This organism's genome is a 'mountain of DNA garbage', and it's growing

South American lungfish (Image credit: Katherine Seghers, Louisiana State University)

Life will always find its own way, even though one of those ways may be "picking up trash."

In a small African pool in August, a large black fish leaped out of the water, opened its mouth wide, and with a sound like a bellows, it swallowed enough air and went back under the water.

This is a lungfish . Lungfish have gills like other fish, but they also have a very primitive lung , the inner surface of which is even covered with a large number of honeycomb-like cavities, where the air it has just swallowed is exchanged, ensuring that it can survive the dry season.

In our impression, lungs seem to be structures unique to terrestrial animals. No wonder before the 1980s, people once believed that lungfish were the ancestors of all tetrapods, including humans. But now we know that our ancestors may have once shared the same habitat with lungfish, but lungfish are not our direct ancestors.

420 million years ago, two species of fish went their separate ways. One of them came to land and gave rise to humans after a long period of evolution, while the other remained almost unchanged. The earliest known lungfish fossils were found in the Early Devonian strata 400 million years ago, but today, 400 million years later, the living Australian lungfish (Neoceratodus forsteri) looks exactly like the fossils. Now, there are only six species of these creatures, known as "living fossils", one of which is in Australia, one in South America, and the other four live in Africa.

Illustration: Brian Choo

Huge genome

The fact that their body shape has barely changed doesn't mean that lungfish have gained nothing in their long evolution - they have gained a huge genome. The DNA of the South American lungfish (Lepidosiren paradoxa) has more than 91 billion base pairs , making it the largest of all species sequenced to date.

Before the South American lungfish genome was sequenced, the record was held by the Australian lungfish and the African lungfish (Protopterus annectens), whose genomes had about 40 billion base pairs. In comparison, the human genome is only 3 billion base pairs . Of the 19 chromosomes of the South American lungfish, 18 of them alone are larger than the entire human genome.

Such a huge genome will of course bring great difficulties to research. The process of genome sequencing is a bit like putting together a jigsaw puzzle. Previous sequencing technologies could only read a very short section of gene sequence each time, which is like fixing the size of each puzzle piece. When the entire puzzle becomes very large, the number of puzzle pieces will also increase sharply.

However, with the development of long-read sequencing technology in recent years, researchers can read sequences containing thousands or even tens of thousands of bases at a time, giving us the opportunity to see the full picture of these huge genomes.

Regardless of whether it has been sequenced or not, the stone lungfish (Protopterus aethiopicus) holds the record for the largest genome in the Earth's animals, followed closely by the Neuse River mud salamander (Necturus lewisi). (Image source: Global Science, March 2022 issue, "Salamanders: A Slow-paced Evolutionary Legend")

In 2021, an international research team led by evolutionary biologist Axel Meyer of the University of Konstanz in Germany and biochemist Manfred Schartl of the University of Würzburg published their results in Nature, reconstructing most of the genome sequence of the Australian lungfish.

Recently, the research team once again appeared in Nature, unlocking the full genome sequence of African lungfish and South American lungfish. This study not only brought the largest genome sequencing results to date, but also showed us the process of the lungfish genome "growing up" .

A burden

A large genome does not mean more effective information. Among the 3 billion base pairs that record human genetic information, there are only about 20,000 genes in the traditional sense, or DNA fragments that encode proteins. The rest was once considered meaningless "junk DNA."

In contrast, the South American lungfish genome is more than 30 times larger than that of humans, but only has about 20,000 sequences that actually encode proteins. This means that there is even more "junk" in their genome. In fact, researchers realized that more than 90% of the genes in the South American lungfish are repetitive sequences.

This 90% of "junk" has another name - transposons , or jumping genes, which are some DNA fragments that can jump around in genes. The problem is that most of them, in addition to "jumping" in genes, can also "photocopy" themselves into a large number of copies and then insert them into the genome. And these "new" fragments can still continue to replicate themselves , thus "reproducing" in large numbers in genes like viruses. It is in this way that transposons continue to reproduce in the genes of lungfish, making their genes so large .

This characteristic once made transposons called "selfish genes" or "gene parasites". Obviously, if transposons are active on a large scale or even inserted into important genes, it will have serious consequences for the "host". So in most cases, we can see that organisms have also evolved a complete set of defense mechanisms. For example, KRAB-type zinc finger proteins can recognize specific DNA sequences and bind to transposons, thereby silencing transposons at the epigenetic level. In germ cells, piRNAs target transposons to form double-stranded RNA to resist the invasion of transposons.

However, lungfish seem to lack this function . Researchers have found that compared with humans and other lungfish, the South American lungfish genome has significantly fewer genes related to piRNA and KRAB-type zinc finger proteins (humans and other lungfish have about 300 copies, while South American lungfish have only 23). Perhaps it is precisely because of the loss of the ability to contain transposons that the South American lungfish has a huge genome.

The end result is that we see the fastest rate of genome expansion in the South American lungfish of any known species: On average, the lungfish genome grows to the size of a human genome every 10 million years , a rate they have maintained for at least 100 million years. “And it’s still growing,” Meyer said. “We have evidence that transposons are still active in the lungfish genome today.”

The cost of expansion

This raises the question of what survival costs come with having a large genome, a cost we can clearly see in another organism with a similarly large genome: the salamander .

The genome size of different salamander species varies greatly, from "only" 10 billion base pairs to as many as 120 billion, also packed with transposons. These "burdens" in the genome make many salamanders grow into "giant babies": like the Neuse River mud salamander, they have young gills, weak limbs and extremely simple brains, and they cannot fully complete the metamorphosis process throughout their lives.

In 2018, a study gave a possible answer. Researchers reconstructed the genome of the Mexican axolotl (Ambystoma mexicanum), which contains a total of 32 billion base pairs. They found that transposons are not simply scattered between genes, but also exist in large numbers in the intron regions within genes. When a gene is expressed, the entire DNA, including introns, will be transcribed into an RNA chain, and then the introns need to be trimmed off so that the remaining sequence can be used as a template to produce proteins.

Mexican axolotl (Photo source: pixabay)

Because they are so packed with transposons, the intron sequences of the Mexican axolotl can be up to 13 times the length of introns in human genes, so their RNA takes longer to produce, and the instructions guiding cell differentiation take longer to take effect, making it difficult for any part of their body to actually grow .

Lungfish do not seem to suffer from similar difficulties. In a study published in Cell in 2021, Northwestern Polytechnical University, South China Agricultural University, Wuhan Institute of Hydrobiology, Chinese Academy of Sciences, Shenzhen Institute of Agricultural Genomics, Chinese Academy of Agricultural Sciences, BGI and other institutions jointly analyzed the first complete and high-quality super-large genome of African lungfish. The results showed that the introns of African lungfish are also very long, with nearly 16Gb of the entire genome being introns.

The longest gene in African lungfish is 18 Mb, much longer than that in the Mexican axolotl (6.7 Mb) and humans (2.5 Mb). By examining the transcriptome data, the researchers found no obvious correlation between gene expression levels and gene length. Even genes longer than 1 Mb showed expression levels similar to other shorter genes. In other words, changes in gene length seem to have little effect on gene expression in African lungfish. "These results," the paper reads, "suggest that the transcription efficiency of ultra-long genes in lungfish may be increased in order to maintain a balance in gene expression."

Every step of the login

When we carefully understand the changes in the lungfish genome, we can also see the evolutionary process that the ancestors of tetrapods went through in the intermediate stage from water to land. This process requires a series of innovations in life: breathing with lungs, supporting limbs, skin that can cope with dryness, and completely different movement postures...

Not only do lungfish have primitive lungs , they have also greatly increased the number of genes encoding pulmonary surfactant protein B, a complex lipoprotein that can maintain the relative stability of alveolar size . The number of related genes in lungfish is 2 to 3 times that of bony and cartilaginous fish, which is consistent with the typical number of tetrapods. At the same time, genes involved in olfaction have also been expanded in lungfish - a pre-adaptation for living in air.

Another important change occurred in the limbs. Lungfish and Latimeria are both lobe-finned fish, and they already had rudimentary bones in their fins, which provided a certain degree of support . The genome sequence also completed this story: researchers saw genes related to limb development in tetrapods in the lungfish genome, a pattern that had never been seen in other fish before. This shows that "early lobe-finned fish had already produced limb-like gene expression, preparing for subsequent quadrupedal adaptation."

However, among the living lungfish, only the Australian lungfish has the same thick fleshy fins as its ancestors. Over the past 100 million years, the pectoral and pelvic fins of African and South American lungfish have degenerated into filaments. (Image source: Katherine Seghers, Louisiana State University)

The researchers even saw some unexpected findings. In a study published in Cell in 2021, the researchers noticed that the protein neuropeptide S and its receptor, which are closely related to anti-anxiety, co-appeared in the ancestors of lungfish and tetrapods. Consistent with this, the amygdala of the brain also began to have a relatively mature multi-partition structure from the ancestors of lungfish and tetrapods. The researchers speculate that the ancestors of lungfish and tetrapods may have been stronger in their ability to handle anxiety in order to adapt to completely different environmental disturbances such as air breathing and terrestrial life.

References

[1]https://www.nature.com/articles/s41586-024-07830-1#author-information

[2]https://www.nature.com/articles/s41586-021-03198-8#ref-CR19

[3]https://www.cell.com/cell/fulltext/S0092-8674(21)00090-8

[4]https://www.eurekalert.org/news-releases/1054265

[5]https://www.eurekalert.org/news-releases/907686

[6]http://www.kiz.ac.cn/xwzx/news5/202102/t20210226_5961028.html

[7] Global Science, March 2022, “Salamanders: A Slow-Paced Evolutionary Legend”

Planning and production

Source: Global Science (ID: huanqiukexue)

Author: Erqi

Editor: He Tong

Proofread by Xu Lailinlin