Unintelligent Design - A Tiny Fern With A Record-Breaking Genome

Tmesipteris oblanceolata

Genome over 50 times larger than a human genome

Record breaker: This tiny fern has the largest genome of any organism on Earth | Kew

Creationists know little of genetics or biology in general, so they are easy prey for frauds who lead their cult and take their money while fooling them into believing their ignorance makes them more expert than the experts and fully qualified to tell millions of working biomedical scientists that they've got it all wrong.

And one of the ideas they've been fooled with is the evolution is a process of increasing complexity and increasing genetic information. This is useful to the frauds who then sell them the idiotic notion that new genetic information can't arise because the Second Law of Thermodynamics [sic] makes it impossible. They also present complexity as evidence of intelligent design, which is also nonsensical, of course, because good intelligent, design is minimally complex.

So, many creationists believe the humans are the most complex organisms because they are the pinnacle of evolution, which is a again nonsensical because there is no such pinnacle; all species are equally well-adapted to their given environment and have been evolving, aimlessly, for the same period of time.

So, the logic of their misconception should be the assumption that humans should have at least one of the largest and most complex genomes of all living organisms or at least that genome size should equate to complexity and complexity to the ranking position in some sort of living hierarchy.

It might come as a shock then to discover that not only do humans have a fairly average size genome, far smaller than some 'primitive' salamanders, for instance, and certainly much small than some plants (e.g., the Norwegian spruce of Christmas tree). But the record genome size goes to a humble miniature fern from the French overseas territor of New Caledonia, Tmesipteris oblanceolata, with a genome size of 148.89 Gbp, or a little over 50 times the size of a human genome!

Is there a relationship between the genome size and complexity of an organism’s genome and the complexity of the organism itself? The relationship between the size and complexity of an organism's genome and the complexity of the organism itself is not straightforward. This topic is often summarized by the "C-value paradox" or "C-value enigma," which describes the lack of correlation between genome size (measured in base pairs or number of genes) and organismal complexity.

Here are some key points to understand this relationship:

1. Genome Size vs. Organismal Complexity:
   • Genome size, or C-value, refers to the total amount of DNA contained within one copy of a single genome.
   • There is no consistent correlation between genome size and the complexity of an organism. For example, some single-celled organisms have larger genomes than humans. The lungfish, for instance, has one of the largest known genomes, which is significantly larger than that of humans, despite being less complex.
2. Non-Coding DNA:
   • A significant portion of an organism's genome is non-coding DNA, which does not directly code for proteins. This includes introns, regulatory sequences, repetitive sequences, and other non-coding elements.
   • The proportion of non-coding DNA varies widely among organisms. In some cases, large genomes are primarily composed of non-coding DNA, which does not necessarily contribute to the organism's complexity.
3. Gene Number and Complexity:
   • The number of genes does not consistently correlate with organismal complexity. Humans have around 20,000-25,000 protein-coding genes, while some simpler organisms, such as the water flea (Daphnia pulex), have over 30,000 genes.
   • This discrepancy is partly because complexity arises not just from the number of genes, but from how they are regulated, expressed, and interact with each other.
4. Gene Regulation and Interaction:
   • The complexity of an organism is often more related to the regulatory networks and interactions between genes, rather than the sheer number of genes or the total genome size.
   • Complex organisms often have sophisticated mechanisms for gene regulation, alternative splicing, and post-translational modifications, which contribute to their complexity.
5. Examples of Genome Size Disparity:
   • Amoeba dubia has one of the largest genomes, around 200 times the size of the human genome, despite being a single-celled organism.
   • Plants, particularly those that have undergone polyploidy (having multiple sets of chromosomes), often have large genomes. For example, the Paris japonica plant has a genome size much larger than humans.

In summary, while it might seem intuitive that more complex organisms should have larger and more complex genomes, this is not necessarily the case. The relationship between genome size, gene number, and organismal complexity is influenced by many factors, including the amount of non-coding DNA, gene regulation, and evolutionary history.

This news comes in the form of a research paper by researchers from Kew Gardens. London, UK who have just published their findings, open access, in the Cell Press journal, iScience, accompanies by a press release from Kew Gardens:

• A New Caledonian fern species awarded 3 GUINNESS WORLD RECORDS™ titles; Largest plant genome, Largest Genome, and Largest fern genome for the amount of DNA in the nucleus
• Stretched out, the Tmesipteris oblanceolata genome is taller than Big Ben’s tower in London
• Discovery poses new questions about just how much DNA can be stored in cells
• Study will help scientists understand how genome size impacts species in face of biodiversity loss and climate change

In a new study published today in the journal iScience, researchers from the Royal Botanic Gardens, Kew and the Institut Botànic de Barcelona (IBB-CSIC) in Spain present a new record-holder for the largest amount of DNA stored in the nucleus of any living organism on the planet.

Coming in at more than 100 metres of unravelled DNA, the New Caledonian fork fern species Tmesipteris oblanceolata was found to contain over 50 times more DNA than humans and has dethroned the Japanese flowering plant species Paris japonica, which has held this record since 2010. In addition, the plant has achieved three Guinness World Records titles for Largest plant genome, Largest Genome, and Largest fern genome for the amount of DNA in the nucleus.

T. oblanceolata is a rare species of fern found on the island nation of New Caledonia, an overseas French territory situated in the Southwest Pacific, about 750 miles east of Australia, and some of the neighbouring islands such as Vanuatu. The genus Tmesipteris is an understudied group of plants consisting of about 15 species, most of which occur across a range of Pacific Islands and Oceania.

Until now, scientists have only estimated the size of the genomes for two species of Tmesipteris – T. tannensis and T. obliqua – both of which were found to contain gigantic genomes, at 73.19 and 147.29 gigabase pairs (Gbp) respectively.

In 2023, lead authors Dr Jaume Pellicer and Dr Oriane Hidalgo, from the IBB and formerly of RBG Kew, travelled to New Caledonia to collect samples of Tmesipteris, which were then analysed to estimate the size of their genomes. This involved isolating the nuclei of thousands of cells, staining them with a dye and then measuring how much dye had bound to the DNA within each nucleus – the more dye, the bigger the genome.

The analysis revealed the species T. oblanceolata to have a record-breaking genome size of 160.45 Gbp, which is about seven per cent larger than that of P. japonica (148.89 Gbp).

When unravelled, the DNA from each cell of this fern would stand taller than the Elizabeth Tower in Westminster, London, which is 96m tall and home to the world-famous Big Ben bell. For comparison, the human genome contains about 3.1 Gbp distributed across 23 chromosomes and when stretched out like a ball of yarn, the length of DNA in each cell only measures about 2m.

Highlights

• Giant genomes are restricted across the eukaryotic Tree of Life
• The genome of T. oblanceolata is over 50 times larger than the human genome.
• Genome size variation among eukaryotes expands over 61,000-fold.

Summary
Vascular plants are exceptional among eukaryotes due to their outstanding genome size diversity which ranges ∼2,400-fold, including the largest genome so far recorded in the angiosperm Paris japonica (148.89 Gbp/1C). Despite available data showing that giant genomes are restricted across the Tree of Life, the biological limits to genome size expansion remain to be established. Here, we report the discovery of an even larger eukaryotic genome in Tmesipteris oblanceolata, a New Caledonian fork fern. At 160.45 Gbp/1C, this record-breaking genome challenges current understanding and opens new avenues to explore the evolutionary dynamics of genomic gigantism.

Graphical Summary

Introduction
The ever expanding exploration of nearly 20,000 eukaryotic genomes has revealed an astounding array of genome sizes distributed across the eukaryotic Tree of Life (Figure 1A), influencing cell sizes, life cycles, physiology and morphology, and ultimately, impacting the ecology and evolution of species.^1,2 Miniature-sized fungal genomes, including the smallest eukaryotic genome found in the microsporidian Encephalitozoon intestinalis (2.6 Mbp/1C,³ i.e., 1C = nuclear DNA content in a gametic nucleus), contrast with those found in other groups where genomes have expanded up to five orders of magnitude. Yet it is only within a few animal and plant lineages that truly extreme genomic expansions beyond 100 Gbp/1C are known.⁴ Among animals, obese genomes exist in just two chordate lineages—lungfishes (class Dipnoi), where they reach up to 129.90 Gbp/1C in Protopterus aethiopicus⁵ and proteid salamanders (class Amphibia), with genomes up to 117.47 Gbp/1C in Necturus lewisi.⁶ In contrast, several vascular plant groups have successfully expanded into the upper end of the genome size spectrum and comprise six of the top ten largest eukaryotic genomes known (Figure 1B). While most of these are angiosperms, especially within the monocot families Liliaceae and Melanthiaceae (e.g., Paris japonica; 148.89 Gbp/1C⁷), extreme genomes have also been reported in the parasitic eudicot Viscum album (Santalaceae; 100.84 Gbp/1C⁸) and within ferns in the Psilotaceae family (Tmesipteris obliqua, 147.60 Gbp/1C⁹). This vast scope of genome size variation, seemingly disconnected from organismal complexity and known as the “C-value paradox” or “C-value enigma”,¹⁰ has intrigued biologists for over half a century. Rapid advances in DNA sequencing are now providing compelling evidence showing that variation in DNA amount arises predominantly from differences in the frequency of polyploidy, abundance of non-coding repetitive DNA and the dynamics of the processes that amplify, erode and delete DNA.¹¹ Yet the question arises as to whether we have uncovered the full extent of genome size diversity.

Figure 1 Genome size diversity across eukaryotes

(A) Current distribution of genome sizes across major lineages of plants, animals, and fungi.

(B) Top 10 of the largest genome size records available in eukaryotes. Image and silhouette credits are provided in supplemental information.

As part of ongoing research addressed to enhance our understanding of how and why giant genomes evolve and function, and based on previous evidence of genomic gigantism in the small genus Tmesipteris,⁹ we conducted a survey using propidium iodide flow cytometry to robustly quantify genome size variation in the genus. Here, we present the discovery of the largest eukaryotic genome so far reported.

Results

The nuclear DNA content of T. oblanceolata

Using Allium cepa “Ailsa Craig” as internal standard, the species Tmesipteris oblanceolata subsp. linearifolia (Figure 2A), a rare species present in New Caledonia and some neighboring archipelagos, was found to have a genome size of 160.75 Gbp/1C (Figure 2B). An additional analysis using an alternative internal standard (Fritillaria lusitanica, 50.47 Gbp/1C), with a larger genome than that of A. cepa, was carried out with a resulting 1C-value of 160.45 ± 0.81 Gbp, that is c. 160,000 Mbp (Figure 2C, see Table S1 and STAR methods for detailed procedures).

Figure 2 Largest eukaryote genome in Tmesipteris oblanceolata

(A) Wild population of the fork fern Tmesipteris oblanceolata sourced for genome size analysis (left), including details of synangia and stomata (right).
(B) Relative fluorescence histogram from the flow cytometry analysis of a combined sample comprising nuclei from the internal calibration standard Allium cepa (peaks 1 and 2) and Tmesipteris oblanceolata (peak 3). Relative fluorescence histograms from the flow cytometry analyses of T. oblanceolata (C) and Paris japonica (D) with the internal standard Fritillaria lusitanica. Peak 1 in both images indicates the relative fluorescence peak of the G₁ stained nuclei from the internal standard Fritillaria lusitanica, and peak 2 for the target sample, i.e., P. japonica or T. oblanceolata.

(E) Relative fluorescence histograms from a combined analysis of T. oblanceolata with the previous record-holder P. japonica, which confirms the larger size of the genome of T. oblanceolata.

Image credits as follows: © Oriane Hidalgo.

Fernández, Pol; Amice, Rémy; Bruy, David; Christenhusz, Maarten J.M.; Leitch, Ilia J.; Leitch, Andrew L.; Pokorny, Lisa; Hidalgo, Oriane; Pellicer, Jaume.
A 160 Gbp fork fern genome shatters size record for eukaryotes
iScience (2024); DOI: 10.1016/j.isci.2024.109889

Copyright: © 2024 The authors.
Published by Cell Press. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

Something that creationists might wish to ignore is the explanation for this massive genome, which has probably come about because of the blundering inefficiency of the replication process in sexually-reproducing plants where gene, and even whole genome duplication is relatively common. As the authors say in the discussion section of their paper:

… unlike angiosperms where polyploidy is also prevalent,¹⁷ post-polyploid diploidization mechanisms in ferns typically involves gene silencing without significant DNA elimination, resulting in high chromosome numbers but reflecting a diploid-like gene expression.¹⁸ Tmesipteris oblanceolata subsp. linearifolia has been reported, like P. japonica, to be an octoploid, but it has a much higher chromosome number (2n = 416 versus 2n = 407,¹⁹). Its massive genome is thus considered to have arisen through the combined effects of repetitive DNA accumulation and polyploidy, as in other species of the genus.²⁰

In other words, even the Heath-Robinson work-around for these blunders used in other examples of polyploidy where duplicate genes are switch off, hasn't worked in this little fern, so every cell in its and its descendants' body has to replicate a vast, unnecessarily complex and wasteful genome, containing vast amounts of redundancy.

If you subscribe to the childish notion of conscious design, a better example of incompetent design leading to unnecessary complexity and waste, would be hard to find in nature. If not then this sort of unintelligent, suboptimal, utilitarian condition is exactly what the theory of evolution predicts.

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