abundance of piRNA. This type of RNA is part of a molecular mechanism that normally silences transposons.
Yet remarkably stable
Because transposons replicate and jump around in the genome, contributing to its growth, they can greatly alter and destabilize an organism’s genetic material. This is not always detrimental, and it can even be an important driver of evolution, because these ‘jumping genes’ sometimes also cause evolutionary innovations by changing gene functions. This makes it all the more surprising that the current study found no correlation between massive transposon excess and genome instability; the lungfish genome is unexpectedly stable and the gene arrangement is surprisingly conservative. This fact allowed the research team to reconstruct the original architecture of the chromosome set (karyotype) of the ancestral tetrapod based on the sequences of the lungfish species that is still alive today.
In addition, the comparison of the lungfish genomes allowed them to draw conclusions about the genetic basis of the differences between the sexes that are still alive today. The Australian lungfish, for example, still has the limb-like fins that once allowed its relatives to move on land. In today’s other species of lungfish from Africa and South America, these fins, which are similar in bone structure to our arms, have evolved back into filamentous fins over the past approximately 100 million years. “In our study, we also used experiments with transgenic CRISPR-Cas mice to show that this simplification of the fins is due to a change in what is known as the Shh signaling pathway,” says Meyer.
During mouse embryonic development, the Shh signaling pathway regulates, among other things, the number and development of the fingers. The study results thus provide additional evidence for the evolutionary link between the ray fins of bony fish and the fingers of terrestrial vertebrates. With the new research now providing scientists with the complete genome sequences of all current lungfish families, additional comparative genomic studies in the future will provide further insight into the lobe-finned ancestors of terrestrial vertebrates – and help solve the mystery of how vertebrates made their way to the found land.
