South American lungfish, Lepidosiren paradoxa
© Katherine Seghers, Louisiana State University
A favourite creationists straw man parody of science says that evolutionary biologists believe evolution is a process of increasing complexity, leading eventually to humans - the most complex of all species.
This is utter nonsense, of course, being intelligently designed to easily attack and make evolutionary biology look like something no rational person would believe, so creationists dupes can feel smugly superior to scientists without bothering to learn any real science.
Creationists dogma also says that a genome was intelligently designed, so does not contain any redundant or non-coding DNA, since an intelligent designer would not have designed needless complexity and prolific waste (both characteristics of a mindless evolutionary process).
So, it leaves creationists floundering when science discovers genomes many times larger (for larger read 'more complex', in creationist terminology) than the human genome. In fact, the human genome is about average for the number of genes and size of the genome compared to other animals and very much smaller than that of many animals and plants.
Do you have examples of animal and plant genomes that are several times larger than that of the human genome? Yes, there are several examples of animal and plant genomes that are significantly larger than the human genome, which is approximately 3.2 billion base pairs (Gb) in size. Here are a few notable examples:Just such a genome has just been fully decoded by an international team of researchers led by the University of Konstanz evolutionary biologist, Axel Meyer and the University of Würzburg biochemist, Manfred Schartl. They have found, for example, that 18 of the 19 chromosomes of the South American lungfish each contain more DNA than the entire human genome.
Animals:Plants:
- Marbled Lungfish (Protopterus aethiopicus):
- Genome Size: ~130 billion base pairs (Gb)
- Description: The marbled lungfish holds the record for the largest known animal genome. Its genome is about 40 times larger than that of humans. Lungfishes are fascinating creatures that can breathe air and are considered close relatives of tetrapods.
- Axolotl (Ambystoma mexicanum):
- Genome Size: ~32 billion base pairs (Gb)
- Description: The axolotl, a type of salamander, has a genome about 10 times larger than the human genome. This amphibian is known for its remarkable ability to regenerate limbs, spinal cord, heart, and other organs.
- Eurasian Wels Catfish (Silurus glanis):
- Genome Size: ~150 billion base pairs (Gb)
- Description: This species of catfish has an enormous genome, although its size has not been fully characterized. It is one of the largest freshwater fish in Europe and is known for its enormous size.
These examples illustrate the incredible diversity in genome sizes across the tree of life. While larger genomes often contain more repetitive sequences and non-coding DNA, the exact reasons for such vast differences in genome sizes are still an active area of research.
- Paris Japonica:
- Genome Size: ~150 billion base pairs (Gb)
- Description: Paris japonica, a rare Japanese plant, has the largest known plant genome. Its genome is about 50 times larger than the human genome. This is the largest known genome of any living organism.
- Fritillaria assyriaca:
- Genome Size: ~130 billion base pairs (Gb)
- Description: This flowering plant, a type of lily, has an extremely large genome, approximately 40 times the size of the human genome. Members of the Fritillaria genus are known for having some of the largest genomes among plants.
- Amphibian Genomes (Some Species of Frogs and Salamanders):
- Genome Sizes: Often in the range of 20-30 billion base pairs (Gb)
- Description: Various species of amphibians, particularly salamanders, often have genomes that are several times larger than the human genome. This is likely due to large amounts of repetitive DNA and whole-genome duplications in their evolutionary history.
In the context of expanding genomes over time, what is piRNA and what does it do?
piRNA (Piwi-interacting RNA) is a class of small non-coding RNA molecules that play a crucial role in the regulation of gene expression, particularly in the suppression of transposable elements (TEs) in animal genomes. Here's a breakdown of what piRNAs are and what they do:
What is piRNA?
- Size: piRNAs are typically 24-31 nucleotides long, making them slightly longer than other small RNAs like microRNAs (miRNAs) and small interfering RNAs (siRNAs).
- Origin: piRNAs are derived from long single-stranded precursor RNAs transcribed from specific genomic regions known as piRNA clusters.
- Associated Proteins: piRNAs interact with a group of proteins called Piwi proteins, which are part of the Argonaute family of proteins. This interaction is essential for the biogenesis and function of piRNAs.
What Does piRNA Do?
Role in Genome Evolution and Expansion
- Suppression of Transposable Elements (TEs):
- Primary Function: The main role of piRNAs is to protect the genome from the potentially harmful activity of transposable elements, often referred to as "jumping genes." These elements can move around the genome, causing mutations, disrupting gene function, and leading to genome instability.
- Mechanism: piRNAs guide Piwi proteins to complementary RNA sequences derived from transposable elements. This targeting leads to the degradation or silencing of the TE transcripts, preventing their expression and mobility.
- Genome Stability:
- By suppressing transposable elements, piRNAs help maintain the integrity and stability of the genome, especially in germ cells (sperm and eggs), where the genome must be faithfully transmitted to the next generation.
- Regulation of Gene Expression:
- Beyond their role in transposon silencing, piRNAs are also involved in the regulation of gene expression during development, particularly in the germline. They can modulate the expression of genes involved in processes like stem cell maintenance, differentiation, and meiosis.
- Epigenetic Regulation:
- piRNAs are involved in establishing and maintaining epigenetic marks on transposable elements, contributing to their long-term silencing. This is achieved by guiding the Piwi proteins to specific genomic loci, where they help recruit enzymes that modify histones and DNA, leading to a repressive chromatin state.
- Genome Size and piRNAs: The presence of piRNAs is thought to have allowed genomes to tolerate a larger load of transposable elements. While transposons can contribute to genome expansion by copying and inserting themselves into new locations, piRNAs help mitigate the potential damage caused by these elements. This balance allows for the potential benefits of transposons, such as creating genetic diversity, while minimizing their harmful effects.
- Evolutionary Significance: The evolution of the piRNA pathway is considered a major event in the development of complex organisms, particularly animals. By controlling transposable elements, piRNAs have likely played a significant role in shaping genome architecture over evolutionary time.
In summary, piRNAs are essential for maintaining genome stability by silencing transposable elements, regulating gene expression, and contributing to the epigenetic landscape of the genome. Their function is crucial for preventing the detrimental effects of unchecked transposon activity, which is particularly important in the context of large and complex genomes.
They have just published their findings in the journal Nature and explained it in a Konstanz University news release:
Decoding the world’s largest animal genomeSadly, the main body of the paper in Nature is behind and expensive paywall, so only the abstract is available:
Thirty times the size of the human genome: An international team of researchers led by Konstanz evolutionary biologist Axel Meyer and Würzburg biochemist Manfred Schartl has sequenced the largest genome of all animals, the lungfish genome. Their data help to 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 in the Devonian period, some 420 to 360 million years ago. In a shallow area near the water’s edge, something happened that would forever change life on our planet: a fish from the class of lobe-finned fishes uses its pair of powerful pectoral fins to pull itself out of the shallow water onto land, moving its body across the sludgy surface at the shoreline. The fish is in no hurry to return to the water. It can easily breathe air, because this fish already has lungs, like we land vertebrates still do today.
This scenario or one similar to it could have been 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 encompasses not only amphibians, reptiles and birds, but also mammals – humans included. Yet one mystery remains: Why were the fish of this lobe-finned lineage so well prepared to conquer land?
A look at its 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 analysed, making it possible to draw conclusions about their appearance. Only three lineages of these closest relatives, the lungfish, are still alive today: 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. Since our genetic material, the DNA, is made up of nucleobases and the sequence of these nucleobases contains the actual genetic information, a comparative analysis of the lungfish genomes is only possible with knowledge of their complete sequences.
We already knew that the genomes of lungfish are huge, but how gigantic they really are and what can be learned from them was not clear until now. Accordingly, the sequencing of the lungfish genomes was very labour intensive and complicated from both a technical and a bioinformatic perspective. However, an international research team led by Konstanz biologist Axel Meyer and Würzburg biochemist Manfred Schartl has now succeeded in fully sequencing the genome of the South American lungfish and of a member of the African lineage. The previously largest genome sequence of the Australian lungfish (Neoceratodus) had already been sequenced by the same team. The findings of their latest research were published in the journal Nature.
Very, very big, but why?
The genetic material of the South American lungfish in particular breaks all records for size:
With over 90 gigabases (in other words, 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 genome of the previous record holder, the Australian lungfish. 18 of the 19 chromosomes of the South American lungfish are each individually larger than the entire human genome with its almost 3 billion bases.
Alex Meyer, co-corresponding author
Evolutionary biologist
Department of Biology
University of Konstanz, Konstanz, Germany.
Autonomous transposons are responsible for the fact that the lungfish genome has ballooned to this enormous size over time. These are DNA sequences that “replicate” and then change their position in the genome, which in turn causes the genome to grow.
Although this occurs in other organisms as well, the research team’s analyses showed that the expansion rate of the genome of the South American lungfish is by far the fastest on record: Every 10 million years in the past, its genome has grown by the size of the entire human genome.
And it continues to grow. We have found evidence that the transposons responsible are still active.
>Alex Meyer.
The researchers identified the mechanism for this gigantic genome growth: The extreme expansion is at least partially due to very low piRNA abundance. This type of RNA is part of a molecular mechanism that normally silences transposons.
Remarkably stable nonetheless
Because transposons replicate and jump around in the genome, thereby contributing to its growth, they can greatly alter and destabilise the genetic material of an organism. This is not always detrimental, and it can even be an important driver of evolution, as these “jumping genes” sometimes also cause evolutionary innovations by altering gene functions. This makes it all the more surprising that the current study found no correlation between the enormous transposon surplus and genome instability – the genome of the lungfish is unexpectedly stable and the gene arrangement is surprisingly conservative. This fact enabled the research team to reconstruct the original architecture of the set of chromosomes (karyotype) of the ancestral tetrapod from the sequences of the lungfish species that are still alive today.
In addition, the comparison of the lungfish genomes enabled them to draw conclusions about the genetic basis of differences between the lineages still alive today. The Australian lungfish, for example, still has the limb-like fins that once enabled its relatives to move on land. In today’s other lungfish species from Africa and South America, these fins, which are similar in bone structure to our arms, evolved back into filamentous fins over the last 100 million years or so. “In our research, we also used experiments with CRISPR-Cas transgenic mice to show that this simplification of the fins is attributable to a change in what is known as the Shh-signalling pathway,” says Meyer.
During the embryonic development of mice, for example, the Shh-signalling pathway controls the number and development of the fingers, among other things. The research findings thus provide additional evidence of the evolutionary link between the ray fins of bony fish and the fingers of land vertebrates. As scientists now have the complete genome sequences of all current lungfish families at their disposal thanks to the new research, additional comparative genomic studies will provide further insights into the lobe-finned ancestors of land vertebrates in the future – and help solve the mystery of how vertebrates made their way onto land.
Abstract
The genomes of living lungfishes can inform on the molecular-developmental basis of the Devonian sarcopterygian fish–tetrapod transition. We de novo sequenced the genomes of the African (Protopterus annectens) and South American lungfishes (Lepidosiren paradoxa). The Lepidosiren genome (about 91 Gb, roughly 30 times the human genome) is the largest animal genome sequenced so far and more than twice the size of the Australian (Neoceratodus forsteri)1 and African2 lungfishes owing to enlarged intergenic regions and introns with high repeat content (about 90%). All lungfish genomes continue to expand as some transposable elements (TEs) are still active today. In particular, Lepidosiren’s genome grew extremely fast during the past 100 million years (Myr), adding the equivalent of one human genome every 10 Myr. This massive genome expansion seems to be related to a reduction of PIWI-interacting RNAs and C2H2 zinc-finger and Krüppel-associated box (KRAB)-domain protein genes that suppress TE expansions. Although TE abundance facilitates chromosomal rearrangements, lungfish chromosomes still conservatively reflect the ur-tetrapod karyotype. Neoceratodus’ limb-like fins still resemble those of their extinct relatives and remained phenotypically static for about 100 Myr. We show that the secondary loss of limb-like appendages in the Lepidosiren–Protopterus ancestor was probably due to loss of sonic hedgehog limb-specific enhancers.
There is a great deal for creationists to lie about, misrepresent or ignore in this work:
- Firstly, there is the massive amount of redundant DNA, which no intelligent designer worthy of the description would have included in its design, since the hallmark of good design is minimal complexity and minimal waste.
- Secondly, there is the evidence that masses of new genetic information, in terms of DNA codons, even those non-functional codons, arose by a natural process with no need for magic and no violation of any laws of physics and/or chemistry, contrary to the nonsense creationist frauds tell their dupes. In fact, the evidence is that the DNA equivalent of a whole human genome has been added to the genome of the South American lungfish every 10 million years for the last 100 million years.
- Thirdly, there is the disconnect between the complexity of the organism and the size of its genome.
- Fourthly, there is the evidence of a mindless, undirected utilitarian process at work in the 'creation' of this massive genome.
- Fifthly, there is the evidence supporting the theory that relatives of the lungfish were the lobe-finned fish that transitioned into the terrestrial tetrapods.
- And lastly, there is the complete absence of any evidence that the researchers considered the Theory of Evolution inadequate for explaining the observable facts.
Overall, another difficult day for creationism and another casual refutation of the childish superstition by science.
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